Contacts of the helix formed by residues 316 - 332 (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 ASP 316 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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217B ARG* 6.2 4.5 - - + -
315B GLY* 1.3 72.0 - - - -
317B GLU* 1.3 70.4 + - - +
318B HIS* 3.3 2.9 + - - -
319B ILE* 3.4 27.2 + - + +
320B ARG* 3.9 5.9 + - - +
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Residues in contact with GLU 317 (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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315B GLY 3.8 0.2 - - - -
316B ASP* 1.3 83.9 + - - +
318B HIS* 1.3 76.2 + - + +
319B ILE 3.5 0.2 + - - -
320B ARG* 3.8 14.5 + - - +
321B ASP* 3.5 25.0 + - - +
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Residues in contact with HIS 318 (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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268B TYR* 3.5 30.2 + - + +
313B ASN* 6.2 3.6 - - + +
315B GLY* 3.6 35.8 - - - -
316B ASP 5.4 0.2 - - - -
317B GLU* 1.3 88.1 + - + +
319B ILE* 1.3 52.8 + - + +
321B ASP* 2.9 11.4 + - - +
322B MET* 2.7 40.8 + - + +
400B GDD 5.0 5.6 - - - +
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Residues in contact with ILE 319 (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 ARG* 4.3 13.5 - - + +
218B TYR* 3.8 50.0 - - + +
221B VAL* 4.2 27.3 - - + +
315B GLY 4.3 14.1 - - - +
316B ASP* 3.4 18.9 + - + +
317B GLU 3.3 1.0 - - - -
318B HIS* 1.3 78.2 - - - +
320B ARG* 1.3 66.5 + - - +
322B MET* 3.2 17.0 + - + +
323B LEU* 3.2 19.8 + - - +
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Residues in contact with ARG 320 (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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221B VAL* 6.4 0.2 - - - -
316B ASP 3.9 4.3 + - - +
317B GLU* 3.8 17.1 + - - +
319B ILE* 1.3 82.6 - - + +
321B ASP* 1.3 76.0 + - - +
323B LEU* 3.0 15.2 + - + +
324B LEU* 2.9 30.2 + - + +
351B ALA* 5.8 3.4 - - + -
352B GLY* 4.4 35.0 + - - +
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Residues in contact with ASP 321 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268B TYR* 4.4 14.1 - - + -
317B GLU* 3.5 17.0 - - - +
318B HIS* 2.9 17.5 + - - +
320B ARG* 1.3 97.3 + - - +
322B MET* 1.3 50.7 + - - +
324B LEU* 3.5 14.5 - - - +
325B ALA* 2.8 37.7 + - - +
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Residues in contact with MET 322 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218B TYR* 4.3 28.5 - - + -
221B VAL* 5.5 7.0 - - + -
225B ASN* 3.7 6.6 + - - +
248B ASN* 4.0 26.2 - - - +
268B TYR* 4.1 40.5 - - + +
318B HIS* 2.7 22.0 + - + +
319B ILE* 3.2 22.9 + - + +
321B ASP* 1.3 72.9 - - - +
323B LEU* 1.3 61.3 + - - +
325B ALA* 3.5 2.9 - - - +
326B CYS* 3.2 24.1 + - - +
400B GDD 4.3 24.0 - - - +
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Residues in contact with LEU 323 (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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220B ARG* 4.9 11.2 - - - +
221B VAL* 4.1 18.3 - - + +
224B ARG* 3.9 25.1 - - + -
225B ASN* 3.4 22.3 - - - +
319B ILE 3.2 8.1 + - - +
320B ARG* 3.0 15.1 + - + +
322B MET* 1.3 75.8 - - - +
324B LEU* 1.3 59.2 - - - +
326B CYS 3.2 1.4 + - - -
327B LEU* 2.9 51.9 + - + +
347B GLU* 4.9 4.9 - - + +
348B LEU* 4.3 13.9 - - + -
351B ALA* 4.1 25.4 - - + -
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Residues in contact with LEU 324 (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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320B ARG* 2.9 21.4 + - + +
321B ASP* 3.5 19.5 - - - +
323B LEU* 1.3 73.6 - - - +
325B ALA* 1.3 67.1 + - - +
327B LEU* 3.9 0.9 - - - +
328B ALA* 3.0 22.0 + - + +
348B LEU* 3.9 26.8 - - + +
358B GLU* 5.5 0.4 - - - +
360B PRO* 4.0 24.9 - - + -
361B PRO* 4.2 19.5 - - + -
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Residues in contact with ALA 325 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268B TYR* 3.5 37.7 - - + +
269B ALA* 4.0 5.3 - - + +
321B ASP 2.8 20.4 + - - +
322B MET 3.5 6.5 - - - +
324B LEU* 1.3 76.1 - - - +
326B CYS* 1.3 64.0 + - - +
328B ALA* 3.1 12.6 + - - +
329B THR* 3.1 18.9 + - - +
363B PRO* 5.4 0.7 - - - +
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Residues in contact with CYS 326 (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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225B ASN* 3.4 44.4 - - - +
228B ALA* 5.0 0.9 - - - -
229B LEU* 3.9 18.4 - - - -
247B ALA* 4.5 1.8 - - - -
248B ASN* 5.0 0.4 - - - +
272B PRO* 3.8 30.7 - - + -
322B MET 3.2 8.5 + - - +
323B LEU 3.2 1.6 + - - -
325B ALA* 1.3 79.4 - - - +
327B LEU* 1.3 65.2 + - - +
329B THR* 2.9 28.2 + - - -
330B VAL* 3.4 6.4 + - - +
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Residues in contact with LEU 327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224B ARG* 4.4 8.7 - - + +
225B ASN* 3.3 25.6 - - - +
228B ALA* 4.0 24.5 - - + -
323B LEU* 2.9 29.4 + - + +
324B LEU 4.1 0.2 - - - +
326B CYS* 1.3 77.7 - - + +
328B ALA* 1.3 56.8 + - - +
330B VAL* 3.6 5.6 + - - +
331B TYR* 3.0 21.5 + - - +
344B VAL* 3.3 41.4 - - + +
347B GLU* 4.1 15.9 - - + -
348B LEU* 3.4 31.4 - - + -
360B PRO* 5.5 0.9 - - - -
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Residues in contact with ALA 328 (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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324B LEU* 3.0 22.2 + - + +
325B ALA* 3.3 7.6 - - - +
326B CYS 3.0 0.4 - - - -
327B LEU* 1.3 74.2 - - - +
329B THR* 1.3 58.5 + - + +
330B VAL 3.1 2.5 - - - -
331B TYR* 3.1 7.4 + - - +
332B HIS* 2.8 35.7 + - - +
348B LEU* 6.0 0.2 - - - +
360B PRO* 3.9 18.4 - - + +
361B PRO* 3.6 24.5 - - + +
363B PRO* 4.8 4.7 - - + -
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Residues in contact with THR 329 (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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269B ALA* 3.8 28.7 - - + +
272B PRO* 3.8 17.8 - - + +
273B GLN* 3.5 27.6 + - - +
276B VAL* 4.0 16.6 - - - +
325B ALA 3.1 18.8 - - - +
326B CYS* 2.9 16.1 + - - +
328B ALA* 1.3 77.4 - - - +
330B VAL* 1.3 58.9 + - - +
332B HIS* 3.9 1.4 - - - +
333B SER* 3.2 22.7 + - - -
363B PRO* 4.2 11.7 - - + -
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Residues in contact with VAL 330 (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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228B ALA* 4.2 19.5 - - + +
229B LEU* 3.7 30.3 - - + -
232B LEU* 3.7 29.2 - - + -
276B VAL* 4.4 1.6 - - + -
326B CYS 3.4 8.4 + - - +
327B LEU* 3.9 7.4 - - - +
329B THR* 1.3 80.5 + - - +
331B TYR* 1.3 69.1 + - - +
332B HIS 3.1 1.3 - - - -
333B SER* 2.8 22.9 + - - -
336B ALA* 3.5 7.3 - - - +
340B VAL* 3.9 19.7 - - + -
344B VAL* 4.1 14.1 - - + -
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Residues in contact with TYR 331 (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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327B LEU 3.0 20.1 + - - +
328B ALA* 3.4 8.3 - - - +
330B VAL* 1.3 80.9 - - - +
332B HIS* 1.3 86.7 + + - +
333B SER 3.4 0.3 + - - -
341B ARG* 3.5 77.4 + - + +
344B VAL* 4.2 9.8 - - + +
345B LEU* 3.3 33.2 - - + +
359B GLU* 3.0 34.2 + - - -
360B PRO* 4.3 10.1 - - + -
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Residues in contact with HIS 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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328B ALA* 2.8 18.6 + - - +
329B THR 3.9 2.2 - - - +
331B TYR* 1.3 103.4 - + - +
333B SER* 1.3 67.7 + - - +
334B LYS* 3.5 5.0 + - - +
341B ARG* 5.4 0.4 - - - +
359B GLU* 4.6 7.5 + - + +
360B PRO* 2.8 28.8 + - + -
361B PRO 4.1 1.0 + - - -
362B PRO* 3.5 35.4 - - + +
363B PRO* 4.3 12.8 - - + -
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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