Contacts of the strand formed by residues 6 - 11 (chain B) in PDB entry 3O5Z
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 GLY 6 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B GLU* 1.3 78.7 - - - +
7B PHE* 1.3 76.0 + - - -
32B VAL* 5.1 2.9 - - - -
33B VAL 3.0 16.6 - - - -
34B SER* 4.2 0.7 - - - -
35B ARG* 4.0 5.2 - - - -
80B PRO* 3.6 2.1 - - - +
81B VAL* 3.0 33.6 + - - +
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Residues in contact with PHE 7 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B GLU* 5.6 1.8 - - + -
6B GLY* 1.3 84.8 - - - -
8B GLN* 1.3 61.9 + - - +
9B TYR* 3.9 17.7 - - + +
31B LEU 3.6 0.9 - - - +
32B VAL* 3.4 5.7 - - - +
33B VAL 2.9 32.4 + - - +
35B ARG* 3.8 49.6 - - + -
38B LEU* 4.0 17.5 - - + -
45B GLU* 4.3 2.0 - - - -
48B GLU* 3.5 51.4 - - + -
49B ARG* 5.4 1.1 - - - -
77B PHE* 4.0 13.5 - + + -
79B GLY 3.7 3.6 - - - -
80B PRO* 3.7 21.5 - - + -
81B VAL* 3.6 5.3 - - - +
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Residues in contact with GLN 8 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B PHE* 1.3 72.7 - - - +
9B TYR* 1.3 68.1 + - - +
30B VAL* 3.8 21.5 - - + +
31B LEU 3.3 5.6 - - - +
32B VAL* 4.8 2.7 - - + +
62B GLU* 3.3 23.4 + - - -
77B PHE* 3.9 1.6 - - - -
78B LEU* 2.9 44.4 + - + +
79B GLY 2.9 18.6 + - - +
80B PRO 4.6 4.3 - - - +
81B VAL* 4.4 26.1 - - + +
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Residues in contact with TYR 9 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B PHE* 3.9 18.4 - - + +
8B GLN* 1.3 74.0 - - - +
10B ARG* 1.3 59.6 + - - +
29B ASP 3.7 0.4 - - - +
30B VAL* 3.3 7.1 - - - +
31B LEU* 2.6 48.4 + - + +
33B VAL* 3.8 33.0 - - + -
38B LEU* 4.2 5.4 - - - +
48B GLU* 2.8 47.3 + - - +
51B PRO* 3.7 17.1 - - + +
57B MET* 4.2 11.6 - - - -
70B PHE* 4.7 4.9 - + + -
75B VAL* 3.7 29.8 - - + -
76B GLU 3.3 4.9 - - - +
77B PHE* 3.6 27.6 - + - -
78B LEU* 4.3 4.5 - - - +
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Residues in contact with ARG 10 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B TYR* 1.3 74.8 - - - +
11B ALA* 1.3 74.9 + - - +
12B LEU* 5.4 1.1 - - + -
28B GLY* 4.1 21.5 - - - -
29B ASP 3.3 8.5 - - - +
30B VAL* 5.1 2.7 - - + -
75B VAL* 3.1 5.4 - - - -
76B GLU* 2.8 60.4 + - + +
78B LEU* 3.5 42.7 - - + +
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Residues in contact with ALA 11 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B ARG* 1.3 78.6 - - - +
12B LEU* 1.3 60.5 + - - +
13B TYR 4.2 10.1 - - - +
25B LEU* 4.2 20.9 - - + -
26B LEU 3.6 19.5 - - - +
27B PRO* 3.5 0.5 - - - +
28B GLY 2.9 24.5 + - - -
29B ASP* 2.9 19.1 + - + +
31B LEU* 4.8 1.1 - - + +
74B TYR 3.4 9.0 - - - +
75B VAL* 3.9 5.3 - - + +
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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