Contacts of the strand formed by residues 32 - 37 (chain E) in PDB entry 3O2Q
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 32 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5E PRO 6.0 0.2 - - - -
6E LEU 3.6 15.5 + - - +
7E ARG* 3.9 28.3 + - - +
8E VAL* 2.9 28.1 + - - +
30E GLY 3.9 1.6 + - - -
31E PHE* 1.3 72.1 - - - +
33E VAL* 1.3 58.6 + - - +
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Residues in contact with VAL 33 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8E VAL* 3.2 13.5 - - + +
10E VAL* 4.6 6.1 - - + -
23E HIS* 3.7 36.6 + - + +
26E LEU* 4.2 26.0 - - + -
27E SER* 3.8 26.5 - - - +
31E PHE* 3.4 15.2 + - + +
32E SER* 1.3 76.1 + - - +
34E ARG* 1.3 83.9 + - - +
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Residues in contact with ARG 34 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7E ARG* 4.8 7.4 - - - +
8E VAL 3.2 5.3 + - - -
9E ALA* 3.3 5.1 - - - -
10E VAL 3.0 22.7 + - - -
23E HIS* 4.0 8.7 - - - -
33E VAL* 1.3 80.8 - - - +
35E SER* 1.3 62.6 + - - +
36E PHE* 3.8 21.9 - - + -
96E GLU* 2.9 34.1 + - - -
101E CYS* 3.4 22.8 - - - -
103E ASP* 2.3 37.0 + - - +
105E PHE* 3.8 19.1 - - + -
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Residues in contact with SER 35 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10E VAL* 3.2 12.3 - - - -
15E ASN* 3.2 13.3 + - - -
19E SER* 3.8 18.2 - - - -
20E MET* 3.3 6.1 - - - -
23E HIS* 2.8 26.9 + - - -
34E ARG* 1.3 78.2 - - - +
36E PHE* 1.3 75.7 + - - +
92E LYS* 3.1 31.0 + - - +
96E GLU* 3.3 4.9 + - - +
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Residues in contact with PHE 36 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9E ALA* 4.1 11.2 - - + -
10E VAL 3.1 4.8 + - - -
11E VAL* 3.2 11.7 - - + -
12E SER 2.9 24.1 + - - -
15E ASN* 3.5 8.5 + - - -
19E SER* 3.7 6.4 + - - -
34E ARG* 3.8 41.1 - - + -
35E SER* 1.3 86.4 - - - +
37E GLY* 1.3 58.6 - - - +
96E GLU* 3.2 25.6 - - + +
97E ARG 4.1 0.9 - - - -
98E PHE* 3.8 43.7 - + + +
101E CYS* 3.7 28.5 - - + -
105E PHE* 3.8 30.5 - + - -
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Residues in contact with GLY 37 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11E VAL* 4.2 0.4 - - - -
12E SER 3.2 9.2 - - - -
13E SER 3.2 15.7 - - - -
14E SER 4.2 0.7 - - - -
15E ASN* 3.5 10.2 - - - +
36E PHE* 1.3 74.1 - - - +
38E THR* 1.3 62.1 + - - -
39E GLY 3.5 0.7 - - - -
57E PHE* 4.3 5.2 - - - -
96E GLU 2.8 9.4 + - - -
97E ARG* 3.4 6.9 - - - +
98E PHE 2.8 26.4 + - - -
99E GLN* 3.7 0.5 + - - -
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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