Contacts of the helix formed by residues 590 - 595 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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172D LEU* 4.7 8.1 - - + -
498D LEU* 3.9 28.3 + - + +
502D LEU* 4.2 25.1 - - + +
588D MET 4.2 0.4 + - - -
589D ARG* 1.3 77.4 - - - +
591D MET* 1.3 67.4 + - - +
592D MET* 4.0 19.7 - - + -
593D MET* 3.1 20.3 + - + +
594D GLU* 3.5 4.3 + - - +
604D LEU 5.0 2.2 - - - +
607D GLN 5.1 0.2 - - - -
608D TYR* 5.0 1.1 - - - -
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Residues in contact with MET 591 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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589D ARG 3.6 1.2 + - - -
590D ALA* 1.3 71.3 - - - +
592D MET* 1.3 65.7 + - - +
593D MET 2.8 2.3 + - - -
594D GLU* 2.8 14.5 + - - +
595D PHE* 2.8 19.1 + - + -
601D CYS* 3.7 23.1 - - + +
604D LEU* 3.6 32.2 + - + -
607D GLN* 3.6 33.1 + - + +
608D TYR* 4.1 13.5 - - - -
609D MET* 3.8 32.8 - - - +
615D MET* 4.2 3.6 - - + -
629D TYR 4.4 0.4 - - - +
631D PRO* 3.6 36.1 - - + -
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Residues in contact with MET 592 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163D TYR* 3.4 52.5 - - + +
172D LEU* 5.9 0.4 - - + -
201D MET* 4.5 1.6 - - + -
202D THR 4.5 1.8 - - - +
203D ASN* 4.1 22.2 - - + -
247D PRO* 4.1 16.1 - - + +
502D LEU* 4.1 20.0 - - - -
590D ALA* 4.0 14.1 - - + -
591D MET* 1.3 78.6 - - - +
593D MET* 1.3 66.9 + - - +
595D PHE 4.1 3.1 - - - -
596D PRO* 3.2 31.5 - - + +
601D CYS* 3.5 27.2 + - - +
602D ASP* 4.5 3.4 - - - +
604D LEU 5.8 0.2 + - - -
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Residues in contact with MET 593 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201D MET* 5.2 0.7 - - + -
247D PRO* 4.2 15.3 - - + +
248D LYS* 3.8 34.5 - - + +
251D LEU* 3.7 22.9 - - + -
498D LEU 5.7 0.2 - - - +
501D GLY 4.4 1.3 - - - +
502D LEU* 3.4 31.4 - - + +
585D THR* 4.8 0.7 - - - -
586D PRO* 3.8 34.3 - - + -
589D ARG* 3.9 16.8 - - + -
590D ALA* 3.1 19.2 + - + +
591D MET 2.8 1.8 + - - -
592D MET* 1.3 91.1 - - - +
594D GLU* 1.3 61.1 + - - +
596D PRO* 3.7 9.7 - - - +
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Residues in contact with GLU 594 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248D LYS* 2.6 36.6 + - - +
589D ARG* 3.1 20.6 + - + -
590D ALA 3.5 3.0 + - - +
591D MET 2.8 7.3 + - - +
593D MET* 1.3 76.8 - - - +
595D PHE* 1.3 92.3 + - + +
596D PRO* 3.3 7.4 - - - +
609D MET* 3.9 20.6 - - + -
611D GLY 5.1 0.2 - - - -
612D ASP* 3.7 16.4 - - - +
664D ARG* 3.0 24.2 + - - +
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Residues in contact with PHE 595 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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591D MET* 2.8 18.1 + - + +
592D MET* 3.6 4.5 - - - +
594D GLU* 1.3 102.1 - - + +
596D PRO* 1.3 63.5 - - - +
597D ASP 3.1 4.3 + - - -
598D ASP* 3.1 24.5 + - + +
601D CYS* 4.1 17.0 - - - +
609D MET* 3.9 16.8 - - - -
631D PRO* 3.5 39.9 - - + -
632D GLU 5.3 3.6 - - - -
635D TRP* 3.8 16.6 - + - -
664D ARG* 3.6 39.3 - - - -
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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