Contacts of the helix formed by residues 590 - 595 (chain B) in PDB entry 1XSK
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 ALA 590 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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172B LEU* 4.5 17.0 - - + -
498B LEU* 4.0 23.2 + - + +
502B LEU* 4.1 26.9 - - + -
588B MET 4.3 0.2 + - - -
589B ARG* 1.3 75.4 - - - +
591B MET* 1.3 67.2 + - - +
592B MET* 4.3 13.5 - - + +
593B MET* 3.0 23.1 + - + +
594B GLU* 3.5 4.2 + - - +
604B LEU 5.0 1.8 - - - +
607B GLN 5.2 0.4 - - - -
608B TYR* 4.9 1.1 - - - -
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Residues in contact with MET 591 (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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589B ARG 3.5 0.4 + - - -
590B ALA* 1.3 72.6 - - - +
592B MET* 1.3 57.5 + - - +
593B MET 3.1 0.7 + - - -
594B GLU* 3.1 1.8 + - - +
595B PHE* 2.8 44.1 + - + +
601B CYS* 3.8 12.1 - - + -
604B LEU* 3.7 37.5 + - + -
607B GLN* 3.4 38.5 + - + +
608B TYR* 4.1 12.0 - - - +
609B MET* 3.7 27.4 - - - +
615B MET* 4.4 2.5 - - + -
629B TYR 4.3 0.2 - - - +
631B PRO* 3.5 37.9 - - + -
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Residues in contact with MET 592 (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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163B TYR* 3.2 59.9 - - + +
172B LEU* 6.0 0.2 - - + -
201B MET* 4.2 8.5 - - + -
202B THR 4.1 16.2 - - - +
203B ASN* 4.2 10.3 - - + -
247B PRO* 4.0 9.2 - - + +
502B LEU* 4.1 11.0 - - - -
590B ALA* 4.3 11.6 - - + +
591B MET* 1.3 78.0 - - - +
593B MET* 1.3 70.9 + - - +
595B PHE 4.3 3.1 - - - -
596B PRO* 3.1 31.3 - - + +
601B CYS* 3.3 27.0 + - - +
602B ASP* 4.5 4.9 - - - +
604B LEU 5.7 0.4 + - - -
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Residues in contact with MET 593 (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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247B PRO* 4.0 19.0 - - + +
248B LYS* 3.9 27.9 - - + +
251B LEU* 3.7 20.9 - - + -
498B LEU 5.5 0.4 - - - +
501B GLY 4.4 0.2 - - - -
502B LEU* 3.3 35.2 - - + +
585B THR* 4.5 8.3 - - - -
586B PRO* 3.8 35.0 - - + -
588B MET 5.4 0.2 - - - +
589B ARG* 3.9 15.0 - - + -
590B ALA 3.0 18.0 + - - +
592B MET* 1.3 92.6 - - - +
594B GLU* 1.3 60.9 + - - +
596B PRO* 3.8 7.1 - - - +
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Residues in contact with GLU 594 (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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248B LYS* 2.8 34.8 + - - +
589B ARG* 3.0 22.5 + - + -
590B ALA 3.5 3.2 + - - +
591B MET 3.1 2.7 + - - +
593B MET* 1.3 78.2 - - - +
595B PHE* 1.3 89.2 + - + +
596B PRO* 3.3 8.7 - - - +
609B MET* 3.8 21.1 - - + -
612B ASP* 3.9 12.4 - - - +
664B ARG* 2.8 27.6 + - - +
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Residues in contact with PHE 595 (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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591B MET* 2.8 21.6 + - + +
592B MET* 3.6 4.4 - - - +
594B GLU* 1.3 99.5 - - + +
596B PRO* 1.3 63.8 - - - +
597B ASP 3.3 2.7 - - - -
598B ASP* 3.2 25.0 + - + +
601B CYS* 4.0 15.3 - - - +
609B MET* 3.8 18.4 - - + -
631B PRO* 3.5 35.2 - - + -
632B GLU 5.3 3.4 - - - -
635B TRP* 3.7 21.8 - + - -
664B ARG* 3.3 38.8 - - - -
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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