Contacts of the helix formed by residues 360 - 368 (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 VAL 360 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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291B ALA 5.3 0.9 - - - +
292B ASP* 2.7 32.7 + - - +
293B SER* 3.7 8.1 - - - -
294B PHE* 4.6 1.6 - - + -
336B ALA* 3.4 41.5 - - + +
337B LEU* 3.9 25.6 - - + +
359B ASP* 1.3 68.7 - - - +
361B GLN* 1.3 63.7 + - + +
363B PHE* 3.1 7.9 + - - +
364B GLU* 2.9 44.0 + - + +
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Residues in contact with GLN 361 (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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292B ASP* 4.4 7.4 + - - +
359B ASP* 2.8 15.9 + - - +
360B VAL* 1.3 75.9 - - + +
362B ALA* 1.3 61.4 + - - +
364B GLU* 3.4 7.2 + - - +
365B ARG* 3.0 44.8 + - - +
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Residues in contact with ALA 362 (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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272B VAL* 5.3 0.4 - - + -
358B MET* 4.5 8.3 - - + -
359B ASP* 3.1 24.9 + - + +
361B GLN* 1.3 72.9 - - - +
363B PHE* 1.3 66.8 + - - +
365B ARG* 3.2 20.4 + - - +
366B LEU* 3.0 29.0 + - - +
278E THR* 3.7 29.4 - - + +
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Residues in contact with PHE 363 (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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258B PHE* 3.9 32.5 - + - -
261B LEU* 5.3 0.7 - - + -
269B ILE* 3.8 19.1 - - + -
294B PHE* 4.1 15.0 - + - -
337B LEU* 3.9 15.5 - - + -
358B MET* 4.0 12.5 - - + +
359B ASP 3.0 15.7 + - - +
360B VAL* 3.1 12.5 + - - +
362B ALA* 1.3 76.9 - - - +
364B GLU* 1.3 61.4 + - + +
366B LEU* 3.3 3.9 + - - +
367B LEU* 2.8 43.8 + - + +
368B GLY 3.8 15.9 - - - -
370B CYS* 4.1 17.9 - - + -
373B ILE* 3.6 28.3 - - + -
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Residues in contact with GLU 364 (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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337B LEU* 4.8 7.0 - - + +
360B VAL* 2.9 34.3 + - + +
361B GLN* 3.8 7.6 - - - +
362B ALA 3.3 0.2 - - - -
363B PHE* 1.3 77.9 - - + +
365B ARG* 1.3 62.2 + - - +
368B GLY* 2.6 42.7 + - - +
369B PRO* 3.7 29.1 - - + +
370B CYS 5.0 2.0 - - - +
285E LYS* 3.7 5.7 - - - +
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Residues in contact with ARG 365 (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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359B ASP* 5.4 0.4 + - - -
361B GLN* 3.0 39.6 + - + +
362B ALA* 3.6 19.6 - - - +
364B GLU* 1.3 77.1 - - + +
366B LEU* 1.3 57.7 + - - +
276E ASP* 4.4 0.6 + - - -
278E THR* 2.7 49.1 + - - +
279E LYS* 3.5 31.4 - - - +
284E LEU* 3.3 14.2 - - + +
285E LYS* 2.9 47.4 + - - +
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Residues in contact with LEU 366 (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 LYS* 3.9 40.3 - - + +
269B ILE* 4.6 1.8 - - + -
272B VAL* 4.0 19.3 - - + -
358B MET* 4.4 8.5 - - + -
362B ALA 3.0 18.1 + - - +
363B PHE* 3.7 3.1 - - - +
365B ARG* 1.3 78.1 - - - +
367B LEU* 1.3 74.1 + - + +
368B GLY 3.7 0.4 - - - -
277E LEU 3.7 8.7 - - - +
278E THR* 4.1 12.8 - - + -
283E ASN* 3.5 40.2 - - - +
284E LEU* 3.8 8.4 - - + -
285E LYS* 3.2 21.8 + - - +
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Residues in contact with LEU 367 (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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261B LEU* 3.5 32.1 - - + -
265B GLU* 3.5 41.7 - - + +
268B LYS* 4.8 7.2 - - + -
269B ILE* 3.9 18.8 - - + -
363B PHE* 2.8 40.4 + - + +
366B LEU* 1.3 83.2 - - + +
368B GLY* 1.3 61.8 + - - +
369B PRO 4.8 0.3 - - - +
373B ILE* 4.0 19.6 - - + +
376B ARG* 4.6 7.2 + - - +
285E LYS* 4.4 4.7 - - - -
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Residues in contact with GLY 368 (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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363B PHE* 3.8 9.4 - - - -
364B GLU* 2.6 38.2 + - - -
366B LEU 3.7 0.6 - - - -
367B LEU* 1.3 78.6 - - - +
369B PRO* 1.3 75.5 - - - +
370B CYS 3.6 1.2 + - - -
373B ILE* 4.7 0.3 - - - +
285E LYS* 4.1 13.7 - - - +
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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