Contacts of the helix formed by residues 100 - 121 (chain C) in PDB entry 5JTM
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 ALA 100 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96C HIS* 3.3 11.8 + - + +
98C LEU 3.3 2.6 + - - -
99C GLY* 1.3 80.2 - - - +
101C TYR* 1.3 61.2 + - - +
102C CYS 3.5 1.1 - - - -
103C PRO* 3.4 7.1 - - - +
104C ASN* 3.1 28.8 + - - +
133C PHE* 3.6 28.9 - - + +
134C ASP* 3.6 23.7 - - - +
137C PHE* 3.8 13.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 101 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A PRO* 3.5 14.8 + - + +
132A ASN* 3.0 42.1 + - - -
9C MET* 5.6 3.7 - - + +
11C PHE* 3.1 44.2 - + - -
96C HIS* 3.0 27.1 + + + +
97C CYS* 3.7 28.5 - - + -
100C ALA* 1.3 76.3 - - - +
102C CYS* 1.3 61.8 + - - +
104C ASN* 3.3 18.7 - - + +
105C ILE* 3.4 18.6 - - + +
134C ASP* 3.5 16.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 102 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C PHE* 3.9 20.6 - - - -
58C VAL* 4.0 11.4 - - + -
84C PHE* 3.4 36.9 - - + -
86C ILE* 5.1 0.7 - - - -
97C CYS* 2.7 51.2 + - - +
98C LEU* 4.2 7.0 - - - +
101C TYR* 1.3 71.0 - - - +
103C PRO* 1.4 61.7 - - + +
104C ASN 3.2 3.8 - - - -
105C ILE* 3.1 29.2 - - - +
106C LEU* 3.5 1.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 103 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58C VAL* 4.0 10.9 - - + -
60C LEU* 3.6 46.9 - - + +
98C LEU 3.0 28.9 - - - +
99C GLY* 4.3 3.4 - - - -
100C ALA* 3.4 20.0 - - - +
102C CYS* 1.4 83.4 - - + +
104C ASN* 1.4 52.0 + - - -
105C ILE 3.3 0.7 - - - -
106C LEU* 3.5 14.1 - - + +
107C PHE* 2.8 31.5 + - - +
133C PHE* 5.9 3.6 - - + -
11G LEU* 6.4 0.4 - - + -
15G PHE* 5.4 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 104 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A ASN 5.8 1.2 + - - -
108A PRO* 3.8 23.3 - - - +
109A TYR* 5.8 2.8 - - - -
100C ALA 3.1 19.5 + - - +
101C TYR* 3.3 13.1 - - + +
103C PRO* 1.4 73.7 - - - +
105C ILE* 1.4 64.6 + - + +
107C PHE* 3.4 10.5 + - - +
108C PRO* 3.4 17.3 - - - +
131C VAL 5.3 6.8 + - - -
132C ASN* 5.1 9.3 - - - +
133C PHE* 6.4 1.6 - - + -
134C ASP* 3.1 24.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 105 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A PRO* 4.5 10.3 - - + +
111A ARG* 3.1 34.9 + - - +
130A PRO* 4.0 22.9 - - + -
11C PHE* 4.7 4.7 - - + -
13C ILE* 3.6 14.1 - - + -
16C ILE* 3.5 28.9 - - + -
84C PHE* 4.0 10.5 - - + -
101C TYR* 3.4 21.5 - - + +
102C CYS* 3.1 17.9 - - - +
104C ASN* 1.4 77.8 - - + +
106C LEU* 1.3 54.3 + - - +
108C PRO* 3.3 11.1 - - - +
109C TYR* 3.1 23.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 106 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C ILE* 3.7 32.5 - - + -
58C VAL* 3.2 38.4 - - + +
59C VAL* 4.8 0.4 - - - -
60C LEU* 4.8 4.3 - - + +
80C GLN* 3.5 30.4 - - + +
81C GLY 4.0 2.5 - - - +
82C GLY* 3.7 11.2 - - - +
84C PHE* 3.6 26.2 - - + -
102C CYS 3.5 9.4 + - - +
103C PRO* 3.3 11.2 + - + +
104C ASN 3.2 0.6 - - - -
105C ILE* 1.3 75.4 - - - +
107C PHE* 1.3 64.7 + - - +
108C PRO* 3.5 0.7 - - - -
109C TYR* 3.3 5.8 + - - -
110C ALA* 3.1 21.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 107 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A TYR* 3.2 31.6 - + - -
60C LEU* 6.2 4.9 - - + -
62C VAL* 6.0 5.4 - - + -
103C PRO 2.8 12.9 + - - +
104C ASN* 3.5 17.3 - - - +
106C LEU* 1.3 78.1 - - - +
108C PRO* 1.4 66.2 - - + +
110C ALA* 3.4 6.0 + - + +
111C ARG* 2.9 44.1 + - + +
128C LEU* 3.8 40.8 - - + +
129C ALA 3.2 25.6 - - - -
130C PRO* 4.2 5.6 - - + -
131C VAL* 4.5 9.0 - - + -
133C PHE* 5.8 3.6 - + - -
8G LEU* 4.7 14.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 108 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A PRO* 3.4 28.3 - - + +
109A TYR* 3.9 24.0 - - + +
112A GLU* 3.4 33.4 - - + +
104C ASN 3.4 10.8 - - - +
105C ILE 3.3 15.5 - - - +
107C PHE* 1.4 97.3 - - + +
109C TYR* 1.4 56.2 + - - +
111C ARG* 3.5 11.3 - - + +
112C GLU* 3.0 24.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 109 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A PRO 4.9 0.4 - - - -
111A ARG* 3.3 24.1 - - - +
112A GLU* 3.6 32.8 - - + -
115A THR* 3.6 25.4 + - + -
116A SER 5.8 0.2 - - - -
125A GLN* 5.5 1.1 - - - -
127A ASN* 2.8 20.5 + - - -
16C ILE* 3.5 33.5 - - + +
17C TYR* 6.2 0.2 - - - -
18C THR* 5.2 1.4 - - + +
80C GLN* 3.4 23.5 + - - +
105C ILE* 3.1 29.2 - - + -
106C LEU* 3.5 8.5 - - - +
107C PHE 3.3 0.4 - - - -
108C PRO* 1.4 74.0 - - + +
110C ALA* 1.4 65.7 + - - +
112C GLU* 4.1 2.1 - - - +
113C CYS* 3.1 24.6 + - - +
120D ARG* 5.2 0.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 110 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62C VAL* 3.8 31.0 - - + -
78C VAL* 4.2 10.4 - - + +
80C GLN* 3.7 21.7 - - + +
106C LEU 3.1 14.5 + - - +
107C PHE* 3.7 5.2 - - - +
109C TYR* 1.4 78.8 - - - +
111C ARG* 1.3 61.7 + - - +
113C CYS* 3.4 2.8 + - - +
114C ILE* 3.1 32.1 + - - +
128C LEU* 6.4 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 111 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A ILE* 4.3 22.2 + - - +
109A TYR* 3.4 31.6 - - - -
119B SER 5.7 1.4 + - - -
120B ARG* 5.9 3.8 + - - +
122B THR* 4.5 8.9 - - - +
107C PHE* 2.9 32.7 + - + +
108C PRO* 3.5 8.7 - - - +
110C ALA* 1.3 77.2 - - - +
112C GLU* 1.4 57.4 + - - +
114C ILE* 3.3 8.9 + - - +
115C THR* 3.0 35.0 + - - +
127C ASN* 3.9 24.0 - - - +
128C LEU* 2.8 55.9 + - + +
129C ALA* 5.4 1.2 - - - +
130C PRO* 5.5 4.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 112 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A GLU* 4.2 8.1 - - - +
116A SER* 3.5 4.0 + - - -
120A ARG* 3.0 20.3 + - - -
112B GLU* 4.0 0.9 - - - +
116B SER* 3.5 10.9 + - - +
119B SER* 5.8 4.9 - - - +
120B ARG* 2.8 41.5 + - + +
108C PRO 3.0 18.0 + - - +
109C TYR 4.1 2.9 - - - +
111C ARG* 1.4 75.5 - - - +
113C CYS* 1.4 57.4 + - - +
115C THR* 4.1 4.8 - - - +
116C SER* 2.9 32.1 + - - -
120D ARG* 3.0 33.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 113 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C THR* 4.2 8.7 - - + -
21C ILE* 3.5 44.2 - - - -
78C VAL* 3.6 21.0 - - + +
109C TYR 3.1 19.7 + - - +
110C ALA 3.7 4.7 - - - +
111C ARG 3.3 0.2 - - - -
112C GLU* 1.4 78.5 - - - +
114C ILE* 1.3 58.9 + - - +
116C SER* 3.9 0.4 - - - -
117C MET* 3.2 35.0 + - - +
120D ARG* 3.5 22.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 114 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62C VAL* 3.3 45.8 - - + +
64C VAL* 3.8 28.3 - - + +
76C CYS* 3.6 24.6 - - + -
78C VAL* 3.6 17.5 - - + -
110C ALA 3.1 23.5 + - - +
111C ARG* 3.7 4.7 - - - +
113C CYS* 1.3 74.6 - - - +
115C THR* 1.4 62.1 + - - +
117C MET* 3.0 6.6 + - - +
118C VAL* 2.9 37.9 + - + +
126C LEU* 5.1 4.7 - - + +
128C LEU* 4.9 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 115 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B SER* 3.2 27.6 - - - +
111C ARG* 3.0 20.1 + - - +
112C GLU* 4.1 4.9 - - - -
114C ILE* 1.4 76.4 - - - +
116C SER* 1.4 61.2 + - - +
118C VAL* 3.6 6.1 + - - +
119C SER* 3.2 22.7 + - - -
125C GLN* 3.8 16.4 + - - +
126C LEU 3.0 34.6 + - - +
127C ASN* 3.6 19.2 + - - +
128C LEU 4.5 1.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 116 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B GLU* 3.3 20.6 + - - +
116B SER* 6.5 0.4 - - - -
112C GLU* 2.9 32.5 + - - -
113C CYS 3.9 4.9 - - - -
115C THR* 1.4 76.7 - - - +
117C MET* 1.4 52.1 + - - +
119C SER* 3.1 8.6 + - - -
120C ARG* 2.8 57.1 + - - +
120D ARG* 3.3 8.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 117 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C ILE* 3.6 19.1 - - + -
22C SER 4.4 2.7 - - - +
23C PHE* 3.5 33.7 - - + -
76C CYS* 3.9 6.1 - - - -
113C CYS* 3.2 23.3 + - - +
114C ILE 3.0 9.1 + - - +
116C SER* 1.4 78.3 - - - +
118C VAL* 1.3 60.5 + - - +
120C ARG* 3.3 27.1 + - - +
121C GLY 3.0 22.5 + - - -
21D ILE* 3.5 42.8 - - + -
113D CYS* 4.1 1.6 - - - -
117D MET* 3.5 23.8 - - + -
120D ARG* 5.7 3.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 118 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B GLN* 5.4 0.2 - - - +
23C PHE* 3.6 10.1 - - + -
74C PHE* 3.7 32.3 - - + -
76C CYS* 5.2 0.2 - - - -
114C ILE* 2.9 31.3 + - + +
115C THR* 3.6 12.8 - - - +
116C SER 3.3 0.2 - - - -
117C MET* 1.3 76.5 - - - +
119C SER* 1.3 57.2 + - - +
121C GLY* 3.2 4.7 + - - -
122C THR 3.1 8.3 + - - -
123C PHE* 3.0 42.0 + - + +
124C PRO 3.4 26.2 - - - +
125C GLN* 5.0 0.4 - - - -
126C LEU* 4.5 13.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 119 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B THR* 3.2 11.7 - - - +
125B GLN* 2.9 22.3 + - - -
127B ASN* 2.9 21.8 + - - +
115C THR 3.2 10.4 + - - -
116C SER* 3.1 11.1 + - - -
118C VAL* 1.3 76.3 - - - +
120C ARG* 1.4 59.4 + - - +
122C THR* 3.2 19.9 + - - +
123C PHE 3.9 9.2 - - - -
125C GLN* 3.6 15.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 120 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B GLU* 3.0 32.8 + - + +
116C SER* 2.8 29.8 + - - +
117C MET* 3.5 43.9 - - - +
118C VAL 3.2 0.2 - - - -
119C SER* 1.4 72.2 - - - +
121C GLY* 1.4 56.4 + - - +
122C THR* 3.1 8.0 + - - +
16D ILE 4.5 0.2 - - - +
17D TYR* 3.2 11.3 - - - +
18D THR* 3.0 34.7 + - + +
21D ILE* 3.9 4.7 - - + -
112D GLU* 2.9 42.6 + - - -
113D CYS* 3.4 22.7 - - - +
116D SER* 3.1 15.9 + - - -
120D ARG* 4.3 2.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 121 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C PHE* 3.6 15.9 - - - -
32C PHE* 3.1 12.3 - - - -
117C MET 3.0 10.1 + - - -
118C VAL 3.2 4.0 + - - -
120C ARG* 1.4 74.9 - - - +
122C THR* 1.4 68.7 + - - +
123C PHE* 3.1 20.7 - - - -
17D TYR* 3.9 2.0 - - - -
18D THR* 3.2 20.1 + - - -
----------------------------------------------------------
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