Contacts of the helix formed by residues 77 - 91 (chain C) in PDB entry 6G2T
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 77 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36C ARG* 4.8 4.2 - - - +
67C LYS* 4.5 10.7 - - - +
69C PRO* 3.9 7.6 + - + +
75C VAL* 4.8 3.7 - - - +
76C THR* 1.3 86.2 + - - +
78C TRP* 1.3 65.8 + - - +
79C ASP* 2.7 33.2 + - - +
80C ASP* 3.0 37.9 + - + +
81C MET* 3.6 10.2 + - - +
204I GLY* 5.6 5.7 - - - -
205I GLN 5.8 0.3 + - - -
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Residues in contact with TRP 78 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75C VAL* 3.3 46.3 + - + -
76C THR 5.4 1.6 - - - -
77C ASN* 1.3 75.4 + - - +
79C ASP* 1.3 65.6 + - - +
81C MET* 3.2 10.9 + - + +
82C GLU* 3.1 19.6 + - - +
85C TRP* 5.1 4.7 - + - -
113C ALA* 4.3 1.8 - - + -
114C ASN* 3.5 30.7 + - + -
117C LYS* 3.4 46.4 - - + +
118C MET* 4.0 18.6 - - + -
121C ILE* 3.3 31.9 - - + +
201I SER 5.4 4.0 + - - -
203I VAL 5.6 6.5 - - - +
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Residues in contact with ASP 79 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C ARG* 4.8 6.1 + - - -
77C ASN* 2.7 41.4 + - - +
78C TRP* 1.3 72.2 - - - +
80C ASP* 1.3 73.5 + - - +
82C GLU* 3.3 11.2 + - + +
83C LYS* 3.1 34.7 + - - +
204I GLY* 6.3 0.2 - - - -
205I GLN* 4.0 26.2 - - + +
206I HIS* 5.7 9.5 - - + +
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Residues in contact with ASP 80 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C VAL* 3.6 30.6 - - + +
36C ARG* 3.1 27.6 + - - -
67C LYS* 4.0 18.5 - - - +
69C PRO* 4.2 10.2 - - + +
77C ASN* 3.0 36.7 + - - +
78C TRP 3.2 0.8 - - - -
79C ASP* 1.3 81.5 + - - +
81C MET* 1.3 66.6 + - - +
83C LYS* 3.2 11.1 + - - +
84C ILE* 3.1 26.6 + - - +
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Residues in contact with MET 81 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11C ASN* 4.2 10.8 - - - +
16C CYS* 5.8 0.7 - - - -
32C SER* 6.0 1.3 - - - -
69C PRO* 4.0 16.2 - - + +
70C ILE* 3.6 38.4 - - + -
75C VAL* 3.7 15.5 - - + -
77C ASN 3.6 8.0 + - - +
78C TRP* 3.2 17.2 + - + +
80C ASP* 1.3 77.0 - - - +
82C GLU* 1.3 59.3 + - - +
84C ILE* 3.1 14.3 + - + +
85C TRP* 2.8 77.9 + - + -
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Residues in contact with GLU 82 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78C TRP 3.1 12.3 + - - +
79C ASP* 3.5 13.7 - - + +
80C ASP 3.2 0.2 - - - -
81C MET* 1.3 77.7 - - - +
83C LYS* 1.3 70.7 + - - +
85C TRP* 3.3 11.8 + - - +
86C HIS* 2.9 34.6 + - - +
121C ILE* 4.8 9.0 - - + -
125C THR* 3.6 34.8 - - + +
126C PHE* 3.8 11.1 - - + -
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Residues in contact with LYS 83 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34C VAL* 4.9 2.2 - - + -
36C ARG* 3.5 33.9 - - - +
50C ASP* 4.5 4.4 + - - +
51C SER* 3.8 22.9 - - - +
53C VAL* 4.0 19.6 - - + +
79C ASP* 3.1 24.5 + - - +
80C ASP* 3.4 15.5 - - - +
82C GLU* 1.3 89.3 + - - +
84C ILE* 1.3 57.7 + - - +
86C HIS* 3.4 7.6 + - - +
87C HIS* 2.9 27.9 + - - +
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Residues in contact with ILE 84 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16C CYS* 3.4 29.6 - - - -
30C PHE* 4.0 15.0 - - + -
32C SER* 4.4 5.4 - - - -
33C ILE 4.3 12.1 - - - +
34C VAL* 4.0 11.4 - - + -
53C VAL* 3.6 20.2 - - + -
69C PRO* 3.4 34.3 - - + -
80C ASP 3.1 15.0 + - - +
81C MET* 3.1 15.4 + - + +
83C LYS* 1.3 74.9 - - - +
85C TRP* 1.3 61.1 + - + +
87C HIS* 3.1 2.6 + - - +
88C THR* 2.8 36.1 + - + +
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Residues in contact with TRP 85 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9C ILE* 4.3 14.8 - - + +
11C ASN* 2.9 29.6 - - - +
78C TRP* 5.1 2.5 - + - -
81C MET* 2.8 48.2 + - + +
82C GLU* 3.7 8.3 - - - +
84C ILE* 1.3 77.9 - - + +
86C HIS* 1.3 62.5 + - - +
88C THR* 2.7 23.7 + - + -
89C PHE* 2.9 22.2 + - + -
104C LEU* 4.4 3.3 - - + +
118C MET* 3.7 38.6 - - + -
121C ILE* 3.6 39.7 - - + -
122C MET* 3.6 33.9 - - + +
126C PHE* 3.9 14.4 - + + -
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Residues in contact with HIS 86 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82C GLU* 2.9 26.9 + - - +
83C LYS* 3.5 8.4 + - - +
85C TRP* 1.3 75.8 - - - +
87C HIS* 1.3 62.6 + - - +
90C TYR* 3.0 73.7 + + + +
91C ASN* 4.7 5.5 + - - -
126C PHE* 3.6 17.9 - + + -
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Residues in contact with HIS 87 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30C PHE* 3.4 28.3 - + - -
53C VAL* 3.0 43.0 + - + -
54C GLY* 4.3 2.7 - - - -
55C ASP* 4.6 7.1 + - - -
56C GLU* 5.0 8.8 + - - +
83C LYS 2.9 18.7 + - - +
84C ILE 3.1 4.9 + - - +
86C HIS* 1.3 79.5 + - - +
88C THR* 1.3 58.5 + - - +
91C ASN* 2.9 47.3 + - - +
92C GLU* 2.8 46.1 + - - +
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Residues in contact with THR 88 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9C ILE* 4.3 10.3 - - + +
16C CYS* 4.5 9.0 - - + -
18C ALA* 4.8 13.7 - - + -
30C PHE* 3.2 28.7 - - + -
84C ILE* 2.8 29.1 + - + +
85C TRP* 2.7 26.0 + - + -
87C HIS* 1.3 74.0 - - - +
89C PHE* 1.3 65.2 + - - +
92C GLU* 3.9 8.5 + - - +
93C LEU* 3.1 38.1 + - - +
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Residues in contact with PHE 89 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7C LEU* 3.6 29.8 - - + -
9C ILE* 3.4 31.9 - - + -
85C TRP* 2.9 36.3 + - + +
88C THR* 1.3 83.4 + - - +
90C TYR* 1.3 69.2 + - + +
93C LEU* 3.2 20.9 - - + +
94C ARG 2.7 32.1 + - - -
95C VAL* 3.4 18.8 + - + +
97C PRO* 4.5 19.5 - - + -
102C VAL* 4.2 15.0 - - + -
122C MET* 4.4 14.6 - - + -
126C PHE* 4.4 18.6 - + - -
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Residues in contact with TYR 90 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86C HIS* 3.0 53.3 + + + +
89C PHE* 1.3 90.1 - - + +
91C ASN* 1.3 66.1 + - - +
94C ARG* 4.0 15.6 - - - +
95C VAL 4.9 7.6 - - - -
96C ALA* 5.9 1.8 - - + -
97C PRO* 4.4 16.5 - - + +
98C GLU* 5.4 2.6 + - - -
126C PHE* 4.0 21.2 - + - -
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Residues in contact with ASN 91 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86C HIS* 4.3 8.3 + - - +
87C HIS* 2.9 53.1 + - + +
90C TYR* 1.3 81.8 + - - +
92C GLU* 1.3 71.2 + - - +
94C ARG* 4.4 12.2 + - - +
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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