Contacts of the strand formed by residues 40 - 45 (chain A) in PDB entry 2GSB
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 SER 40 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32A LEU* 3.6 8.7 - - - +
36A GLY* 4.6 1.4 - - - -
37A GLN* 2.4 39.0 + - - +
38A VAL 3.5 1.9 + - - -
39A CYS* 1.3 80.7 + - - +
41A PHE* 1.3 61.2 + - - +
57A PHE* 3.2 4.4 - - - -
58A ARG* 3.0 25.9 + - - +
106A GLU* 3.2 20.8 + - - +
107A PRO 4.9 1.5 + - - -
108A VAL* 4.2 14.1 - - - -
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Residues in contact with PHE 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A TRP* 4.3 11.0 - + + -
32A LEU* 4.3 2.2 - - - -
40A SER* 1.3 75.2 - - - +
42A LEU* 1.3 78.1 + - - +
43A VAL* 4.3 3.6 - - + -
55A LEU* 3.7 25.4 - - + -
56A TYR 3.2 13.5 - - - +
57A PHE* 3.8 14.6 - - + -
90A ILE* 3.4 55.6 - - + -
94A ARG* 5.8 0.2 - - - -
104A LEU* 3.8 33.4 - - + -
105A LYS 6.0 0.2 - - - -
106A GLU* 3.8 4.5 + - - -
107A PRO* 3.2 34.3 - - + +
108A VAL* 3.0 25.3 + - - +
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Residues in contact with LEU 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A TRP 3.6 13.2 - - - +
20A HIS* 4.0 22.9 - - + +
23A ILE* 4.9 1.6 - - + -
28A ALA* 4.3 20.2 - - + +
31A LEU* 5.3 1.6 - - + -
32A LEU* 3.5 31.0 - - + +
41A PHE* 1.3 85.7 - - - +
43A VAL* 1.3 80.4 + - - +
44A ARG* 4.1 16.2 - - + +
54A SER 3.9 0.2 - - - +
55A LEU* 3.7 2.8 - - - -
56A TYR* 3.0 38.2 + - + -
108A VAL* 4.2 13.0 - - + -
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Residues in contact with VAL 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A TRP* 3.1 38.2 + - + -
19A PHE* 3.7 6.4 - - + -
20A HIS* 2.9 30.0 + - - +
41A PHE* 4.3 6.5 - - + -
42A LEU* 1.3 73.1 - - - +
44A ARG* 1.3 65.2 + - - +
53A TYR* 4.1 27.4 - - + -
54A SER 4.0 5.8 - - - +
55A LEU* 3.4 28.0 - - + -
68A ILE* 5.4 2.2 - - + -
86A ILE* 4.2 23.8 - - + -
90A ILE* 4.8 0.7 - - + -
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Residues in contact with ARG 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A PHE* 4.9 0.2 - - - -
20A HIS 3.7 5.2 + - - +
21A GLY* 5.4 1.4 + - - -
23A ILE* 3.6 27.9 + - - +
24A SER* 3.1 41.9 + - - +
25A LYS* 3.1 13.7 - - - +
28A ALA* 4.1 8.0 - - - +
42A LEU* 4.1 5.2 - - + -
43A VAL* 1.3 78.5 - - - +
45A PRO* 1.3 77.8 + - + +
46A SER* 3.4 0.9 + - - +
47A ASP* 4.1 20.8 + - - +
53A TYR* 3.7 6.9 - - - -
54A SER* 3.2 38.3 + - - +
56A TYR* 3.2 34.9 + - + -
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Residues in contact with PRO 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A PHE* 4.0 18.6 - - + -
20A HIS 2.9 18.8 - - - +
21A GLY* 4.3 10.5 - - - +
44A ARG* 1.3 94.3 + - + +
46A SER* 1.3 67.2 + - - +
47A ASP* 2.9 20.8 + - - +
52A ASP 4.0 7.0 - - - +
53A TYR* 4.0 13.9 - - + -
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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