Contacts of the strand formed by residues 5 - 13 (chain E) in PDB entry 2WP9
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 VAL 5 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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130B ALA* 3.6 22.2 - - - +
131B ARG* 5.0 5.7 - - - +
1E MET* 3.8 26.9 - - + -
3E LEU 3.5 9.6 - - - +
4E PRO* 1.3 78.9 - - - +
6E ARG* 1.3 65.1 + - - +
7E GLU* 4.0 4.0 + - + +
192E TYR* 3.4 22.2 - - + -
194E LYS* 3.9 32.5 - - + -
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Residues in contact with ARG 6 (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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128B PRO* 2.9 29.5 + - - +
129B PRO* 4.1 2.0 - - - +
130B ALA* 3.9 32.1 - - + +
4E PRO* 5.4 2.3 - - + +
5E VAL* 1.3 74.6 - - - +
7E GLU* 1.3 60.4 + - - +
8E PHE* 3.7 20.7 - - + -
161E PHE* 3.8 25.6 - - - -
164E TRP* 4.9 7.9 - - - -
189E GLU* 5.3 7.1 + - - -
191E VAL* 4.0 21.5 - - + +
192E TYR 2.9 10.6 + - - +
193E PHE* 3.4 31.8 - - + -
194E LYS* 2.9 25.3 + - - +
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Residues in contact with GLU 7 (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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94A GLU* 5.7 1.4 - - - +
130B ALA 5.3 3.2 + - - -
5E VAL* 4.0 5.3 + - + +
6E ARG* 1.3 71.6 - - - +
8E PHE* 1.3 82.6 - - - +
32E THR* 5.0 0.7 + - - -
194E LYS* 3.3 48.2 + - + +
195E ALA* 5.8 0.2 - - - -
196E ARG* 6.0 1.9 - - - -
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Residues in contact with PHE 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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128B PRO* 4.9 10.1 - - + -
6E ARG* 3.7 33.4 - - + -
7E GLU* 1.3 86.6 - - - +
9E ASP* 1.3 67.2 + - - +
10E ALA 3.3 19.1 - - - +
11E VAL* 4.5 7.4 - - + -
32E THR* 3.7 14.8 - - - +
33E CYS 3.9 9.6 - - - -
34E ALA* 3.6 39.5 - - + -
159E THR* 4.3 14.1 - - + -
161E PHE* 3.7 18.2 - + - -
193E PHE* 4.0 6.5 - + - -
194E LYS 3.0 6.6 + - - +
195E ALA* 3.2 18.9 - - - -
196E ARG* 3.7 2.5 + - - -
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Residues in contact with ASP 9 (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 PHE* 1.3 71.1 - - - +
10E ALA* 1.3 60.2 + - + +
31E GLN* 3.4 25.5 - - + +
32E THR* 3.0 40.2 + - - +
196E ARG* 2.9 64.9 + - - +
197E ALA* 3.0 8.5 + - - +
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Residues in contact with ALA 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 PHE* 3.3 8.3 - - - +
9E ASP* 1.3 79.6 - - + +
11E VAL* 1.3 65.7 + - - +
12E VAL* 4.1 1.1 - - + -
26E ILE* 4.2 33.7 - - + -
32E THR 3.1 10.9 + - - +
33E CYS* 3.3 4.5 - - - -
34E ALA 3.0 22.2 + - - -
197E ALA* 3.2 18.4 - - + +
199E VAL* 5.0 1.8 - - + -
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Residues in contact with VAL 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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8E PHE* 4.5 12.1 - - + -
10E ALA* 1.3 76.1 - - - +
12E VAL* 1.3 62.9 + - - +
13E ILE* 3.8 17.6 + - + -
34E ALA* 3.5 4.9 - - + -
36E LEU* 4.2 27.6 - - + -
179E GLY* 5.8 0.2 - - - -
180E CYS* 4.7 5.6 - - - -
193E PHE* 4.0 25.8 - - + +
194E LYS 4.4 4.9 - - - +
195E ALA* 3.5 24.5 - - + -
197E ALA 2.9 6.8 + - - +
198E THR* 3.5 6.9 - - + +
199E VAL 2.8 25.3 + - - -
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Residues in contact with VAL 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 ALA* 5.0 0.2 - - + -
11E VAL* 1.3 74.8 - - - +
13E ILE* 1.3 61.3 + - - +
14E GLY 3.3 13.2 + - - +
19E GLY* 3.7 17.5 - - - +
22E ALA* 4.8 2.0 - - + -
23E ALA* 4.5 6.5 - - - +
26E ILE* 4.0 20.0 - - + -
33E CYS* 3.8 22.2 - - - -
34E ALA 2.8 11.5 + - - +
35E LEU* 3.6 24.3 - - + -
36E LEU* 2.8 29.1 + - - +
199E VAL* 3.5 21.1 - - + +
201E ALA* 4.4 4.9 - - + -
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Residues in contact with ILE 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 VAL* 4.2 15.3 - - + +
12E VAL* 1.3 71.7 - - - +
14E GLY* 1.3 58.1 + - - +
36E LEU* 4.2 10.8 - - + -
166E ALA* 3.7 24.9 - - + -
180E CYS* 3.6 27.4 - - - -
198E THR* 3.9 18.6 - - + -
199E VAL 2.7 16.7 + - - +
200E LEU* 3.9 18.8 - - + -
201E ALA* 2.8 28.8 + - - -
202E THR* 3.5 18.2 - - + +
225E MET* 4.2 7.0 - - + -
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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