Contacts of the helix formed by residues 380 - 390 (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 HIS 380 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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377B ASN* 2.9 34.9 + - + +
378B ILE 3.0 0.6 - - - -
379B SER* 1.3 98.8 + - - +
381B TYR* 1.3 63.6 + - - +
382B GLU 3.4 2.0 - - - -
383B GLU* 2.9 34.7 + - - +
384B GLN* 2.9 41.9 + - + +
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Residues in contact with TYR 381 (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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371B MET* 3.7 22.4 + - + +
374B MET* 3.6 30.5 - - + +
375B LYS* 3.5 52.6 + - + +
377B ASN 3.3 3.0 + - - -
378B ILE* 3.3 27.6 + - + +
380B HIS* 1.3 78.1 - - - +
382B GLU* 1.3 64.8 + - - +
384B GLN* 3.2 2.5 + - - +
385B LEU* 2.9 58.5 + - + +
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Residues in contact with GLU 382 (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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378B ILE 4.7 1.2 + - - -
379B SER 5.3 2.2 - - - +
380B HIS* 3.4 0.4 - - - +
381B TYR* 1.3 78.2 - - - +
383B GLU* 1.3 68.2 + - - +
385B LEU* 2.9 24.2 + - + +
386B VAL* 2.9 35.8 + - + +
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Residues in contact with GLU 383 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256B PRO* 5.5 6.9 - - - +
379B SER 5.5 1.3 + - - +
380B HIS* 2.9 44.3 + - - +
382B GLU* 1.3 82.5 + - - +
384B GLN* 1.3 69.5 + - - +
386B VAL* 3.3 6.0 + - - +
387B LYS* 3.0 23.5 + - + +
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Residues in contact with GLN 384 (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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256B PRO* 3.6 19.7 + - - +
257B LEU* 3.8 34.1 - - - +
259B LYS* 5.7 0.5 - - - +
260B SER* 5.9 2.1 + - - -
374B MET* 3.9 39.0 - - + +
380B HIS* 2.9 36.7 + - + +
381B TYR 3.4 6.7 - - - +
383B GLU* 1.3 82.7 + - + +
385B LEU* 1.3 62.3 + - - +
387B LYS* 3.1 12.2 + - - +
388B MET* 3.0 24.4 + - - +
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Residues in contact with LEU 385 (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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371B MET* 4.0 20.2 - - + -
374B MET* 4.2 10.5 - - + -
381B TYR* 2.9 63.1 + - + +
382B GLU* 2.9 14.7 + - + +
384B GLN* 1.3 77.6 - - - +
386B VAL* 1.3 58.5 + - + +
388B MET 3.3 0.7 + - - -
389B PHE* 2.9 47.3 + - + +
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Residues in contact with VAL 386 (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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382B GLU* 2.9 35.9 + - + +
383B GLU* 3.7 8.7 - - - +
385B LEU* 1.3 77.0 - - + +
387B LYS* 1.3 57.2 + - - +
389B PHE 5.0 0.2 - - - -
390B GLY* 2.7 40.3 + - - +
391B SER* 5.5 2.5 - - - +
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Residues in contact with LYS 387 (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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256B PRO* 6.3 3.8 - - + -
257B LEU* 6.4 0.9 - - + -
331B TYR* 3.9 30.1 + - - +
334B GLU* 4.5 14.0 + - - +
383B GLU* 3.0 15.4 + - + +
384B GLN* 3.1 17.9 + - - +
386B VAL* 1.3 80.7 - - - +
388B MET* 1.3 63.1 + - + +
390B GLY* 4.1 4.3 + - - +
392B ASN 5.0 14.5 + - - +
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Residues in contact with MET 388 (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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257B LEU* 3.9 29.6 - - + -
331B TYR* 6.1 0.2 - - - +
334B GLU* 3.9 33.4 - - + +
335B LEU* 3.8 24.7 - - + +
337B LEU* 5.0 2.0 - - + -
338B VAL* 3.6 43.3 - - + -
370B CYS* 5.1 0.2 - - - -
374B MET* 4.2 14.4 - - + -
384B GLN 3.0 14.7 + - - +
387B LYS* 1.3 81.4 - - - +
389B PHE* 1.3 77.7 + - + +
390B GLY 3.5 0.6 - - - +
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Residues in contact with PHE 389 (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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335B LEU* 4.3 6.7 - - + -
338B VAL* 3.9 25.6 - - + -
339B THR* 4.2 16.4 - - + -
371B MET* 4.5 12.6 - - + -
374B MET* 4.9 0.4 - - + -
385B LEU* 2.9 39.4 + - + +
386B VAL* 5.0 0.4 - - - -
388B MET* 1.3 101.6 - - + +
390B GLY* 1.3 62.3 + - - +
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Residues in contact with GLY 390 (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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386B VAL* 2.7 33.5 + - - -
387B LYS 4.1 3.1 + - - +
388B MET 3.5 2.1 - - - +
389B PHE* 1.3 82.1 - - - +
391B SER* 1.3 69.3 + - - +
392B ASN 3.8 5.3 - - - -
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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