Contacts of the strand formed by residues 26 - 33 (chain C) in PDB entry 2GYR
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 LEU 26 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11C LEU* 4.2 24.3 - - + +
12C VAL* 3.6 29.8 - - - +
13C PRO* 3.7 14.1 - - + -
25C GLU* 1.3 80.4 - - - +
27C VAL* 1.3 64.1 + - - +
51E LEU* 4.0 38.8 - - + +
52E GLY* 5.6 0.2 - - - -
63E ARG* 3.5 35.2 - - - +
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Residues in contact with VAL 27 (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 LEU* 3.3 6.4 - - - -
12C VAL* 3.0 41.3 + - + +
14C VAL* 3.8 15.9 - - + -
17C LEU* 4.1 19.1 - - + -
25C GLU* 3.8 13.7 - - - +
26C LEU* 1.3 79.1 - - - +
28C ARG* 1.3 66.8 + - - +
29C PHE* 3.5 2.1 + - + -
78C VAL* 4.2 13.2 - - + -
79C SER 3.3 27.4 - - - +
80C PHE* 3.8 8.5 - - + -
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Residues in contact with ARG 28 (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 SER* 3.5 23.9 + - - -
10C GLN* 3.6 23.8 + - - +
11C LEU* 3.7 36.4 - - + +
27C VAL* 1.3 77.2 - - - +
29C PHE* 1.3 62.2 + - - +
30C ARG* 3.8 36.9 - - - +
78C VAL* 4.3 14.2 - - - +
94C SER* 4.1 6.3 + - - -
52E GLY 4.8 2.0 + - - -
53E ALA* 5.3 5.9 - - - +
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Residues in contact with PHE 29 (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 SER* 3.3 18.2 - - - -
10C GLN* 3.1 14.5 + - - +
12C VAL* 4.1 20.2 - - + -
17C LEU* 3.9 22.4 - - + -
27C VAL* 3.5 1.5 + - + +
28C ARG* 1.3 76.2 - - - +
30C ARG* 1.3 70.5 + - - +
31C PHE* 4.1 12.4 + + + -
78C VAL* 4.7 5.8 - - + -
93C LEU* 2.8 36.1 - - + -
94C SER* 3.7 6.3 - - - -
43D HIS* 3.8 17.0 - + - -
46D SER* 4.1 5.4 - - - -
47D LEU* 4.1 25.1 - - + -
50D LEU* 3.4 26.7 - - + -
56D LEU* 4.4 7.4 - - + +
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Residues in contact with ARG 30 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C LEU* 4.2 24.7 - - + -
8C ARG 2.8 9.9 - - - +
9C SER* 3.3 22.0 + - - -
28C ARG* 3.8 31.8 - - - +
29C PHE* 1.3 77.0 - - - +
31C PHE* 1.3 62.5 + - - +
76C GLU* 3.8 20.4 + - - -
94C SER* 2.8 13.7 + - - +
95C ALA* 3.1 40.4 + - - +
96C THR* 5.7 0.7 - - - +
43D HIS* 3.5 5.5 + - - -
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Residues in contact with PHE 31 (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* 3.5 2.2 - - - -
8C ARG* 2.6 65.1 + - + +
9C SER* 4.0 8.3 - - - -
10C GLN* 4.4 10.1 - - - -
29C PHE* 4.2 15.0 - + + -
30C ARG* 1.3 76.7 - - - +
32C CYS* 1.3 72.9 + - - +
33C SER* 3.5 24.2 - - - -
95C ALA* 4.1 3.1 - - - +
43D HIS* 3.9 18.2 - - + +
47D LEU* 4.4 10.5 - - + -
56D LEU* 4.2 31.2 - - + -
57D ARG 5.3 0.9 - - - -
59D PRO* 4.2 19.5 - - + -
64D PRO* 4.3 15.0 - - + -
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Residues in contact with CYS 32 (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 ARG 3.8 0.2 - - - -
7C LEU* 3.9 4.5 - - - -
31C PHE* 1.3 76.9 - - - +
33C SER* 1.3 63.8 + - - +
70C CYS* 4.0 13.5 - - - +
71C ARG* 3.9 5.8 - - - -
72C PRO* 3.5 36.7 - - + +
95C ALA* 4.2 1.0 - - - +
97C ALA 3.5 3.4 - - - -
98C CYS* 2.0 57.7 - - + -
43D HIS* 5.0 3.8 + - - -
47D LEU* 5.4 2.6 - - - +
64D PRO* 3.4 16.5 - - - +
65D VAL 5.1 2.1 + - - +
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Residues in contact with SER 33 (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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4C GLY 3.3 2.1 - - - +
6C ARG 2.9 31.6 + - - +
8C ARG* 3.7 11.6 + - - -
31C PHE* 3.5 22.9 + - - -
32C CYS* 1.3 77.7 - - - +
34C GLY* 1.3 62.5 + - - +
70C CYS* 3.3 9.6 - - - -
59D PRO* 2.8 27.0 - - - +
62D SER 3.2 11.1 + - - -
64D PRO* 3.8 12.1 - - - +
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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