Contacts of the strand formed by residues 7 - 15 (chain C) in PDB entry 6QPA
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 ILE 7 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5C ASN 4.8 4.0 - - - +
6C PRO* 1.3 79.9 - - - +
8C ILE* 1.3 65.0 + - - +
80C THR 3.9 0.7 - - - +
81C VAL* 3.4 3.1 - - - +
82C TRP* 2.8 39.7 + - + +
83C LYS 4.5 2.7 - - - +
84C ASP* 4.1 25.1 - - - -
85C VAL* 4.2 8.1 - - + +
118C TYR* 3.8 29.8 - - + -
119C PHE 3.7 9.9 - - - +
120C GLU* 4.7 9.0 - - + -
202C PHE* 3.8 29.4 - - + -
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Residues in contact with ILE 8 (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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6C PRO 4.8 0.4 - - - +
7C ILE* 1.3 80.3 - - - +
9C ALA* 1.3 62.1 + - - +
10C ILE* 3.7 25.6 - - + -
79C TYR* 4.0 21.5 - - + -
80C THR 3.6 4.3 - - - +
81C VAL* 4.2 16.6 - - + -
118C TYR 3.6 0.5 - - - -
119C PHE* 2.8 48.2 + - + +
121C VAL* 3.7 28.5 - - + -
197C MET* 3.9 26.2 - - + -
199C MET* 4.0 5.6 - - - -
308C TRP* 4.0 15.3 - - + -
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Residues in contact with ALA 9 (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 ILE 4.1 1.0 - - - -
8C ILE* 1.3 71.7 - - - +
10C ILE* 1.3 61.1 + - - +
11C ASN 3.8 0.4 - - - -
78C GLN 3.2 3.1 - - - +
79C TYR* 3.3 2.3 - - - -
80C THR* 2.8 49.6 + - - +
82C TRP* 4.4 4.6 - - + +
88C HIS* 4.0 12.6 - - + +
116C GLU* 3.6 26.4 - - + +
117C PRO 3.5 7.0 - - - +
118C TYR* 4.2 15.0 - - + -
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Residues in contact with ILE 10 (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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8C ILE* 3.7 13.7 - - + -
9C ALA* 1.3 75.5 - - - +
11C ASN* 1.3 61.4 + - - +
12C MET* 3.3 21.1 + - + +
77C PHE* 3.8 27.4 - - + -
78C GLN 3.4 2.9 - - - +
79C TYR* 3.6 25.8 - - + -
115C TRP 3.3 0.3 - - - +
116C GLU* 3.3 2.5 - - - -
117C PRO* 3.1 33.8 + - - +
119C PHE* 3.7 29.6 - - + -
199C MET* 3.7 26.9 - - + -
254C LEU* 3.9 8.7 - - + -
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Residues in contact with ASN 11 (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 ALA 3.8 0.6 + - - -
10C ILE* 1.3 69.3 - - - +
12C MET* 1.3 61.2 + - - +
13C ALA* 4.6 4.7 - - - +
76C MET 3.4 3.1 - - - +
77C PHE* 3.4 4.2 - - - -
78C GLN* 2.9 46.3 + - + +
92C HIS* 6.0 1.6 - - - -
114C PRO* 3.4 24.0 - - - +
115C TRP 3.8 0.7 - - - -
116C GLU* 3.7 25.4 + - - +
208C GLY* 3.3 25.1 + - - -
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Residues in contact with MET 12 (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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10C ILE* 3.6 29.2 - - + +
11C ASN* 1.3 72.7 + - - +
13C ALA* 1.3 61.0 + - - +
76C MET 3.8 2.9 - - - -
77C PHE* 3.8 27.1 - - + -
113C GLY* 3.9 2.9 - - - -
114C PRO* 3.2 3.5 - - - +
115C TRP* 2.8 48.7 + - + +
117C PRO* 4.2 16.2 - - + -
119C PHE* 4.0 15.7 - - + -
252C GLN* 4.7 7.9 - - - +
254C LEU* 3.7 31.6 - - + -
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Residues in contact with ALA 13 (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* 4.6 6.5 - - - +
12C MET* 1.3 75.2 - - - +
14C LYS* 1.3 62.5 + - - +
15C ILE* 4.2 15.3 - - + -
75C GLY* 3.6 3.5 - - - -
76C MET* 2.8 45.0 + - + +
77C PHE* 4.6 2.6 - - - -
110C VAL* 5.1 8.1 - - + -
112C GLU 3.4 12.6 - - - +
113C GLY* 4.5 0.7 - - - -
114C PRO* 4.5 10.3 - - + -
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Residues in contact with LYS 14 (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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13C ALA* 1.3 77.7 - - - +
15C ILE* 1.3 62.6 + - - +
50C GLN* 4.3 16.0 + - - +
71C LEU* 6.4 0.2 - - - +
73C PRO* 3.6 32.4 + - + +
74C MET 3.4 3.8 - - - +
75C GLY* 4.4 9.3 - - - +
77C PHE* 6.4 0.7 - - + -
110C VAL* 3.8 0.9 - - - +
111C ILE 2.8 24.8 + - - -
112C GLU* 2.9 47.2 + - + +
297C MET* 4.7 9.3 - - - +
14E LYS* 5.2 14.2 - - - +
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Residues in contact with ILE 15 (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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13C ALA* 4.4 11.0 - - + -
14C LYS* 1.3 79.0 - - - +
16C ALA* 1.3 70.6 + - - +
21C SER* 4.5 2.5 - - - -
25C MET* 4.0 31.6 - - + -
49C LEU* 4.2 9.0 - - + -
73C PRO* 3.2 6.6 - - - +
74C MET* 2.9 49.8 + - + +
76C MET* 4.1 25.4 - - + -
109C MET* 3.2 42.0 - - + +
110C VAL* 4.7 5.2 - - + -
111C ILE* 4.1 0.9 - - - -
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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