Contacts of the strand formed by residues 335 - 342 (chain B) in PDB entry 5WRS
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 LEU 335 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285B ILE* 3.6 27.1 - - + +
286B VAL 3.4 2.2 - - - +
287B ASN* 3.9 33.0 - - + +
330B CYS 4.5 0.3 - - - +
331B GLY* 3.2 2.3 - - - -
332B LYS* 3.1 28.9 + - - +
333B PRO* 6.4 0.7 - - + -
334B HIS* 1.3 76.4 - - - +
336B LEU* 1.3 58.5 + - - +
337B GLU 4.4 0.2 - - - -
1D NAG 4.2 28.0 - - + +
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Residues in contact with LEU 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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236B PHE* 4.3 9.0 - - + -
238B PRO* 3.8 13.7 - - + -
239B MET* 4.5 7.4 - - + +
241B GLN* 3.4 34.5 - - + +
284B ARG 3.7 0.5 - - - +
285B ILE* 4.4 2.0 - - - -
286B VAL* 2.8 41.6 + - - +
288B VAL* 3.7 29.8 - - + -
315B PHE* 4.8 2.2 - - + -
329B VAL* 3.8 29.4 - - + -
330B CYS 3.6 11.2 - - - +
331B GLY* 4.3 1.3 - - - -
335B LEU* 1.3 75.8 - - - +
337B GLU* 1.3 77.2 + - - +
338B GLY 3.9 0.2 + - - -
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Residues in contact with GLU 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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236B PHE* 4.6 0.2 - - - -
239B MET* 3.0 45.8 + - + +
260B HIS* 2.5 37.0 + - + +
261B ASN* 4.2 2.1 + - - +
284B ARG 3.7 5.6 - - - -
285B ILE* 4.4 10.0 - - + +
336B LEU* 1.3 82.5 - - - +
338B GLY* 1.3 60.6 + - - +
486B LEU* 3.6 34.9 - - + +
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Residues in contact with GLY 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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236B PHE* 3.6 15.7 - - - -
237B LYS 3.4 12.1 - - - -
239B MET 4.0 2.9 - - - -
260B HIS* 4.0 9.9 - - - -
283B GLY* 3.4 5.2 - - - -
284B ARG* 3.1 31.4 + - - +
336B LEU 3.9 0.6 + - - -
337B GLU* 1.3 77.8 - - - +
339B SER* 1.3 60.7 + - - -
486B LEU* 3.5 5.1 - - - +
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Residues in contact with SER 339 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235B MET 3.3 2.0 + - - +
236B PHE* 3.3 6.5 - - - -
237B LYS* 2.9 50.9 + - - +
260B HIS* 3.5 28.4 - - - +
263B GLU* 3.7 21.7 - - - +
264B ILE* 4.1 8.1 - - - -
281B THR* 4.4 1.7 - - - +
282B VAL 3.6 4.3 - - - -
283B GLY* 4.5 0.7 - - - -
338B GLY* 1.3 73.9 - - - -
340B LEU* 1.3 61.8 + - - +
341B SER* 5.9 0.9 - - - -
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Residues in contact with LEU 340 (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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188B MET* 3.5 29.8 - - + +
226B LEU* 4.0 14.8 - - + -
228B PHE* 3.8 14.4 - - + -
234B ALA* 3.6 23.8 - - + -
235B MET 3.5 0.4 - - - -
236B PHE* 3.6 38.1 - - + +
280B PRO 4.0 0.3 - - - +
281B THR* 3.1 5.6 - - - -
282B VAL* 2.7 47.7 + - + +
284B ARG* 3.7 26.2 - - + -
286B VAL* 5.3 0.4 - - + -
339B SER* 1.3 75.5 - - - +
341B SER* 1.3 59.8 + - - +
342B ALA 4.3 0.2 + - - -
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Residues in contact with SER 341 (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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234B ALA* 3.2 4.5 - - - -
235B MET* 2.8 43.6 + - - +
237B LYS* 6.4 1.8 - - - -
263B GLU* 5.4 9.0 + - - -
279B PRO* 3.8 9.2 + - - +
280B PRO 3.6 3.8 - - - -
281B THR* 3.4 19.0 + - - -
339B SER* 5.9 0.7 - - - -
340B LEU* 1.3 73.9 - - - +
342B ALA* 1.3 65.2 + - - +
343B PHE* 4.2 0.3 - - - -
604B ATP 3.1 29.8 + - - -
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Residues in contact with ALA 342 (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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161B TRP* 6.3 1.1 - - + -
164B PHE* 4.3 12.6 - - + -
184B LEU* 4.0 24.7 - - + -
188B MET* 3.7 24.2 - - - -
233B LYS 4.0 4.7 - - - +
279B PRO* 3.5 8.7 - - - +
280B PRO* 2.9 18.6 + - + +
341B SER* 1.3 72.2 + - - +
343B PHE* 1.3 59.9 + - - +
604B ATP 2.6 24.7 + - - -
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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