Contacts of the strand formed by residues 255 - 265 (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 ASN 255 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18A ILE* 3.6 13.8 - - + +
19A GLY 3.0 20.6 + - - +
20A SER* 3.7 6.5 - - - +
21A PHE* 4.6 1.8 - - - +
122A MET* 3.2 30.4 + - - +
221A PHE* 3.6 30.9 - - - +
253A GLY* 2.9 23.8 + - - -
254A ILE* 1.3 79.4 + - - +
256A ASP* 1.3 66.1 - - - +
352A GLY* 3.1 12.9 - - - -
353A HIS 2.9 23.5 + - - +
354A PRO* 3.3 10.3 - - - +
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Residues in contact with ASP 256 (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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18A ILE* 3.4 6.6 - - - +
19A GLY* 2.8 29.5 + - - +
20A SER 3.9 8.3 - - - +
21A PHE* 5.4 0.2 - - - -
25A LEU* 3.7 21.8 + - + +
26A ALA* 3.8 14.2 + - - -
33A LEU* 4.6 1.1 - - + -
120A GLU 3.4 7.9 - - - +
121A ASN* 3.4 15.2 - - - +
122A MET 2.8 28.1 + - - -
123A SER* 2.6 33.1 + - - -
255A ASN* 1.3 78.1 - - - +
257A GLY* 1.3 58.0 + - - +
354A PRO* 3.6 4.5 - - - -
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Residues in contact with GLY 257 (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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16A THR* 3.3 13.0 - - - -
17A ILE 4.0 2.2 - - - -
18A ILE* 4.9 2.7 - - - -
25A LEU* 4.4 0.9 - - - -
33A LEU* 3.9 12.2 - - - +
119A MET* 4.3 0.2 - - - +
120A GLU 2.9 33.7 + - - +
256A ASP* 1.3 74.6 - - - +
258A ALA* 1.3 62.3 + - - +
354A PRO* 3.7 8.0 - - - +
357A ALA* 3.4 10.7 - - - +
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Residues in contact with ALA 258 (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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15A ARG* 3.4 2.8 - - - +
16A THR* 2.9 33.3 + - + +
33A LEU* 3.7 36.3 - - + +
34A GLY* 4.0 0.4 - - - +
37A VAL* 4.0 8.1 - - + -
118A GLY 3.2 13.2 - - - +
119A MET* 3.9 9.2 - - + -
257A GLY* 1.3 76.9 - - - +
259A ALA* 1.3 65.0 + - - +
357A ALA* 3.9 4.7 - - - +
361A ARG* 5.3 2.1 - - - +
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Residues in contact with ALA 259 (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 3.4 12.6 - - - +
15A ARG* 3.9 6.7 - - + +
37A VAL* 3.8 3.8 - - - -
57A PHE* 3.7 3.3 - - - -
117A GLY* 3.1 1.9 - - - -
118A GLY 3.0 30.3 + - - +
258A ALA* 1.3 77.7 - - - +
260A ALA* 1.3 63.2 + - - +
357A ALA* 4.3 2.7 - - - +
360A CYS* 3.8 9.2 - - + -
361A ARG* 3.5 38.4 - - + +
364A VAL* 4.2 2.0 - - + -
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Residues in contact with ALA 260 (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* 3.4 0.5 - - - -
14A ALA 2.9 33.0 + - - +
37A VAL* 3.8 22.4 - - + +
41A VAL* 3.5 20.7 - - + +
57A PHE* 3.9 8.7 - - + -
115A VAL* 4.2 5.8 - - + -
116A ALA 3.2 12.6 - - - +
259A ALA* 1.3 76.6 - - - +
261A VAL* 1.3 68.8 + - - +
360A CYS* 3.9 2.7 - - - -
364A VAL* 3.8 1.2 - - - +
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Residues in contact with VAL 261 (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* 3.8 14.4 - - + -
12A SER 3.2 7.9 - - - +
13A ALA* 3.8 20.6 - - + -
41A VAL* 4.4 1.8 - - - -
99A VAL* 3.9 24.0 - - + -
114A VAL 3.8 0.5 - - - +
115A VAL* 3.5 5.5 - - - +
116A ALA* 2.8 40.3 + - + +
260A ALA* 1.3 81.1 - - - +
262A VAL* 1.3 62.0 + - - +
263A LEU* 3.3 20.0 - - + -
360A CYS* 4.2 10.3 - - - -
363A LEU* 4.4 11.7 - - + -
364A VAL* 4.3 4.5 - - + -
367A LEU* 4.4 1.6 - - + -
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Residues in contact with VAL 262 (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* 3.4 4.5 - - - -
11A VAL* 2.9 29.9 + - + +
12A SER* 3.0 15.1 + - - +
41A VAL* 3.5 44.6 - - + +
42A LEU* 4.2 13.7 - - + +
45A ALA* 4.4 11.7 - - + -
47A VAL* 4.7 3.4 - - + -
113A ILE* 4.2 16.6 - - + -
114A VAL 3.6 3.8 - - - +
115A VAL* 4.3 4.0 - - + -
261A VAL* 1.3 72.1 - - - +
263A LEU* 1.3 61.4 - - - +
264A MET* 4.2 23.1 - - + -
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Residues in contact with LEU 263 (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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8A VAL* 3.8 11.4 - - + -
9A VAL 3.2 11.2 - - - +
10A ILE* 3.9 13.7 - - + -
99A VAL* 3.8 24.2 - - + +
102A ALA* 3.9 12.3 - - + -
103A VAL* 4.0 1.6 - - + +
106A ILE* 3.6 13.6 - - + +
113A ILE* 3.3 5.9 - - - +
114A VAL* 3.0 37.1 + - + +
116A ALA* 5.0 2.7 - - + -
261A VAL* 3.3 35.0 - - + +
262A VAL* 1.3 78.8 - - - +
264A MET* 1.3 64.7 + - - +
280A ILE* 3.7 23.1 - - + -
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Residues in contact with MET 264 (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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8A VAL* 3.6 1.6 - - - -
9A VAL* 2.9 30.3 + - + +
11A VAL* 4.1 15.7 - - + -
47A VAL* 4.0 19.7 - - + -
106A ILE* 4.1 9.4 - - - -
112A SER 3.5 17.7 - - - +
113A ILE* 4.2 14.4 - - + -
262A VAL* 4.2 13.5 - - + -
263A LEU* 1.3 77.8 - - - +
265A LYS* 1.3 70.8 + - - +
268A GLU* 3.8 15.3 - - + -
269A ALA* 3.5 34.3 - - + +
272A ARG* 4.1 6.5 - - - -
274A LEU* 4.0 19.1 - - + -
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Residues in contact with LYS 265 (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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6A ASP* 3.6 31.1 + - - +
7A PRO 3.6 5.2 - - - +
8A VAL* 4.4 3.1 - - + +
9A VAL* 4.1 0.7 - - - -
106A ILE* 3.5 40.0 + - + +
107A GLY* 4.7 11.1 + - - -
109A GLY* 4.9 8.6 - - - -
111A SER 5.8 0.7 - - - -
112A SER* 4.2 3.0 + - - +
264A MET* 1.3 80.8 - - - +
266A LYS* 1.3 66.7 + - - +
267A SER* 3.7 14.8 - - - +
268A GLU* 2.9 18.1 + - + +
269A ALA* 3.0 11.1 + - - +
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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