Contacts of the helix formed by residues 590 - 595 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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172C LEU* 4.7 10.3 - - + -
498C LEU* 3.7 25.7 + - + +
502C LEU* 4.2 22.7 - - + -
588C MET 4.3 0.2 + - - -
589C ARG* 1.3 75.6 - - - +
591C MET* 1.3 66.5 + - - +
592C MET* 4.0 19.7 - - + -
593C MET* 3.0 26.0 + - + +
594C GLU* 3.3 4.9 + - - +
604C LEU 5.1 1.6 - - - +
607C GLN 5.2 0.4 - - - -
608C TYR* 5.0 0.9 - - - +
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Residues in contact with MET 591 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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589C ARG 3.5 1.0 + - - -
590C ALA* 1.3 71.5 - - - +
592C MET* 1.3 55.8 + - - +
594C GLU* 2.9 3.2 + - - +
595C PHE* 2.7 39.0 + - + +
601C CYS* 3.9 18.4 - - + -
604C LEU* 3.8 22.4 + - + -
607C GLN* 3.0 48.2 + - + +
608C TYR* 3.9 13.7 - - - +
609C MET* 3.7 29.2 - - - +
615C MET* 4.0 7.6 - - + -
629C TYR 4.1 0.9 - - - +
631C PRO* 3.9 33.9 - - + -
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Residues in contact with MET 592 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163C TYR* 3.8 46.7 - - + +
172C LEU* 5.8 0.9 - - + -
201C MET* 4.8 1.3 - - - -
202C THR 5.0 1.1 - - - +
203C ASN* 4.3 19.1 - - + -
247C PRO* 3.8 21.5 - - + -
502C LEU* 4.2 15.9 - - - -
590C ALA* 4.0 13.0 - - + +
591C MET* 1.3 78.1 - - - +
593C MET* 1.3 84.1 + - - +
595C PHE 4.3 2.9 - - - -
596C PRO* 3.2 27.5 - - + +
601C CYS* 3.4 28.0 + - - +
602C ASP* 4.5 3.8 - - - +
604C LEU 5.7 0.4 + - - -
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Residues in contact with MET 593 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247C PRO* 4.1 19.1 - - + +
248C LYS* 3.8 33.3 - - + +
251C LEU* 4.1 11.0 - - + -
498C LEU 5.3 0.7 - - - +
501C GLY* 4.6 2.7 - - - +
502C LEU* 3.6 27.6 - - + +
585C THR* 4.8 0.2 - - - -
586C PRO* 3.6 39.9 - - + -
588C MET 4.9 0.7 - - - +
589C ARG* 4.1 13.2 - - + -
590C ALA 3.0 25.6 + - - +
592C MET* 1.3 96.6 - - - +
594C GLU* 1.3 59.1 + - - +
596C PRO* 3.8 7.8 - - - +
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Residues in contact with GLU 594 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248C LYS* 2.8 36.0 + - - +
589C ARG* 2.9 27.5 + - + -
590C ALA 3.3 3.7 + - - +
591C MET 2.9 6.2 + - - +
593C MET* 1.3 75.6 - - - +
595C PHE* 1.3 82.9 + - + +
596C PRO* 3.1 14.3 - - - +
609C MET* 3.9 23.3 - - + -
611C GLY 5.0 0.2 - - - -
612C ASP* 3.9 10.3 - - - +
664C ARG* 3.2 24.6 + - - +
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Residues in contact with PHE 595 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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591C MET* 2.7 26.5 + - + +
592C MET* 3.4 8.9 - - - +
594C GLU* 1.3 92.0 - - + +
596C PRO* 1.3 64.6 - - - +
597C ASP 3.0 4.7 + - - -
598C ASP* 3.1 29.8 + - + +
601C CYS* 4.0 5.0 - - - +
609C MET* 4.0 17.7 - - - -
631C PRO* 3.4 42.6 - - + -
632C GLU* 5.0 8.3 - - + -
635C TRP* 3.7 20.9 - + - -
664C ARG* 3.8 31.9 - - - -
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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