Contacts of the helix formed by residues 494 - 501 (chain B) in PDB entry 2P1Q
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 GLY 494 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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470B ASP* 2.7 22.9 + - - +
473B MET* 4.3 3.5 - - - +
493B PHE* 1.3 75.7 - - - +
495B ASP* 1.3 68.3 + - - -
498B LEU* 3.5 19.9 + - - +
513B MET* 4.4 0.2 - - - +
517B SER* 3.8 20.2 - - - -
518B VAL* 3.9 9.9 - - - +
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Residues in contact with ASP 495 (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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470B ASP* 3.9 0.8 + - - -
494B GLY* 1.3 74.2 - - - -
496B LYS* 1.3 70.8 + - + +
498B LEU* 3.7 3.0 - - - +
499B LEU* 3.0 34.5 + - + +
517B SER 3.6 3.2 + - - +
518B VAL* 3.3 5.2 - - - -
519B SER* 2.6 47.2 + - - -
522B ALA* 3.3 24.7 - - + +
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Residues in contact with LYS 496 (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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470B ASP* 3.5 29.9 + - + +
494B GLY 3.3 1.4 - - - -
495B ASP* 1.3 83.4 - - + +
497B ALA* 1.3 57.9 + - - +
499B LEU* 4.3 1.4 - - - +
500B ALA* 3.0 32.1 + - - +
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Residues in contact with ALA 497 (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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470B ASP* 3.1 39.3 + - + +
473B MET* 3.9 17.9 - - + -
474B HIS* 3.6 22.2 - - + +
477B LEU* 4.0 0.9 - - + +
496B LYS* 1.3 75.8 - - - +
498B LEU* 1.3 65.2 + - - +
500B ALA* 4.4 2.0 - - - -
501B ASN* 2.9 33.2 + - - +
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Residues in contact with LEU 498 (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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473B MET* 3.7 12.9 - - + +
477B LEU* 4.8 2.6 - - + +
494B GLY 3.5 15.4 + - - +
495B ASP 3.5 2.7 + - - +
496B LYS 3.3 0.4 - - - -
497B ALA* 1.3 81.1 - - - +
499B LEU* 1.3 64.0 + - + +
501B ASN 3.5 2.9 + - - +
502B ALA* 3.3 20.8 + - - +
505B LEU* 4.1 11.8 - - + +
511B LEU* 3.5 31.9 - - + -
513B MET* 4.5 2.7 - - - -
518B VAL* 3.7 33.7 - - + -
522B ALA* 5.0 10.1 - - + +
523B CYS* 5.5 2.5 - - - +
526B LEU* 4.1 21.4 - - + +
556B VAL* 5.4 0.9 - - + -
558B ILE* 3.9 15.9 - - + -
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Residues in contact with LEU 499 (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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495B ASP* 3.0 23.5 + - + +
496B LYS* 4.5 1.8 - - - +
498B LEU* 1.3 79.8 - - + +
500B ALA* 1.3 66.5 + - - +
501B ASN 3.1 1.4 + - - -
502B ALA* 3.4 16.9 + - + +
522B ALA* 3.8 30.5 - - + +
525B LEU* 4.6 20.6 - - + -
526B LEU* 3.8 39.5 - - + +
529B LYS* 5.1 9.6 - - + +
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Residues in contact with ALA 500 (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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474B HIS* 4.8 8.2 - - + +
496B LYS 3.0 21.1 + - - +
497B ALA* 3.9 5.2 - - - +
499B LEU* 1.3 77.5 - - - +
501B ASN* 1.3 68.7 + - - +
502B ALA 3.6 0.6 + - - -
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Residues in contact with ASN 501 (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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474B HIS* 3.1 39.0 + - - -
477B LEU* 3.7 27.8 + - + +
478B SER* 3.9 21.2 - - - +
497B ALA 2.9 24.8 + - - +
498B LEU 3.6 3.8 - - - -
499B LEU 3.1 0.4 - - - -
500B ALA* 1.3 84.8 + - - +
502B ALA* 1.3 62.6 + - - +
503B SER* 3.3 4.9 - - - -
504B LYS* 3.1 21.1 + - + +
505B LEU* 3.9 6.2 + - - +
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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