Contacts of the helix formed by residues 90 - 115 (chain C) in PDB entry 3GTU
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLU 90 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88C GLU 3.9 0.2 + - - -
89C SER* 1.3 72.6 - - - +
91C LYS* 1.3 84.1 + - - +
93C GLN* 3.2 16.2 + - - +
94C ILE* 2.8 43.5 + - + +
70D LYS* 5.1 1.6 - - - -
71D ASN* 3.5 12.5 - - - +
82D TYR* 3.5 15.7 - - + -
85D ARG* 4.0 14.6 + - - +
86D LYS* 3.2 29.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 91 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89C SER* 3.1 10.5 - - - +
90C GLU* 1.3 105.3 + - + +
92C GLU* 1.3 63.7 + - + +
94C ILE* 3.3 10.7 + - - +
95C ARG* 3.1 27.5 + - - +
70D LYS* 4.7 18.6 - - - +
71D ASN* 4.8 14.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 92 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87C GLY* 3.8 11.2 - - - -
88C GLU* 3.0 28.2 + - - +
89C SER* 3.0 26.3 + - - +
91C LYS* 1.3 76.2 - - + +
93C GLN* 1.3 57.9 + - - +
95C ARG* 3.2 6.5 + - - +
96C GLU* 2.8 25.9 + - - +
148C LEU* 3.0 35.6 - - + +
151C LYS* 3.3 37.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 93 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87C GLY* 3.4 21.1 + - - +
88C GLU* 3.3 19.6 + - - +
89C SER 2.9 10.6 + - - +
90C GLU* 3.2 21.7 + - - +
92C GLU* 1.3 77.4 - - - +
94C ILE* 1.3 56.4 + - - +
96C GLU* 3.2 14.2 + - - +
97C ASP* 2.8 37.6 + - - +
85D ARG* 3.1 41.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 94 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90C GLU* 2.8 31.2 + - + +
91C LYS* 3.6 8.3 - - - +
92C GLU 3.3 0.2 - - - -
93C GLN* 1.3 71.6 - - - +
95C ARG* 1.3 58.3 + - + +
97C ASP* 3.4 7.6 + - + +
98C ILE* 2.9 50.4 + - + +
71D ASN* 3.7 35.9 - - + +
72D LYS 5.2 1.6 - - - +
73D ILE* 3.6 26.2 - - + -
78D ALA 6.0 0.4 - - - +
82D TYR* 3.8 29.4 - - + -
85D ARG* 4.2 5.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 95 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91C LYS* 3.1 14.6 + - - +
92C GLU* 3.4 11.4 - - - +
94C ILE* 1.3 78.3 - - + +
96C GLU* 1.3 54.2 + - - +
98C ILE* 3.8 4.5 - - - +
99C LEU* 2.8 45.0 + - + +
140C PHE* 3.1 65.0 + - + -
144C GLN* 3.2 23.9 + - - +
147C PHE* 2.5 35.6 + - - +
148C LEU* 4.0 14.4 - - + +
59D ASP* 5.6 0.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 96 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77C ARG* 4.3 9.9 + - - +
86C CYS* 3.5 7.8 - - - +
87C GLY* 2.9 36.2 + - - +
92C GLU 2.8 13.0 + - - +
93C GLN* 3.2 15.3 - - - +
95C ARG* 1.3 75.8 - - - +
97C ASP* 1.3 63.1 + - - +
99C LEU* 4.0 1.1 - - - +
100C GLU* 2.9 32.6 + - - +
148C LEU* 4.0 5.8 - - + +
153C THR* 4.4 5.0 + - - -
154C PHE* 3.2 33.2 - - + -
155C VAL* 3.6 26.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 97 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77C ARG* 3.1 24.2 + - - +
93C GLN* 2.8 21.4 + - - +
94C ILE* 3.7 4.2 - - - +
96C GLU* 1.3 74.9 - - - +
98C ILE* 1.3 63.4 + - - +
100C GLU* 3.8 3.7 - - - +
101C ASN* 2.7 36.2 + - - +
78D ALA* 3.7 21.4 - - + +
81D ARG* 3.3 25.5 - - - +
85D ARG* 2.7 30.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 98 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94C ILE* 2.9 40.3 + - + +
95C ARG* 3.8 4.9 - - - +
97C ASP* 1.3 75.3 - - - +
99C LEU* 1.3 59.3 + - + +
101C ASN* 3.8 2.3 - - - +
102C GLN* 2.8 32.4 + - + +
140C PHE* 5.6 7.4 - - + -
59D ASP* 5.9 5.2 - - + +
60D PHE* 4.0 30.1 - - + -
72D LYS 4.4 5.2 - - - +
73D ILE* 3.7 32.3 - - + -
74D THR* 3.9 18.8 - - - +
75D GLN* 3.8 9.1 - - + +
78D ALA* 4.0 5.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 99 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95C ARG* 2.8 26.4 + - + +
96C GLU 4.0 0.2 - - - +
98C ILE* 1.3 70.3 - - - +
100C GLU* 1.3 55.8 + - - +
102C GLN* 4.1 2.2 - - + -
103C PHE* 2.7 63.8 + - + -
137C TYR* 4.4 3.6 - - + -
140C PHE* 3.3 40.4 - - + -
147C PHE* 3.7 30.7 - - + +
148C LEU* 4.5 4.0 - - + -
155C VAL* 3.6 20.9 - - + -
60D PHE* 4.2 18.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 100 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73C ASN* 3.3 41.8 + - - +
77C ARG* 2.8 46.4 + - - +
96C GLU 2.9 22.7 + - - +
97C ASP* 3.8 3.2 - - - +
99C LEU* 1.3 72.3 - - - +
101C ASN* 1.3 73.6 + - - +
103C PHE* 3.6 2.9 + - - +
104C MET* 3.3 20.1 + - - +
154C PHE* 3.8 14.0 - - + -
155C VAL* 4.6 2.8 - - + +
158C ILE* 4.5 20.8 - - + +
81D ARG* 4.7 1.6 + - - -
104D GLU* 4.3 9.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 101 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73C ASN* 6.1 0.7 - - - +
97C ASP* 2.7 28.3 + - - +
99C LEU 3.2 0.4 - - - -
100C GLU* 1.3 88.3 + - - +
102C GLN* 1.3 67.1 + - - +
104C MET* 3.2 8.3 + - - +
105C ASP* 3.1 21.5 + - - +
75D GLN* 3.4 30.5 + - + +
77D ASN* 3.5 41.7 + - - +
78D ALA* 4.0 6.3 - - - +
81D ARG* 6.0 1.2 - - - +
104D GLU* 6.0 0.2 - - - -
108D MET* 4.5 6.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 102 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98C ILE* 2.8 26.7 + - + +
99C LEU* 3.7 6.1 - - - +
101C ASN* 1.3 72.6 - - - +
103C PHE* 1.3 59.3 + - - +
105C ASP* 2.9 35.6 + - - +
106C SER* 3.2 6.4 + - - -
133C MET* 6.1 1.8 - - - +
136C LEU* 6.1 1.0 - - - +
137C TYR* 3.2 26.3 + - + +
60D PHE* 3.7 46.1 - - + +
62D ASN* 4.6 5.9 + - - +
74D THR* 6.1 0.2 - - - -
75D GLN* 3.0 25.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 103 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99C LEU* 2.7 50.0 + - + +
100C GLU 4.0 1.3 - - - +
102C GLN* 1.3 70.2 - - - +
104C MET* 1.3 64.3 + - - +
106C SER* 3.3 4.8 + - - -
107C ARG* 3.0 23.7 + - - +
137C TYR* 3.3 42.8 - + - -
147C PHE* 3.9 14.1 - + - -
155C VAL* 4.1 13.9 - - + -
158C ILE* 3.7 22.7 - - + -
159C ALA* 3.5 32.8 - - + -
162C VAL* 3.5 33.7 - - + +
163C LEU* 4.8 5.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 104 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C LEU* 4.8 8.3 - - + -
72C SER* 4.9 7.0 - - - -
73C ASN* 3.8 30.7 - - - +
100C GLU 3.3 11.4 + - - +
101C ASN* 3.2 12.0 + - - +
103C PHE* 1.3 74.5 - - - +
105C ASP* 1.3 66.6 + - - +
107C ARG* 3.1 31.8 + - - +
108C MET* 2.9 61.5 + - + +
158C ILE* 5.2 0.2 - - - +
108D MET* 6.6 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 105 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101C ASN 3.1 9.5 + - - +
102C GLN* 2.9 28.0 - - - +
104C MET* 1.3 78.1 - - - +
106C SER* 1.3 60.5 + - - +
108C MET* 3.4 4.9 + - - +
109C GLN* 3.1 28.2 + - - +
62D ASN* 4.7 5.5 + - - -
75D GLN* 3.4 23.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 106 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102C GLN* 3.2 4.1 + - - -
103C PHE* 3.7 7.9 - - - -
105C ASP* 1.3 74.2 - - - +
107C ARG* 1.3 66.0 + - - +
109C GLN* 3.1 18.9 + - - +
110C LEU* 3.1 14.2 + - - +
126C TYR* 4.7 3.5 + - - -
133C MET* 3.6 29.9 - - - +
137C TYR* 2.7 35.3 + - - -
162C VAL* 5.1 11.9 - - - -
166C ASN* 5.5 0.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 107 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C LEU* 3.8 24.5 + - - +
15C SER* 3.7 10.9 + - - -
72C SER* 5.7 2.6 - - - -
73C ASN* 5.1 2.2 + - - -
76C LEU* 6.2 0.8 - - - +
103C PHE 3.0 13.9 + - - +
104C MET* 3.1 38.2 + - - +
106C SER* 1.3 76.3 - - - +
108C MET* 1.3 85.8 + - + +
110C LEU* 3.3 5.7 + - - +
111C ALA* 3.0 22.4 + - + +
158C ILE* 3.7 29.7 + - - +
161C ASP* 3.1 27.3 + - - -
162C VAL* 3.9 21.6 - - + +
165C ARG* 4.7 21.0 + - - +
208C PHE* 5.5 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 108 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C LEU* 4.4 11.0 - - + -
104C MET* 2.9 48.6 + - + +
105C ASP* 3.9 4.7 - - - +
107C ARG* 1.3 100.8 - - + +
109C GLN* 1.3 57.4 + - - +
111C ALA* 3.6 11.3 - - + +
112C LYS* 2.9 34.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 109 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105C ASP* 3.1 20.3 + - - +
106C SER* 3.1 12.5 + - - +
108C MET* 1.3 77.1 - - - +
110C LEU* 1.3 60.3 + - - +
112C LYS* 4.4 10.0 - - - +
113C LEU* 3.5 19.9 + - - +
126C TYR* 3.5 29.6 - - + -
129C ALA* 5.2 9.9 - - - +
130C LEU* 5.8 0.5 + - - -
133C MET* 4.2 20.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 110 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106C SER 3.1 9.8 + - - +
107C ARG* 3.8 7.0 - - - +
109C GLN* 1.3 74.8 - - - +
111C ALA* 1.3 68.4 - - - +
113C LEU* 3.1 10.9 + - + +
114C CYS* 2.9 51.5 + - - -
126C TYR* 3.9 34.9 - - + +
162C VAL 5.5 0.7 - - - +
165C ARG* 3.7 41.7 - - + +
166C ASN* 4.2 14.8 - - - +
169C PHE* 4.0 17.7 - - + -
208C PHE* 4.4 5.6 - - + -
214C TRP* 5.2 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 111 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107C ARG* 3.0 18.8 + - + +
108C MET* 3.6 18.6 - - + +
110C LEU* 1.3 75.4 - - - +
112C LYS* 1.3 63.6 + - - +
114C CYS* 3.1 3.3 + - - -
115C TYR* 3.0 36.8 + - + -
208C PHE* 3.7 28.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 112 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108C MET 2.9 20.0 + - - +
109C GLN* 4.4 9.9 - - - +
111C ALA* 1.3 72.6 - - - +
113C LEU* 1.3 57.1 + - - +
115C TYR* 3.4 5.7 + - - +
116C ASP* 3.0 36.0 + - - +
116D ARG* 5.0 14.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 113 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109C GLN 3.5 13.9 + - - +
110C LEU* 3.1 13.8 + - + +
112C LYS* 1.3 79.3 - - - +
114C CYS* 1.3 70.2 + - - +
116C ASP* 3.1 19.5 + - - +
119C PHE* 3.5 35.1 - - + +
122C LEU* 3.5 44.2 - - + +
123C LYS* 3.9 3.8 - - - +
126C TYR* 4.1 20.9 - - + -
169C PHE* 3.8 17.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 114 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110C LEU* 2.9 39.2 + - - +
111C ALA 3.8 1.6 - - - +
113C LEU* 1.3 79.3 - - - +
115C TYR* 1.3 52.3 + - - +
116C ASP 3.5 0.2 - - - -
119C PHE* 3.9 8.5 - - - -
169C PHE* 4.2 1.1 - - - -
208C PHE* 3.4 31.4 - - + -
212C ALA* 3.7 0.9 - - - -
213C VAL* 2.7 35.6 + - - +
214C TRP* 3.1 45.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 115 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111C ALA* 3.0 33.1 + - + +
112C LYS* 3.8 5.2 - - - +
114C CYS* 1.3 79.3 - - - +
116C ASP* 1.3 64.1 + - - +
117C PRO* 3.4 7.8 - - - +
208C PHE* 3.2 35.7 - + + +
209C THR* 2.9 45.1 + - - +
211C MET* 4.0 17.0 - - + +
212C ALA* 3.6 20.9 - - + -
213C VAL* 3.6 10.1 - - - +
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il