Contacts of the helix formed by residues 591 - 600 (chain B) in PDB entry 2XER
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 ARG 591 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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519B ARG* 5.5 0.6 - - - +
589B CYS 3.9 2.8 + - - -
590B ILE* 1.3 72.8 - - - +
592B LYS* 1.3 56.8 + - - +
594B LYS* 3.5 3.8 + - - +
595B ARG* 3.0 31.5 + - + +
629B GLN 5.3 0.6 + - - -
630B ASP* 3.6 52.2 + - - +
632B VAL* 3.7 37.0 - - + +
1767B SO4 3.3 33.2 + - - +
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Residues in contact with LYS 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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523B LEU* 6.1 2.5 - - + -
526B ILE* 4.3 12.1 - - + -
527B GLU* 2.9 36.0 + - - +
530B TYR* 3.9 35.3 - - + -
590B ILE* 3.1 8.8 - - + +
591B ARG* 1.3 74.1 - - - +
593B GLY* 1.3 60.5 + - - +
595B ARG* 3.2 32.5 + - - +
596B MET* 2.8 30.9 + - - +
1767B SO4 3.1 28.6 + - - +
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Residues in contact with GLY 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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526B ILE* 3.6 21.4 - - - +
587B ILE* 3.3 27.1 - - - -
590B ILE 2.9 4.0 + - - -
592B LYS* 1.3 78.6 - - - +
594B LYS* 1.3 57.1 + - - +
596B MET* 3.4 5.9 - - - +
597B VAL* 2.9 35.2 + - - +
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Residues in contact with LYS 594 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
587B ILE 3.7 0.2 + - - -
588B MET* 3.0 46.5 + - + +
589B CYS 4.0 4.2 + - - -
590B ILE 3.0 20.8 + - - +
591B ARG 3.7 1.7 - - - +
593B GLY* 1.3 73.9 - - - +
595B ARG* 1.3 61.2 + - - +
596B MET 3.0 4.9 + - - -
597B VAL 3.5 0.2 + - - -
598B ALA* 3.5 20.4 + - - +
626B LYS 3.3 17.4 + - - -
627B ASP* 2.8 46.9 + - - +
630B ASP* 3.5 13.1 + - - +
632B VAL* 3.4 22.6 - - + +
633B LEU* 4.4 15.3 - - + -
635B CYS* 4.0 4.5 - - - -
636B LEU* 3.9 10.6 - - + +
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Residues in contact with ARG 595 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
530B TYR* 4.6 10.3 + - - -
591B ARG* 3.0 24.1 + - + +
592B LYS* 3.2 38.9 - - - +
594B LYS* 1.3 75.4 - - - +
596B MET* 1.3 56.5 + - - +
598B ALA* 4.3 3.3 - - - +
599B ARG* 3.1 39.9 + - + +
632B VAL* 4.8 5.8 - - + +
635B CYS* 4.1 16.4 - - - -
1767B SO4 2.6 32.1 + - - -
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Residues in contact with MET 596 (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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525B ILE* 6.1 0.4 - - + -
526B ILE* 3.5 35.0 - - - +
529B THR* 4.0 15.0 - - + -
530B TYR* 3.7 37.0 - - + -
533B LEU* 4.2 9.2 - - + -
569B LEU* 4.1 14.1 - - + -
587B ILE* 4.4 16.8 - - + -
592B LYS 2.8 16.3 + - - +
593B GLY* 3.4 4.5 - - - +
594B LYS 3.0 0.2 - - - -
595B ARG* 1.3 77.6 - - - +
597B VAL* 1.3 66.1 + - - +
598B ALA 3.1 1.6 - - - -
599B ARG* 3.0 15.3 + - - +
600B ILE* 2.9 41.4 + - + +
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Residues in contact with VAL 597 (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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569B LEU* 4.1 30.7 - - + -
584B PHE* 4.3 4.5 - - + -
587B ILE* 4.5 4.5 - - + -
588B MET* 3.8 21.8 - - + -
593B GLY 2.9 20.3 + - - +
594B LYS 3.5 0.6 + - - +
596B MET* 1.3 75.8 - - + +
598B ALA* 1.3 62.5 + - - +
600B ILE* 3.2 9.4 + - + +
601B LEU* 3.1 35.3 + - + +
604B LEU* 6.3 0.4 - - + -
612B ILE* 4.1 19.3 - - + -
636B LEU* 3.7 19.5 - - + -
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Residues in contact with ALA 598 (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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594B LYS 3.5 4.6 + - - +
595B ARG 4.4 5.2 - - - +
596B MET 3.1 0.6 - - - -
597B VAL* 1.3 78.9 - - - +
599B ARG* 1.3 62.0 + - + +
601B LEU* 3.8 4.2 + - - -
602B PRO* 3.3 16.6 - - - +
635B CYS* 3.6 40.2 - - + +
636B LEU* 3.5 19.2 - - + +
639B PRO* 3.4 15.2 - - + +
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Residues in contact with ARG 599 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
530B TYR* 3.5 35.5 + - - -
533B LEU* 3.5 20.3 - - + +
534B LEU* 4.2 8.1 - - - +
537B GLU* 3.0 33.1 + - - +
595B ARG* 3.1 39.3 + - - +
596B MET 3.0 6.2 + - - +
598B ALA* 1.3 78.5 - - + +
600B ILE* 1.3 58.6 + - - +
601B LEU 3.5 0.2 - - - -
602B PRO* 3.2 10.1 - - - +
603B PHE* 3.2 25.1 - - - -
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Residues in contact with ILE 600 (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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529B THR* 4.2 5.4 - - + -
533B LEU* 4.3 3.8 - - + -
562B ILE* 6.2 0.2 - - + -
565B MET* 3.5 45.5 - - + -
569B LEU* 4.2 15.7 - - + -
596B MET* 2.9 48.0 + - + +
597B VAL* 3.2 12.5 + - + +
599B ARG* 1.3 80.2 - - - +
601B LEU* 1.3 65.5 + - + +
602B PRO 3.3 0.2 - - - -
603B PHE* 3.0 22.3 + - + +
604B LEU* 3.5 28.7 + - + +
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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