Contacts of the strand formed by residues 190 - 200 (chain A) 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 190 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3A LEU* 3.6 29.4 - - + +
4A PRO* 3.6 8.3 - - - +
167A LEU* 4.2 4.7 - - + -
181A THR* 4.7 0.2 - - - -
182A ALA 3.4 9.6 - - - +
183A LEU* 3.8 17.7 - - + -
188A GLY 3.7 9.0 - - - +
189A GLU* 1.3 79.1 - - - +
191A VAL* 1.3 73.2 + - - +
441A LEU* 3.8 29.2 - - + -
444A LEU* 3.9 18.2 - - + -
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Residues in contact with VAL 191 (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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3A LEU* 4.3 6.1 - - - -
4A PRO* 3.7 26.5 - - + +
6A ARG* 3.9 30.3 - - + +
164A TRP* 3.9 22.9 - - + -
181A THR* 3.1 6.4 - - - -
182A ALA 3.0 31.0 + - - -
189A GLU* 4.0 19.5 + - - -
190A VAL* 1.3 80.7 - - - +
192A TYR* 1.3 76.3 + - - +
193A PHE* 3.9 10.8 + - + -
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Residues in contact with TYR 192 (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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1A MET* 4.9 5.6 - - + -
3A LEU* 4.2 15.5 - - + +
4A PRO 3.0 12.5 + - - +
5A VAL* 3.5 24.8 - - + -
6A ARG 2.9 25.5 + - - -
170A VAL* 3.9 22.4 - - + -
178A VAL* 2.8 38.2 + - - +
180A CYS 3.5 10.8 - - - -
181A THR* 4.3 4.0 - - + -
191A VAL* 1.3 76.9 - - - +
193A PHE* 1.3 76.9 + - - +
194A LYS* 3.5 23.9 + - + +
432A ALA* 3.7 15.4 + - + +
437A VAL* 3.7 22.7 - - + -
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Residues in contact with PHE 193 (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 ARG* 3.4 28.0 - - + -
8A PHE* 4.0 18.4 - + - -
11A VAL* 4.0 19.0 - - + +
34A ALA* 4.6 1.6 - - + -
36A LEU* 3.9 30.7 - - + -
161A PHE* 3.9 29.4 - + - -
164A TRP* 3.7 37.9 - + - -
179A GLY* 3.1 7.3 - - - -
180A CYS* 2.8 37.2 + - - +
182A ALA* 3.7 21.5 - - + -
191A VAL* 3.9 10.1 - - + -
192A TYR* 1.3 71.3 - - - +
194A LYS* 1.3 61.2 + - - +
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Residues in contact with LYS 194 (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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5A VAL* 3.9 24.5 - - + -
6A ARG 2.9 9.1 + - - +
7A GLU* 3.3 39.5 + - + +
8A PHE* 2.9 28.3 + - - +
11A VAL* 4.4 0.7 - - - +
178A VAL* 3.7 7.4 - - + +
192A TYR* 3.5 26.9 + - + +
193A PHE* 1.3 69.7 - - - +
195A ALA* 1.3 65.3 + - - +
431A ASP* 3.2 32.5 + - - +
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Residues in contact with ALA 195 (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 GLU* 5.7 0.4 - - - -
8A PHE 3.2 10.3 - - - +
9A ASP 3.9 0.4 - - - +
11A VAL* 3.5 28.5 - - + +
177A VAL 4.6 0.2 - - - +
178A VAL* 3.2 31.0 + - - +
179A GLY* 4.2 1.5 + - - -
194A LYS* 1.3 80.8 - - - +
196A ARG* 1.3 64.7 + - - +
197A ALA 3.6 20.2 - - - +
198A THR* 4.1 8.0 + - - +
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Residues in contact with ARG 196 (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 GLU* 6.0 2.2 - - - -
8A PHE 3.7 2.5 + - - -
9A ASP* 2.9 44.0 + - - +
31A GLN* 4.5 8.9 - - - +
195A ALA* 1.3 74.4 - - - +
197A ALA* 1.3 59.6 + - - +
382A GLY* 3.7 9.6 - - - -
423A ILE* 4.0 42.3 - - + +
426A GLN* 2.9 29.5 + - - +
428A ALA* 6.6 0.2 - - - -
429A LEU* 4.1 13.9 - - + +
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Residues in contact with ALA 197 (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 ASP 3.1 8.4 + - - +
10A ALA* 3.2 5.0 - - + +
11A VAL 3.0 26.0 + - - +
195A ALA* 3.6 2.1 - - - +
196A ARG* 1.3 78.8 - - - +
198A THR* 1.3 61.8 + - - +
199A VAL* 3.9 2.6 - - + +
382A GLY 3.5 5.4 - - - -
384A PHE* 3.5 22.7 - - + -
419A LEU* 3.9 27.6 - - + -
423A ILE* 4.3 5.6 - - + -
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Residues in contact with THR 198 (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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11A VAL* 3.5 10.0 - - + +
13A ILE* 3.8 28.7 - - + -
169A LEU* 4.1 18.2 - - + -
177A VAL* 3.8 9.3 - - - +
178A VAL* 4.3 0.3 - - - -
179A GLY* 3.2 36.7 + - - +
180A CYS* 5.0 0.2 - - + -
195A ALA* 4.1 4.5 + - - +
197A ALA* 1.3 71.9 - - - +
199A VAL* 1.3 61.4 + - - +
200A LEU* 5.0 0.4 - - + +
382A GLY 2.8 15.2 + - - -
383A LEU* 3.5 6.6 - - + +
384A PHE* 2.9 25.7 + - - +
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Residues in contact with VAL 199 (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 ALA* 5.1 0.9 - - + -
11A VAL 2.9 14.5 + - - +
12A VAL* 3.5 23.8 - - + +
13A ILE* 2.7 32.9 + - - -
22A ALA* 5.1 4.9 - - + -
26A ILE* 4.6 12.6 - - + -
197A ALA* 4.5 11.0 - - + +
198A THR* 1.3 74.3 - - - +
200A LEU* 1.3 61.2 + - - +
201A ALA 3.5 0.7 + - - -
384A PHE* 3.5 28.0 - - + +
386A VAL* 4.0 31.4 - - + -
415A ALA* 5.3 4.9 - - + -
419A LEU* 5.0 4.0 - - + -
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Residues in contact with LEU 200 (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 ILE* 4.0 24.7 - - + -
169A LEU* 4.5 14.8 - - + -
198A THR* 5.2 0.7 - - + -
199A VAL* 1.3 72.8 - - - +
201A ALA* 1.3 58.9 + - - +
202A THR* 3.8 17.7 - - + -
222A GLY* 4.3 14.8 - - - +
225A MET* 4.5 11.9 - - + -
226A ALA* 5.0 2.2 - - + +
360A ILE* 3.5 28.3 - - + -
383A LEU* 3.8 26.7 - - + -
384A PHE 2.8 14.3 + - - +
385A ALA* 3.2 7.2 - - + -
386A VAL 3.0 25.1 + - - -
389A ILE* 3.3 10.5 - - + +
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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