Contacts of the strand formed by residues 11 - 16 (chain C) in PDB entry 3Q2K
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 11 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6C ILE* 3.3 45.5 - - + +
9C ARG 3.4 0.8 + - - -
10C LYS* 1.3 70.0 - - - +
12C ARG* 1.3 67.8 + - - +
13C PHE* 3.7 24.2 + - + -
35C ARG 2.7 19.7 + - - +
36C ALA* 3.3 6.8 - - + +
37C GLU* 2.8 31.4 + - - +
74C ASP* 3.9 7.4 - - + +
75C ALA* 5.2 0.9 - - + -
309C ILE* 4.6 14.8 - - + -
312C LEU* 3.8 36.1 - - + -
313C ARG* 4.7 5.8 - - + -
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Residues in contact with ARG 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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9C ARG* 3.4 48.3 - - - +
10C LYS 3.4 7.0 + - - -
11C ILE* 1.3 72.7 - - - +
13C PHE* 1.3 58.5 + - - +
37C GLU* 3.6 15.1 + - - +
39C VAL* 3.5 27.8 - - + -
72C ASN* 3.3 30.8 + - - +
73C ALA* 3.3 8.1 - - - -
74C ASP* 2.5 52.0 + - - +
75C ALA 3.3 4.7 + - - -
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Residues in contact with PHE 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 ILE* 3.8 17.0 - - + -
12C ARG* 1.3 73.6 - - - +
14C GLY* 1.3 59.6 + - - +
29C ILE* 3.9 26.7 - - + -
36C ALA* 3.5 32.8 - - + -
37C GLU 3.0 13.7 + - - +
38C LEU* 3.7 5.4 - - + +
39C VAL* 3.2 24.4 + - - +
40C GLU 3.9 1.4 + - - -
73C ALA* 3.8 4.3 - - - +
75C ALA* 3.4 24.7 - - + -
77C VAL* 4.0 20.0 - - + -
100C VAL* 4.4 3.1 - - + -
305C TYR* 3.7 33.2 - + - -
308C VAL* 4.2 19.1 - - + -
309C ILE* 4.4 8.1 - - + -
312C LEU* 4.7 2.0 - - + -
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Residues in contact with GLY 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 PHE* 1.3 75.5 - - - +
15C LEU* 1.3 56.1 + - - -
38C LEU* 4.4 1.3 - - - -
40C GLU* 3.7 3.4 - - - -
67C MET* 3.6 11.7 - - - -
73C ALA* 3.5 5.2 - - - +
75C ALA 2.8 9.9 + - - +
76C LEU* 3.3 21.0 - - - -
77C VAL* 2.6 38.1 + - - +
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Residues in contact with LEU 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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14C GLY* 1.3 72.7 - - - -
16C VAL* 1.3 62.9 + - - +
17C GLY 3.8 7.9 - - - +
18C CYS* 5.0 8.2 - - - -
22C SER* 3.6 28.0 - - - +
25C HIS* 4.3 11.7 - - + -
26C ILE* 3.9 25.1 - - + +
29C ILE* 5.8 0.9 - - + -
38C LEU* 3.8 15.4 - - + +
40C GLU 3.2 9.3 + - - +
41C ILE* 3.3 10.1 - - + +
42C CYS* 2.9 26.9 + - - +
67C MET* 3.9 1.9 - - - +
77C VAL* 3.5 30.3 - - + -
79C ALA* 3.8 18.6 - - + -
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Residues in contact with VAL 16 (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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15C LEU* 1.3 76.0 - - - +
17C GLY* 1.3 61.3 + - - +
42C CYS* 3.7 11.7 - - - -
64C LEU* 4.0 21.8 - - + -
67C MET* 4.4 4.5 - - - -
76C LEU* 3.9 23.6 - - + -
77C VAL 2.8 18.6 + - - +
78C LEU* 4.0 13.5 - - + -
79C ALA* 2.8 34.2 + - - +
80C THR* 3.6 1.5 + - + -
88C GLN* 3.8 30.7 - - - +
500C NAI 3.8 13.2 - - + -
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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