Contacts of the strand formed by residues 7 - 13 (chain E) in PDB entry 2FRV
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 PRO 7 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5E LYS 3.7 4.6 - - - +
6E ARG* 1.3 87.1 - - + +
8E SER* 1.3 57.6 + - - +
9E VAL* 4.8 1.3 - - + -
39E VAL 3.5 20.0 - - - +
40E ILE* 3.3 7.1 - - + +
41E SER 2.5 31.9 + - - -
67E ASP 5.6 0.4 - - - +
69E VAL* 6.1 2.2 - - + -
163E LEU* 3.6 35.7 - - + -
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Residues in contact with SER 8 (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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6E ARG 3.5 3.7 + - - -
7E PRO* 1.3 73.8 - - - +
9E VAL* 1.3 63.1 + - - +
10E VAL* 4.8 1.4 - - - +
41E SER* 3.6 7.4 - - - -
43E ASP* 2.6 24.8 + - - +
63E ALA* 4.7 6.9 + - - +
67E ASP 3.5 20.5 + - - -
68E PHE* 3.2 13.3 - - - +
69E VAL* 2.9 27.4 + - - +
166F GLN* 5.3 2.2 - - - -
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Residues in contact with VAL 9 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7E PRO* 4.2 2.0 - - + +
8E SER* 1.3 79.8 - - - +
10E VAL* 1.3 68.7 + - - +
11E TYR* 4.1 0.7 - - + -
40E ILE* 3.8 43.1 - - + -
41E SER 2.9 8.9 + - - +
42E MET* 3.8 17.0 - - + +
43E ASP* 2.9 29.1 + - - +
44E TYR 3.7 1.0 + - - -
69E VAL* 3.4 16.2 - - + +
71E VAL* 3.6 30.3 - - + -
155E PHE* 6.0 0.7 - - + -
159E VAL* 5.6 7.6 - - + -
163E LEU* 6.4 1.3 - - + -
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Residues in contact with VAL 10 (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 SER* 4.8 0.7 - - - +
9E VAL* 1.3 78.6 - - - +
11E TYR* 1.3 58.9 + - - +
12E LEU* 4.0 6.2 + - + -
43E ASP* 4.4 2.0 - - + -
44E TYR* 4.1 12.1 - - + -
60E LEU* 3.2 30.1 - - + -
63E ALA* 3.7 30.1 - - + -
64E ILE* 4.2 6.1 - - + -
68E PHE* 3.9 23.8 - - + -
69E VAL 3.0 5.3 + - - -
70E CYS* 3.5 4.0 - - - -
71E VAL* 2.9 26.0 + - - +
99E VAL* 4.2 20.0 - - + -
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Residues in contact with TYR 11 (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 VAL* 4.1 0.6 - - + -
10E VAL* 1.3 70.8 - - - +
12E LEU* 1.4 65.1 - - - +
13E HIS* 3.4 30.0 - + - -
21E SER* 3.6 13.1 + - - -
24E VAL* 4.5 11.3 - - + +
42E MET* 4.1 17.3 - - + -
44E TYR* 2.9 38.6 + - - +
45E HIS* 3.6 26.0 - + + -
71E VAL* 3.3 36.8 - - + -
73E GLU* 2.6 40.7 + - + -
109E ILE* 3.5 17.4 - - + +
155E PHE* 4.5 11.4 - + - -
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Residues in contact with LEU 12 (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* 4.5 2.9 - - + -
11E TYR* 1.4 74.2 - - - +
13E HIS* 1.3 63.2 + - - +
14E ASN* 4.3 10.1 - - - +
44E TYR* 4.2 21.8 - - + -
46E GLU* 5.8 0.7 - - - +
60E LEU* 4.2 23.6 - - + -
70E CYS* 4.3 13.5 - - - -
71E VAL 2.7 16.4 + - - +
72E ILE* 3.8 5.3 - - + -
73E GLU* 2.9 32.2 + - - +
95E ILE* 4.3 12.8 - - + -
96E CYS* 4.0 28.0 - - - -
99E VAL* 4.1 26.2 - - + -
100E ALA 5.3 0.2 - - - +
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Residues in contact with HIS 13 (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 TYR* 3.4 22.1 - + - -
12E LEU* 1.3 78.8 - - - +
14E ASN* 1.3 63.0 + - - +
16E GLU* 2.7 30.0 + - - +
18E THR* 4.5 3.3 + - + -
21E SER* 2.9 27.1 - - - -
45E HIS* 3.1 23.8 + + - -
46E GLU* 4.3 25.3 + - + +
47E THR* 3.1 23.7 + - - -
73E GLU* 3.7 5.4 - - - -
87E VAL* 4.3 8.8 - - - +
92E MET* 4.7 0.2 - - - +
20F HIS* 3.1 25.9 - - + -
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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