Contacts of the strand formed by residues 346 - 359 (chain B) in PDB entry 2QVS
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 SER 346 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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283B ARG* 4.7 1.4 + - - -
285B ILE 3.0 12.1 - - - -
286B ALA* 3.7 2.9 - - - -
287B GLN* 2.7 29.3 + - - +
304B ILE* 3.4 6.7 - - - +
305B LEU* 2.8 35.7 + - - -
307B ARG* 6.1 1.0 - - - +
320B GLU* 5.6 1.3 - - - -
345B ALA* 1.3 74.9 - - - +
347B ALA* 1.3 59.9 + - - +
348B TYR* 3.4 31.2 + - - -
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Residues in contact with ALA 347 (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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283B ARG* 3.6 2.9 - - - +
284B ILE* 2.7 33.5 + - + -
285B ILE* 2.6 37.2 + - + +
302B VAL* 3.9 8.7 - - + -
303B SER 3.3 4.9 - - - -
304B ILE* 3.5 24.0 - - + -
332B PHE* 4.2 7.6 - - + -
346B SER* 1.3 74.1 - - - +
348B TYR* 1.3 57.1 + - - +
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Residues in contact with TYR 348 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281B GLY* 3.8 18.4 - - - +
282B GLU 3.7 4.0 - - - +
283B ARG* 3.5 40.1 + - + -
284B ILE* 4.3 1.1 - - - +
302B VAL* 3.4 6.0 - - - -
303B SER* 2.8 41.1 + - - +
305B LEU* 3.9 28.9 - - + -
320B GLU* 3.9 12.0 + - - -
346B SER* 3.4 33.7 + - - -
347B ALA* 1.3 76.5 - - - +
349B GLY* 1.3 65.3 + - - +
350B VAL* 3.7 1.4 - - - +
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Residues in contact with GLY 349 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278B TYR* 5.2 2.2 - - - -
279B LYS 5.1 2.0 - - - -
280B ASP* 4.3 0.2 - - - +
281B GLY* 2.6 33.1 + - - -
282B GLU 3.0 17.9 + - - -
284B ILE* 4.0 11.1 - - - +
301B GLU 3.9 5.4 - - - -
348B TYR* 1.3 72.7 - - - +
350B VAL* 1.3 60.3 + - - +
351B GLY 3.4 4.7 - - - -
353B VAL* 3.9 14.4 - - - -
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Residues in contact with VAL 350 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280B ASP* 3.7 4.3 - - - +
300B GLY* 4.9 1.0 - - - -
301B GLU* 2.7 45.8 + - + +
302B VAL 3.6 2.9 - - - -
303B SER* 3.2 43.3 - - - +
325B HIS* 4.0 19.3 - - + +
348B TYR* 3.7 1.6 - - + +
349B GLY* 1.3 68.4 - - - -
351B GLY* 1.3 58.5 + - - +
352B ASP 4.3 0.2 + - - -
353B VAL* 4.0 0.4 - - - +
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Residues in contact with GLY 351 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279B LYS 3.6 1.4 - - - -
280B ASP* 2.7 52.9 + - - -
349B GLY 3.4 2.0 + - - -
350B VAL* 1.3 74.9 - - - +
352B ASP* 1.3 65.4 + - - -
353B VAL* 3.5 7.6 + - - +
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Residues in contact with ASP 352 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277B ILE* 5.2 8.4 - - + +
278B TYR 3.5 7.5 - - - +
279B LYS* 4.3 6.1 - - - +
280B ASP* 4.0 11.6 + - - +
299B SER* 3.9 2.7 + - - +
300B GLY* 3.4 21.7 + - - -
351B GLY* 1.3 70.9 - - - -
353B VAL* 1.3 58.9 + - - +
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Residues in contact with VAL 353 (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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276B LYS 4.4 0.2 - - - -
277B ILE* 3.3 8.9 - - - +
278B TYR* 2.8 52.0 + - + +
284B ILE* 4.5 1.1 - - + -
297B ILE* 4.7 1.1 - - + -
299B SER* 3.5 10.8 - - - +
301B GLU 3.2 33.0 - - - +
302B VAL* 4.2 9.6 - - + -
349B GLY* 3.9 11.7 - - - -
350B VAL 4.0 0.2 - - - +
351B GLY 3.7 10.1 - - - +
352B ASP* 1.3 78.6 - - - +
354B LYS* 1.3 65.5 + - - +
355B CYS* 3.3 29.8 - - - -
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Residues in contact with LYS 354 (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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247B MET* 5.3 7.4 - - + +
275B GLU* 3.0 34.7 + - - -
276B LYS 3.4 9.6 - - - +
277B ILE* 4.1 24.9 - - + +
297B ILE* 3.8 0.9 - - - -
298B GLU* 2.8 45.5 + - + +
299B SER* 3.1 25.4 + - - +
353B VAL* 1.3 75.8 - - - +
355B CYS* 1.3 64.4 + - - +
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Residues in contact with CYS 355 (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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275B GLU* 3.4 4.7 - - - -
276B LYS 3.1 30.7 + - - -
278B TYR* 4.5 14.4 - - + -
284B ILE* 4.6 1.8 - - - -
295B TYR* 4.1 20.4 - - + -
296B ILE 3.4 7.2 - - - +
297B ILE* 4.3 9.0 - - - -
298B GLU* 3.5 6.3 - - - +
332B PHE* 4.1 29.2 - - - -
353B VAL* 3.3 26.9 - - - -
354B LYS* 1.3 74.1 - - - +
356B LEU* 1.3 63.0 + - - +
357B VAL* 3.8 1.5 + - + +
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Residues in contact with LEU 356 (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 PHE* 3.3 52.9 - - + +
251B PHE* 3.8 34.3 - - + -
252B ILE* 4.6 8.7 - - + -
273B ILE* 4.0 17.3 - - + -
274B GLY 3.1 10.5 - - - +
275B GLU* 3.6 10.1 - - + -
294B PHE* 3.6 1.4 - - - +
295B TYR* 3.2 7.6 - - - +
296B ILE* 2.9 45.1 + - + +
298B GLU* 3.3 16.2 - - - +
355B CYS* 1.3 73.4 - - - +
357B VAL* 1.3 58.7 + - - +
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Residues in contact with VAL 357 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273B ILE* 3.6 2.3 - - - +
274B GLY* 2.7 36.5 + - - +
276B LYS* 3.3 46.4 - - + +
293B SER* 3.6 24.2 - - - +
294B PHE 3.6 2.7 - - - +
295B TYR* 3.6 28.7 - - + +
355B CYS* 4.1 8.3 - - + +
356B LEU* 1.3 74.2 - - - +
358B MET* 1.3 63.7 + - - +
359B ASP 4.2 0.9 + - - +
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Residues in contact with MET 358 (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 ILE* 3.6 33.9 - - + -
272B VAL* 3.7 30.5 - - + +
273B ILE* 4.0 25.4 - - + -
293B SER* 2.8 21.3 - - - -
294B PHE* 3.0 56.1 + - + -
356B LEU 4.1 0.4 + - - -
357B VAL* 1.3 73.6 - - - +
359B ASP* 1.3 71.1 + - - +
360B VAL 3.5 0.3 + - - -
362B ALA* 4.5 3.4 - - + -
363B PHE* 4.0 24.9 - - + +
366B LEU* 4.4 3.8 - - + -
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Residues in contact with ASP 359 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292B ASP* 3.7 20.9 - - - +
293B SER* 3.8 4.9 - - - -
357B VAL* 4.2 1.8 + - - +
358B MET* 1.3 78.0 - - - +
360B VAL* 1.3 59.2 + - - +
361B GLN* 2.8 37.3 + - - +
362B ALA* 3.1 20.9 + - + +
363B PHE* 3.0 27.7 + - - +
365B ARG* 5.4 0.3 + - - -
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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