Contacts of the helix formed by residues 499 - 511 (chain A) in PDB entry 2BV5
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 499 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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258A SER* 2.5 26.9 + - - -
259A ARG 2.9 30.4 + - - +
260A VAL* 3.5 10.9 - - + +
488A CYS* 4.4 0.9 - - - -
491A GLN* 2.9 23.9 + - - +
498A VAL* 1.3 74.4 - - - +
500A ILE* 1.3 60.8 + - - +
501A LEU 3.6 1.2 + - - -
502A LYS* 2.9 39.6 + - + +
503A THR* 2.9 28.1 + - - -
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Residues in contact with ILE 500 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259A ARG 4.6 1.8 + - - -
261A LEU* 4.8 3.1 - - + +
266A LEU* 4.4 1.8 - - + -
484A ALA* 5.5 2.0 - - + -
488A CYS* 3.8 23.6 - - - -
498A VAL* 3.8 17.8 + - + +
499A ASP* 1.3 70.0 - - - +
501A LEU* 1.3 61.2 + - - +
503A THR* 3.7 0.8 - - - -
504A THR* 2.8 39.6 + - - +
515A ILE* 5.4 0.9 - - + -
521A TYR* 3.8 13.5 - - + -
524A VAL* 4.1 19.1 - - + -
525A HIS* 3.6 61.5 - - + +
528A MET* 4.0 17.7 - - + -
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Residues in contact with LEU 501 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257A PRO* 4.0 16.2 - - + -
258A SER 3.9 26.9 - - - +
259A ARG* 4.0 14.5 + - + +
279A GLU* 3.9 24.1 + - + +
283A ILE* 3.6 34.3 - - + -
499A ASP* 3.3 6.5 + - - +
500A ILE* 1.3 79.2 - - - +
502A LYS* 1.3 62.7 + - - +
504A THR* 3.2 1.5 + - - -
505A CYS* 3.0 33.0 + - - -
521A TYR* 3.5 16.0 + - - +
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Residues in contact with LYS 502 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256A SER* 4.2 19.1 + - - +
257A PRO 3.3 19.5 - - - +
258A SER* 4.5 8.3 - - - +
491A GLN* 6.3 0.7 - - - +
499A ASP* 2.9 37.0 + - + +
501A LEU* 1.3 76.8 - - - +
503A THR* 1.3 63.6 + - - +
505A CYS* 3.3 3.6 + - - +
506A GLN* 2.9 28.3 + - + +
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Residues in contact with THR 503 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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484A ALA* 3.9 30.7 - - + +
487A ILE* 3.9 36.9 - - + +
488A CYS* 3.6 13.9 - - - -
491A GLN* 4.3 4.3 + - - -
499A ASP 2.9 19.0 + - - -
500A ILE* 3.7 4.0 - - - -
502A LYS* 1.3 77.6 - - - +
504A THR* 1.3 57.3 + - - +
506A GLN* 3.2 10.9 + - + +
507A LEU* 2.9 29.3 + - + +
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Residues in contact with THR 504 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283A ILE* 3.8 20.6 - - + -
484A ALA* 4.9 1.6 - - - +
500A ILE* 2.8 26.4 + - - +
501A LEU 3.7 3.6 - - - -
503A THR* 1.3 74.1 - - - +
505A CYS* 1.3 58.5 + - - +
507A LEU* 3.2 11.0 + - - +
508A ARG* 2.9 44.4 + - + +
514A MET 4.1 18.4 - - - +
515A ILE* 3.5 21.6 - - + +
521A TYR* 3.5 20.9 - - + -
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Residues in contact with CYS 505 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256A SER* 3.7 16.4 - - - +
257A PRO* 3.7 35.4 - - + -
283A ILE* 3.8 24.2 - - - -
284A PRO* 5.5 2.5 - - - -
501A LEU* 3.0 24.5 + - - +
502A LYS* 3.6 7.6 - - - +
504A THR* 1.3 77.4 - - - +
506A GLN* 1.3 59.7 + - - +
508A ARG* 3.3 8.5 + - - +
509A GLN* 3.1 28.4 + - - +
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Residues in contact with GLN 506 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256A SER* 4.8 1.7 + - - +
336A ARG* 3.1 70.0 + - - +
337A GLY 3.1 26.6 + - - -
338A TYR* 5.3 0.4 - - - +
339A GLY* 5.1 1.6 + - - -
340A GLY* 4.3 12.1 + - - -
487A ILE* 4.3 10.9 - - - +
502A LYS* 2.9 20.1 + - + +
503A THR* 3.4 13.0 - - - +
505A CYS* 1.3 72.5 - - - +
507A LEU* 1.3 65.8 + - - +
509A GLN* 3.3 13.4 + - - +
510A ASP* 3.3 7.9 + - - +
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Residues in contact with LEU 507 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335A ILE* 3.4 30.9 - - + +
336A ARG 4.6 1.3 - - - +
480A GLY 3.9 8.3 - - - +
483A ILE* 3.6 15.0 - - + -
484A ALA* 3.7 37.9 - - + +
487A ILE* 4.2 8.5 - - + -
503A THR* 2.9 22.1 + - + +
504A THR* 3.2 11.4 + - - +
506A GLN* 1.3 79.2 - - + +
508A ARG* 1.3 57.6 + - - +
510A ASP* 3.0 9.0 + - - +
511A ARG 2.9 26.2 + - - +
514A MET* 3.6 28.2 - - + +
515A ILE* 5.0 2.9 - - + -
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Residues in contact with ARG 508 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280A PHE* 3.3 12.9 - - - -
283A ILE* 3.1 26.0 + - + +
284A PRO 3.0 29.7 + - - +
285A MET* 3.5 30.2 - - - +
286A ASN* 2.8 31.3 + - + +
504A THR* 2.9 22.5 + - - +
505A CYS* 3.3 9.2 + - - +
507A LEU* 1.3 73.4 - - - +
509A GLN* 1.3 57.9 + - - +
510A ASP 3.4 0.3 + - - -
511A ARG 3.5 15.3 + - - +
513A GLY 3.6 9.1 - - - +
514A MET 2.8 22.9 + - - +
515A ILE 2.8 23.8 + - - -
1539A GOL 2.9 30.1 + - - -
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Residues in contact with GLN 509 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256A SER* 4.8 14.8 + - - +
286A ASN* 3.8 12.5 + - - +
310A ASN* 4.8 0.2 + - - -
312A HIS* 2.9 27.3 + - - +
336A ARG* 2.9 27.0 + - - +
505A CYS* 3.1 16.0 + - - +
506A GLN* 3.4 12.2 - - - +
508A ARG* 1.3 77.1 - - - +
510A ASP* 1.3 59.9 + - - +
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Residues in contact with ASP 510 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310A ASN* 4.1 3.1 - - - +
312A HIS* 4.3 6.6 + - - -
313A SER* 2.6 30.0 + - - -
333A ASN* 3.6 6.4 + - - +
334A TYR 3.7 5.8 - - - +
335A ILE* 3.6 24.9 - - + +
336A ARG* 2.9 61.9 + - - +
506A GLN* 3.3 12.5 + - - +
507A LEU* 3.0 8.2 + - - +
509A GLN* 1.3 80.2 - - - +
511A ARG* 1.3 61.0 + - - +
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Residues in contact with ARG 511 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307A ILE* 4.5 6.2 - - - +
308A LEU 4.5 3.8 + - - +
309A PRO* 4.0 6.3 - - - +
310A ASN* 3.4 6.5 - - - +
331A ASN* 2.9 31.2 + - - -
332A ALA* 3.9 10.9 - - - +
333A ASN* 2.8 38.1 + - - +
335A ILE* 3.9 8.5 - - + -
347A ALA* 3.6 31.1 + - - -
349A GLN 4.1 6.7 - - - +
474A ALA 2.9 26.9 + - - -
475A GLY* 2.9 20.5 + - - -
476A ILE* 3.6 8.6 - - + +
507A LEU 2.9 9.2 + - - +
508A ARG* 3.5 7.0 + - - +
510A ASP* 1.3 80.5 - - - +
512A GLY* 1.3 73.3 - - - +
513A GLY 3.4 1.2 + - - -
514A MET* 3.0 27.3 + - + +
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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