Contacts of the helix formed by residues 503 - 515 (chain B) in PDB entry 2HIW
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 503 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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373B GLU* 3.2 23.7 + - - -
436B ILE* 5.7 0.4 - - - -
437B LYS* 3.6 11.2 - - - +
440B VAL* 4.7 2.7 - - - -
502B PRO* 1.3 74.6 - - - +
504B PHE* 1.3 60.1 + - - +
505B ALA* 3.8 5.4 + - - +
506B GLU* 3.0 30.3 + - - +
507B ILE* 2.9 30.2 + - - +
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Residues in contact with PHE 504 (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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366B SER* 4.0 11.1 - - - +
369B MET* 3.2 41.7 - - + -
370B GLU* 3.5 23.3 - - - +
373B GLU* 2.8 19.7 + - - +
382B LEU* 4.6 0.2 - - + -
436B ILE* 3.4 35.0 - - + -
439B ASP* 3.5 26.7 - - + -
440B VAL* 3.4 20.6 - - + -
443B PHE* 3.5 26.7 - + + -
503B SER* 1.3 72.7 - - - +
505B ALA* 1.3 53.5 + - - +
507B ILE* 3.8 13.5 - - + -
508B HIS* 2.7 37.6 + - - +
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Residues in contact with ALA 505 (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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370B GLU* 3.5 28.6 - - + +
373B GLU* 3.3 15.3 + - - +
374B LYS* 6.3 1.1 - - - +
503B SER* 3.2 7.1 - - - +
504B PHE* 1.3 78.9 - - - +
506B GLU* 1.3 56.7 + - - +
508B HIS* 4.3 1.0 - - - +
509B GLN* 3.2 28.2 + - - +
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Residues in contact with GLU 506 (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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437B LYS* 5.1 1.0 + - - -
489B LEU* 5.8 0.7 - - - -
502B PRO* 3.2 20.7 - - + +
503B SER* 3.0 43.0 + - - +
505B ALA* 1.3 74.8 - - - +
507B ILE* 1.3 57.6 + - - +
509B GLN* 3.7 5.6 - - - +
510B ALA* 2.8 30.3 + - - +
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Residues in contact with ILE 507 (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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366B SER* 3.7 11.9 - - - -
440B VAL* 3.7 30.5 - - + -
443B PHE* 3.6 28.3 - - + -
489B LEU* 4.5 11.0 - - + -
493B CYS* 3.8 13.9 - - - -
502B PRO* 3.9 16.4 - - + -
503B SER 2.9 21.7 + - - +
504B PHE* 3.3 19.3 + - + +
506B GLU* 1.3 73.6 - - - +
508B HIS* 1.3 61.0 + - - +
510B ALA* 3.3 6.1 + - - +
511B PHE* 2.8 39.1 + - + -
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Residues in contact with HIS 508 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363B THR* 3.1 41.0 + - + +
366B SER* 3.3 20.0 - - - +
367B SER* 3.7 21.0 + - - -
370B GLU* 2.9 28.9 - - - +
504B PHE 2.7 20.4 + - - +
505B ALA 5.1 0.2 - - - -
507B ILE* 1.3 73.2 - - - +
509B GLN* 1.3 54.5 - - + +
511B PHE* 4.3 0.4 - - - -
512B GLU* 2.5 65.6 + - + +
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Residues in contact with GLN 509 (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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505B ALA 3.2 19.1 + - - +
506B GLU* 3.7 7.0 - - - +
508B HIS* 1.3 79.5 - - + +
510B ALA* 1.3 57.9 + - - +
512B GLU* 3.4 27.3 + - - +
513B THR* 3.1 34.4 + - - +
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Residues in contact with ALA 510 (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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489B LEU* 3.8 26.5 - - + -
506B GLU 2.8 19.4 + - - +
507B ILE 3.3 4.7 + - - +
509B GLN* 1.3 76.1 - - - +
511B PHE* 1.3 57.9 + - - +
513B THR* 3.6 6.2 + - - +
514B MET* 3.1 36.5 + - + +
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Residues in contact with PHE 511 (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 LEU* 3.7 32.5 - - + -
362B ALA* 3.6 21.5 - - + -
363B THR* 3.1 20.2 + - - +
366B SER* 4.2 2.7 - - - +
443B PHE* 4.0 11.9 - + - -
447B LEU* 3.4 40.4 - - + -
486B VAL* 4.4 15.9 - - + -
489B LEU* 3.5 27.1 - - + -
507B ILE* 2.8 32.3 + - + +
508B HIS 3.8 2.7 - - - +
510B ALA* 1.3 74.0 - - - +
512B GLU* 1.3 59.3 + - - +
513B THR 3.3 0.2 - - - -
514B MET* 4.0 5.9 - - + +
515B PHE* 3.0 33.4 + - - +
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Residues in contact with GLU 512 (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 THR* 4.0 12.7 - - + +
508B HIS* 2.5 48.6 + - + +
509B GLN* 3.4 28.4 + - - +
511B PHE* 1.3 73.9 - - - +
513B THR* 1.3 62.3 + - - +
515B PHE* 3.7 12.7 + - - +
516B GLN* 4.0 13.6 + - - +
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Residues in contact with THR 513 (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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485B LYS* 5.4 5.2 - - - +
509B GLN* 3.1 27.5 + - - -
510B ALA* 3.8 7.4 - - - +
512B GLU* 1.3 77.0 - - - +
514B MET* 1.3 67.3 + - + +
516B GLN* 3.2 31.5 - - - +
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Residues in contact with MET 514 (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 LEU* 3.2 30.8 - - + +
483B PRO* 5.8 0.7 - - - -
485B LYS* 3.7 54.7 - - + +
486B VAL* 3.8 27.4 - - - -
489B LEU* 3.8 25.1 - - + -
510B ALA* 3.1 23.2 + - + +
511B PHE* 4.0 9.6 - - - -
513B THR* 1.3 77.6 - - + +
515B PHE* 1.3 54.2 + - - +
516B GLN 2.7 26.0 + - - +
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Residues in contact with PHE 515 (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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356B VAL* 3.8 27.1 - - + -
359B LEU* 3.8 10.8 - - + -
360B TYR* 3.5 57.7 - + + -
363B THR* 3.5 21.3 - - + +
511B PHE 3.0 20.9 + - - +
512B GLU 3.9 6.3 - - - +
513B THR 3.2 0.6 - - - -
514B MET* 1.3 73.5 - - - +
516B GLN* 1.3 66.0 + - - +
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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