Contacts of the strand formed by residues 8 - 15 (chain A) in PDB entry 1WL4
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 8 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A ASP 5.4 0.7 - - - +
7A PRO* 1.3 76.0 - - - +
9A VAL* 1.3 62.2 + - - +
103A VAL* 4.0 34.5 - - + +
106A ILE* 3.8 28.7 - - + -
107A GLY* 4.3 7.0 - - - +
263A LEU* 3.8 36.6 - - + -
264A MET 3.6 10.3 - - - +
265A LYS* 4.4 2.2 - - + +
279A ARG* 3.7 0.7 - - - -
280A ILE* 2.8 36.4 + - + +
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Residues in contact with VAL 9 (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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7A PRO* 3.9 10.3 - - + +
8A VAL* 1.3 79.6 - - - +
10A ILE* 1.3 62.7 + - - +
11A VAL* 4.0 2.4 + - + -
263A LEU* 3.2 8.3 - - - +
264A MET* 2.9 43.1 + - + +
265A LYS 4.2 0.2 - - - +
266A LYS* 3.9 18.6 - - + +
269A ALA* 4.0 19.5 - - + -
276A PRO* 3.8 29.8 - - + -
278A ALA 3.4 9.6 - - - +
279A ARG* 4.0 18.2 - - + +
280A ILE 4.5 0.2 - - - +
397A GLU* 4.4 4.7 - - - +
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Residues in contact with ILE 10 (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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9A VAL* 1.3 74.6 - - - +
11A VAL* 1.3 61.0 + - - +
12A SER 3.5 24.9 - - - +
261A VAL* 3.8 11.4 - - + -
262A VAL 3.4 3.8 - - - +
263A LEU* 3.9 11.4 - - + -
276A PRO* 3.3 2.8 - - - +
277A LEU* 2.8 27.3 + - + +
278A ALA* 2.9 14.5 + - + +
280A ILE* 3.8 33.4 - - + -
363A LEU* 4.0 22.2 - - + -
367A LEU* 3.8 41.1 - - + -
394A VAL* 4.7 3.6 - - + -
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Residues in contact with VAL 11 (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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9A VAL* 4.3 10.5 - - + +
10A ILE* 1.3 76.0 - - - +
12A SER* 1.3 60.2 + - - +
45A ALA* 3.7 29.8 - - + +
262A VAL* 2.9 14.2 + - + +
264A MET* 4.1 33.4 - - + -
269A ALA* 4.4 8.3 - - + -
274A LEU* 4.1 22.4 - - + -
275A THR 4.5 8.5 - - - +
276A PRO* 4.1 8.5 - - + -
277A LEU* 3.8 16.1 + - - +
3001A SO4 4.2 5.0 + - - -
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Residues in contact with SER 12 (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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10A ILE* 3.5 5.4 - - - +
11A VAL* 1.3 79.3 - - - +
13A ALA* 1.3 64.3 + - - +
41A VAL* 3.5 28.6 + - - +
44A ARG* 3.1 21.3 - - - +
45A ALA* 4.0 9.6 - - - -
261A VAL* 3.2 4.4 - - - -
262A VAL* 3.0 26.2 + - - +
277A LEU* 4.0 2.5 - - - -
3001A SO4 2.7 25.7 + - - -
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Residues in contact with ALA 13 (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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12A SER* 1.3 78.2 + - - +
14A ALA* 1.3 62.7 + - - +
41A VAL* 4.1 0.2 - - - -
44A ARG* 3.7 3.1 + - - -
201A GLU* 4.5 0.3 - - - -
260A ALA 3.4 7.4 - - - -
261A VAL* 3.8 15.7 - - + -
277A LEU* 3.7 17.0 - - + -
364A VAL* 3.9 13.7 - - + -
367A LEU* 3.8 12.6 - - + -
368A HIS* 2.8 31.8 + - + +
3001A SO4 2.7 11.0 + - - -
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Residues in contact with ALA 14 (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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13A ALA* 1.3 75.0 - - - +
15A ARG* 1.3 63.0 + - - +
37A VAL* 4.1 4.5 - - + +
40A GLU* 4.3 10.3 - - + -
41A VAL* 3.5 16.7 - - + +
44A ARG* 3.7 22.0 - - - +
201A GLU 3.3 12.8 - - - +
203A VAL* 4.4 6.5 - - + -
259A ALA* 3.4 1.9 - - - -
260A ALA 2.9 32.3 + - - +
364A VAL* 3.6 8.0 - - - +
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Residues in contact with ARG 15 (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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14A ALA* 1.3 76.6 - - - +
16A THR* 1.3 83.0 + - - +
17A ILE* 3.7 3.6 - - - +
18A ILE* 4.0 9.5 - - - +
37A VAL* 3.9 7.2 - - - -
198A PHE* 3.5 32.9 - - - +
201A GLU* 2.8 37.2 + - + +
202A ILE* 3.2 9.1 - - - +
203A VAL* 2.9 25.1 + - - -
219A ASP* 2.8 43.4 + - - -
258A ALA 3.4 12.8 - - - +
259A ALA* 3.9 10.1 - - + -
351A LEU* 4.3 5.1 - - - +
361A ARG* 3.5 30.4 - - + +
364A VAL* 4.3 6.1 - - + -
365A THR* 4.0 1.5 + - - -
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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