Contacts of the helix formed by residues 88 - 109 (chain C) in PDB entry 4IXU
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 ASN 88 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C GLN* 3.3 53.6 + - + +
37C GLN 4.8 2.6 - - - +
79C ASP* 3.0 32.9 + - - +
81C LEU* 4.8 1.2 - - - +
87C VAL* 1.3 93.2 - - - +
89C PRO* 1.3 70.1 - - - +
91C SER* 4.1 1.1 + - - -
92C VAL* 3.0 21.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 89 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79C ASP* 3.3 11.9 - - - +
80C ASP 3.7 10.1 - - - +
82C TYR* 3.9 22.4 - - + -
86C ILE* 3.5 14.4 - - + +
87C VAL 3.2 4.9 - - - -
88C ASN* 1.3 89.3 - - - +
90C ARG* 1.3 69.4 + - - +
93C GLY* 2.8 24.8 + - - -
159C LEU* 3.8 18.6 - - + -
178C LEU* 4.5 9.6 - - + -
179C PRO* 3.4 20.1 - - + +
181C PHE* 3.2 10.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 90 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76C VAL* 3.7 27.8 - - + +
77C PRO 5.4 0.4 - - - -
78C LYS 4.6 4.9 + - - -
79C ASP* 2.7 40.4 + - - +
80C ASP* 2.9 36.7 + - - +
81C LEU 5.0 3.4 + - - -
82C TYR* 5.8 0.8 - - - +
89C PRO* 1.3 82.5 - - - +
91C SER* 1.3 57.7 + - - +
94C LEU* 2.9 32.1 + - - +
179C PRO* 3.6 45.3 - - + +
180C GLY* 4.3 6.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 91 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C GLN* 3.4 37.5 + - - -
74C THR 5.2 4.3 - - - +
75C PRO* 5.5 1.3 - - - +
76C VAL* 4.0 20.9 + - - +
79C ASP* 2.6 35.5 + - - +
88C ASN* 3.7 4.7 - - - +
90C ARG* 1.3 73.7 - - - +
92C VAL* 1.3 59.0 + - - +
94C LEU* 4.1 0.7 - - - +
95C ALA* 2.8 33.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 92 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C PHE* 4.5 8.5 - - + -
35C GLN* 3.6 35.2 - - + +
36C GLY* 3.9 5.2 - - - +
88C ASN 3.0 20.8 + - - +
91C SER* 1.3 75.0 - - - +
93C GLY* 1.3 64.3 + - - +
95C ALA* 4.1 0.2 - - - +
96C ASN* 3.0 49.4 + - - +
121C SER* 3.7 19.1 - - - +
124C ILE* 4.7 0.9 - - + -
159C LEU* 3.7 26.7 - - + -
181C PHE* 4.1 8.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 93 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89C PRO 2.8 17.8 + - - -
90C ARG 3.9 0.4 - - - -
92C VAL* 1.3 79.0 - - - +
94C LEU* 1.3 55.0 + - - +
96C ASN* 4.7 1.6 - - - -
97C GLN* 3.0 22.3 + - - +
180C GLY 3.2 22.2 - - - -
181C PHE* 3.6 14.3 - - - -
183C TRP* 3.0 15.8 + - - -
184C ILE* 5.8 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 94 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74C THR* 3.6 39.9 - - + +
75C PRO 4.7 0.4 - - - +
76C VAL* 3.9 16.2 - - + -
90C ARG 2.9 18.0 + - - +
91C SER 4.1 1.3 - - - +
93C GLY* 1.3 73.5 - - - +
95C ALA* 1.3 66.4 + - - +
97C GLN* 3.2 21.7 + - - +
98C GLU* 3.0 45.1 + - + +
180C GLY* 4.0 2.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 95 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C PHE* 3.4 26.0 - - + -
35C GLN* 6.3 0.7 - - - +
73C PHE* 3.5 40.4 - - + -
74C THR 5.3 1.4 + - - +
91C SER 2.8 19.5 + - - +
94C LEU* 1.3 76.0 - - - +
96C ASN* 1.3 58.2 + - - +
98C GLU* 3.2 2.3 + - - -
99C LEU* 2.8 28.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 96 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C PHE* 3.4 10.4 - - - -
92C VAL* 3.0 40.1 + - - +
93C GLY* 3.8 1.5 - - - +
95C ALA* 1.3 74.7 - - - +
97C GLN* 1.3 59.8 + - - +
99C LEU* 4.2 2.7 - - - +
100C ALA* 2.9 31.0 + - - +
121C SER 2.9 18.5 + - - -
122C LEU* 3.2 18.9 - - - +
124C ILE* 3.8 10.1 - - + +
125C GLY* 2.9 30.5 + - - +
183C TRP* 3.5 15.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 97 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93C GLY 3.0 10.9 + - - +
94C LEU* 3.2 26.8 + - + +
96C ASN* 1.3 76.8 - - - +
98C GLU* 1.3 62.9 + - + +
100C ALA* 3.4 3.3 + - - +
101C GLU* 3.3 20.8 + - - +
132C ARG* 5.1 3.1 + - - +
180C GLY 5.3 0.2 - - - +
183C TRP* 3.3 58.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 98 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71C LEU* 5.5 0.4 - - + -
72C SER 4.3 2.9 - - - +
73C PHE* 3.5 20.5 - - + +
74C THR* 2.6 48.7 + - - -
94C LEU* 3.0 31.4 + - + +
95C ALA* 3.6 6.1 - - - +
97C GLN* 1.3 75.7 - - + +
99C LEU* 1.3 64.7 + - - +
101C GLU* 3.3 14.7 + - - +
102C VAL* 3.3 18.7 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
29C ILE* 4.1 15.0 - - + -
31C ALA* 4.2 10.5 - - + -
33C PHE* 4.0 9.2 - - + -
71C LEU* 3.9 22.9 - - + -
73C PHE* 4.2 8.4 - - + -
95C ALA 2.8 15.7 + - - +
96C ASN* 3.7 6.1 - - - +
98C GLU* 1.3 76.3 - - - +
100C ALA* 1.3 57.9 + - - +
102C VAL* 3.0 3.3 + - - +
103C VAL* 2.9 39.2 + - + +
115C THR* 4.4 4.9 - - + -
122C LEU* 3.6 39.5 - - + +
126C THR* 3.7 19.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 100 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96C ASN 2.9 18.1 + - - +
97C GLN 3.6 5.6 - - - +
98C GLU 3.3 0.2 - - - -
99C LEU* 1.3 75.3 - - - +
101C GLU* 1.3 54.6 + - - +
103C VAL* 4.4 0.7 - - - -
104C SER* 2.8 37.2 + - - -
125C GLY 3.3 24.0 + - - +
129C GLY* 3.3 10.4 - - - +
132C ARG* 3.8 24.2 - - - +
183C TRP* 4.0 9.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 101 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97C GLN 3.3 9.6 + - - +
98C GLU* 3.3 12.1 + - - +
99C LEU 3.1 0.4 - - - -
100C ALA* 1.3 80.6 - - - +
102C VAL* 1.3 58.3 + - + +
104C SER* 3.7 4.4 - - - -
105C ARG* 3.0 30.5 + - + +
132C ARG* 3.7 17.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 102 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C ILE* 3.7 18.6 - - + -
68C PHE* 3.6 34.1 - - + -
71C LEU* 3.9 29.6 - - + -
98C GLU 3.5 13.5 - - - +
99C LEU 3.0 7.0 + - - +
101C GLU* 1.3 79.3 - - + +
103C VAL* 1.3 56.7 + - - +
105C ARG* 3.3 7.2 + - - +
106C ALA* 2.9 27.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 103 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C ILE* 4.1 4.3 - - + -
99C LEU* 2.9 35.6 + - + +
100C ALA* 3.8 3.8 - - - +
102C VAL* 1.3 72.9 - - - +
104C SER* 1.3 66.6 + - - +
106C ALA* 3.2 1.7 + - - +
107C VAL* 2.9 29.5 + - + +
113C CYS* 4.0 29.8 - - + -
115C THR* 4.2 0.2 - - - +
126C THR* 3.6 42.8 - - + +
129C GLY* 4.3 2.9 - - - -
130C HIS* 3.6 16.6 - - + +
291C ALA* 5.5 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 104 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100C ALA 2.8 24.1 + - - -
101C GLU* 3.7 7.2 - - - -
103C VAL* 1.3 72.5 - - - +
105C ARG* 1.3 63.9 + - - +
107C VAL* 3.6 1.2 + - - -
108C SER* 3.0 22.3 + - - -
129C GLY* 3.5 20.3 + - - -
132C ARG* 3.9 19.1 - - - +
133C HIS* 2.8 38.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 105 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68C PHE* 5.9 6.1 - - + -
101C GLU* 3.0 20.2 + - + +
102C VAL* 3.6 7.4 - - - +
104C SER* 1.3 76.0 - - - +
106C ALA* 1.3 57.6 + - - +
108C SER* 2.8 24.0 + - - -
109C ASP* 3.0 51.2 + - - +
133C HIS* 5.4 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 106 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C ALA* 4.0 26.2 - - + -
29C ILE* 4.9 0.9 - - + -
68C PHE* 4.1 16.1 - - + -
102C VAL 2.9 16.3 + - - +
103C VAL* 3.7 4.0 - - - +
105C ARG* 1.3 76.1 - - - +
107C VAL* 1.3 60.5 + - - +
109C ASP* 3.2 8.8 + - - -
110C GLY 3.3 0.5 + - - -
111C TYR* 3.0 34.9 + - + -
113C CYS* 4.2 14.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 107 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103C VAL* 2.9 26.0 + - + +
104C SER* 4.1 3.4 - - - +
106C ALA* 1.3 75.6 - - - +
108C SER* 1.3 58.2 + - - +
110C GLY* 3.0 18.7 + - - -
111C TYR 3.6 18.1 - - - +
113C CYS* 4.0 17.5 - - + -
130C HIS* 4.1 22.9 - - + +
133C HIS* 4.3 11.9 - - + -
134C CYS* 3.8 28.7 - - - -
290C SER* 4.6 8.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 108 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104C SER 3.0 15.4 + - - -
105C ARG* 2.8 30.7 + - - -
107C VAL* 1.3 77.9 - - - +
109C ASP* 1.3 63.4 + - - +
110C GLY* 3.1 3.3 + - - -
133C HIS* 3.6 31.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 109 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66C LYS* 4.8 10.9 + - - -
68C PHE* 6.0 0.2 - - - -
105C ARG* 3.0 57.6 + - - +
106C ALA* 3.7 6.4 - - - +
107C VAL 3.2 0.6 - - - -
108C SER* 1.3 78.5 + - - +
110C GLY* 1.3 59.0 + - - +
111C TYR* 3.5 23.8 - - + -
----------------------------------------------------------
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