Contacts of the strand formed by residues 331 - 338 (chain B) in PDB entry 1W5A
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 331 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255B GLU* 3.0 23.9 - - - +
256B SER 2.9 12.9 + - - +
261B ARG* 3.2 50.7 - - + +
262B ALA* 4.5 11.0 - - + -
265B ALA* 3.8 12.8 - - + +
289B VAL* 4.1 20.6 - - + -
290B MET 3.3 8.1 - - - +
291B GLY* 4.2 4.7 - - - -
292B PRO* 4.2 7.0 - - + -
295B LEU* 4.4 7.0 - - + -
299B GLU* 4.1 4.3 - - - +
329B ASN 4.1 0.2 + - - -
330B THR* 1.3 76.4 - - - +
332B ARG* 1.3 65.8 + - - +
333B VAL* 4.5 1.6 - - + -
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Residues in contact with ARG 332 (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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217B ASN* 3.5 31.5 + - - +
253B ILE* 5.0 11.2 - - + +
254B GLY 3.5 8.7 - - - +
255B GLU* 3.0 31.0 + - + +
288B HIS 3.7 1.4 - - - +
289B VAL* 3.6 2.3 - - - -
290B MET* 2.7 75.1 + - + +
324B ASP* 4.3 6.3 + - - -
327B LEU* 4.0 29.7 - - + +
330B THR* 4.1 2.5 + - + +
331B VAL* 1.3 75.0 - - - +
333B VAL* 1.3 69.3 + - - +
334B LEU* 5.6 0.4 - - - -
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Residues in contact with VAL 333 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252B GLY 3.6 1.0 - - - +
253B ILE* 3.5 6.8 - - - +
254B GLY 2.7 34.3 + - - +
265B ALA* 3.5 25.8 - - + +
266B VAL* 3.8 14.4 - - - +
269B ALA* 4.0 7.3 - - + +
287B ILE* 4.7 2.2 - - + -
288B HIS 3.7 4.3 - - - +
289B VAL* 4.7 4.5 - - + -
303B VAL* 4.1 31.4 - - + -
331B VAL* 4.5 5.4 - - + -
332B ARG* 1.3 80.0 - - - +
334B LEU* 1.3 61.6 + - - +
335B LEU* 3.3 30.1 - - + -
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Residues in contact with LEU 334 (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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217B ASN* 3.8 8.3 - - + +
218B ALA* 3.8 11.2 - - - +
221B GLY* 3.6 37.2 - - - +
222B LEU* 3.7 5.2 - - - +
251B ILE* 4.3 13.9 - - + -
252B GLY 3.6 7.6 - - - +
253B ILE* 3.9 20.2 - - + +
286B LEU 3.8 1.0 - - - +
287B ILE* 3.7 1.6 - - - -
288B HIS* 3.0 36.5 + - + +
290B MET* 3.9 17.2 - - + +
332B ARG* 5.6 0.2 - - + -
333B VAL* 1.3 73.6 - - - +
335B LEU* 1.3 76.2 + - - +
336B VAL* 4.2 16.6 - - + -
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Residues in contact with LEU 335 (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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251B ILE* 3.0 11.1 - - - +
252B GLY 2.7 42.5 + - - +
266B VAL* 4.6 0.4 - - + +
269B ALA* 3.7 20.9 - - + +
270B LEU* 3.7 36.6 - - + +
275B LEU* 4.6 6.7 - - + -
286B LEU 3.9 1.1 - - - -
287B ILE* 4.1 16.2 - - + -
307B VAL* 4.0 20.6 - - + -
333B VAL* 3.3 29.8 - - + -
334B LEU* 1.3 75.7 - - - +
336B VAL* 1.3 64.8 + - - +
337B ILE* 4.1 13.5 - - + -
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Residues in contact with VAL 336 (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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186B THR* 5.8 0.9 - - + -
188B VAL* 4.2 23.8 - - + -
222B LEU* 4.3 23.1 - - + -
249B ALA* 4.3 9.0 - - + -
250B MET 3.5 7.4 - - - +
251B ILE* 4.2 11.4 - - + -
285B ALA* 3.1 7.4 - - - +
286B LEU* 3.0 55.3 + - + +
334B LEU* 4.2 15.9 - - + -
335B LEU* 1.3 80.7 - - - +
337B ILE* 1.3 64.0 + - - +
338B THR* 3.8 3.6 + - + +
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Residues in contact with ILE 337 (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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248B LEU 4.0 0.3 - - - +
249B ALA* 3.0 23.5 - - - -
250B MET* 2.9 17.6 + - + +
270B LEU* 5.8 0.2 - - + -
275B LEU* 4.2 17.9 - - + -
277B VAL* 6.2 0.2 - - + -
279B ILE* 3.9 25.4 - - + -
282B ALA* 3.3 34.1 - - + -
284B GLY 3.7 2.7 - - - +
285B ALA* 3.8 17.7 - - + -
307B VAL* 4.8 5.8 - - + -
311B LEU* 4.5 11.2 - - + -
335B LEU* 4.6 15.0 - - + -
336B VAL* 1.3 85.1 - - - +
338B THR* 1.3 60.5 + - - +
340B VAL* 3.8 16.2 - - + +
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Residues in contact with THR 338 (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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186B THR* 4.4 8.7 - - + +
242B VAL* 4.1 17.7 - - + +
243B MET* 5.5 0.7 - - + -
246B GLY* 3.5 22.4 - - - -
249B ALA* 3.9 14.1 - - + -
282B ALA* 3.7 5.7 - - - +
283B THR* 3.1 26.4 + - - +
284B GLY* 3.1 29.6 + - - +
286B LEU* 4.5 12.8 - - + -
336B VAL* 4.4 8.7 - - + +
337B ILE* 1.3 76.8 - - - +
339B GLY* 1.3 65.6 + - - +
340B VAL* 3.4 2.1 + - - +
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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