Contacts of the strand formed by residues 298 - 304 (chain B) in PDB entry 2WVL
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 298 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14B VAL* 3.1 7.3 + - + +
15B VAL* 4.1 13.8 - - + +
16B ARG* 2.6 36.2 + - - +
194B PHE* 3.1 20.2 - - + +
258B LEU* 3.8 23.6 - - + -
278B LEU* 4.2 11.2 - - + -
282B TYR* 3.9 22.2 - - + -
293B VAL* 3.9 20.6 - - + -
297B GLY* 1.3 77.7 - - - +
299B GLU* 1.3 65.3 + - - +
300B ILE* 4.1 8.7 - - + -
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Residues in contact with GLU 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B ARG* 3.4 22.0 + - + +
18B HIS* 3.1 30.2 + - + -
189B MET 4.1 3.3 - - - +
190B ALA* 3.5 7.1 - - + -
191B LYS* 2.6 49.6 + - - +
192B THR* 3.7 12.8 + - + +
194B PHE 3.1 6.1 + - - +
195B ALA* 3.2 3.5 - - - +
196B MET 2.9 24.4 + - - +
298B VAL* 1.3 74.5 - - - +
300B ILE* 1.3 63.1 + - - +
301B PHE* 3.5 22.2 - - + -
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Residues in contact with ILE 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B VAL* 3.8 20.6 - - + -
16B ARG 2.9 10.3 + - - +
17B LEU* 3.9 18.8 - - + -
18B HIS* 2.8 35.0 + - - +
196B MET* 3.3 14.1 - - + +
198B ARG* 4.0 22.9 - - - -
275B LEU* 3.7 16.2 - - + +
278B LEU* 3.3 35.0 - - + -
279B LEU* 5.8 1.1 - - + -
298B VAL* 4.5 5.2 - - + -
299B GLU* 1.3 78.8 - - - +
301B PHE* 1.3 72.7 + - - +
302B GLN* 4.7 7.2 - - + -
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Residues in contact with PHE 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B PRO* 5.8 1.3 - - + -
18B HIS* 3.8 16.8 - + - -
21B GLN* 3.2 22.9 - - - +
41B ARG* 5.5 3.8 - - - -
186B GLY* 3.8 17.7 - - - -
189B MET* 3.6 34.8 - - + -
190B ALA* 3.7 24.9 - - + -
195B ALA* 5.0 1.3 - - + -
196B MET 2.7 19.0 + - - +
197B VAL* 3.6 8.5 - - + -
198B ARG* 2.8 26.5 + - - +
299B GLU* 3.5 40.2 - - + -
300B ILE* 1.3 78.7 - - - +
302B GLN* 1.3 69.0 - - - +
303B ILE* 4.4 11.2 - - + -
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Residues in contact with GLN 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B LEU* 5.3 5.7 - - - +
18B HIS 2.8 23.3 + - - +
19B GLU* 4.1 1.7 + - - +
20B VAL* 3.3 18.0 + - + -
21B GLN* 2.9 29.4 + - - +
198B ARG* 3.1 7.6 - - - +
200B LEU* 4.5 1.6 - - - -
243B VAL* 2.8 23.1 + - - +
244B VAL* 3.8 6.2 - - - +
245B LYS* 2.9 27.3 - - - +
246B THR* 2.7 37.7 + - + +
275B LEU* 5.7 1.4 - - - +
300B ILE* 4.7 9.8 - - + +
301B PHE* 1.3 79.8 - - - +
303B ILE* 1.3 63.1 + - - +
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Residues in contact with ILE 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3B LEU* 3.8 29.6 - - + -
21B GLN* 3.5 12.8 - - - +
23B ILE* 3.8 20.6 - - + -
182B ALA* 3.6 26.7 - - + +
185B ALA* 5.0 0.2 - - + -
186B GLY* 4.2 11.9 - - - +
189B MET* 4.6 6.3 - - + -
197B VAL* 3.4 29.8 - - + -
198B ARG 2.8 10.6 + - - +
199B ILE* 3.3 13.7 - - + +
200B LEU* 3.2 21.4 + - - +
301B PHE* 4.4 4.9 - - + -
302B GLN* 1.3 77.3 - - - +
304B GLU* 1.3 64.7 + - - +
305B THR* 3.5 2.1 + - - +
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Residues in contact with GLU 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B VAL* 3.8 14.1 - - + +
21B GLN 2.9 10.7 + - - +
22B ARG* 3.2 36.4 + - - +
23B ILE* 3.4 25.3 + - - +
200B LEU* 3.4 20.7 - - + +
201B TRP* 4.7 4.3 - - - -
202B ARG* 3.1 54.9 + - - +
302B GLN 4.0 0.4 + - - -
303B ILE* 1.3 72.4 - - - +
305B THR* 1.3 73.2 + - - +
306B ARG 3.9 0.2 + - - -
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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