Contacts of the helix formed by residues 595 - 600 (chain B) in PDB entry 2HX4
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 VAL 595 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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686A SER* 2.9 30.0 + - - +
687A ILE* 5.0 1.3 - - + -
591B THR* 2.9 32.5 + - + +
594B GLY* 1.3 71.6 - - - +
596B ARG* 1.3 60.4 + - - +
599B CYS* 3.0 30.1 + - - +
600B ASP* 3.4 3.5 + - - +
630B LEU* 3.9 16.6 - - + -
634B ASN* 3.4 24.2 - - - +
682B PRO* 3.6 22.2 - - + +
683B MET* 3.6 18.6 - - + -
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Residues in contact with ARG 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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686A SER* 3.6 22.5 - - - -
691A PHE* 3.8 15.8 - - - -
692A HIS* 3.6 14.6 + - - -
591B THR 3.2 10.3 + - - +
592B GLU* 3.4 11.9 - - - +
595B VAL* 1.3 73.1 - - - +
597B ASP* 1.3 71.9 + - - +
598B TYR 3.3 0.9 - - - -
600B ASP* 2.9 63.7 + - - +
603B ARG* 3.5 7.0 - - - +
682B PRO* 3.7 19.7 - - + +
750B HEM 4.6 5.3 + - - +
760B H4B 3.2 42.6 + - - -
799B 4HX 6.2 0.9 - - - +
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Residues in contact with ASP 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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561B TRP* 3.4 44.0 + - + -
588B TYR* 4.3 6.4 + - - -
592B GLU 3.0 21.4 + - - +
593B ILE* 3.5 17.5 + - - +
596B ARG* 1.3 72.7 - - - +
598B TYR* 1.3 61.8 + - + +
603B ARG* 2.6 37.7 + - - +
604B TYR* 3.1 31.4 + - - +
799B 4HX 4.6 13.1 + - - +
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Residues in contact with TYR 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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517B PHE* 5.0 1.3 - + - -
546B ILE* 3.3 22.8 - - + +
554B PHE* 5.9 0.2 - + - -
559B LEU* 4.3 23.3 - - + -
560B LYS 3.1 25.6 + - - -
561B TRP* 3.7 25.1 - + - +
593B ILE* 2.9 34.0 + - + +
594B GLY 3.8 7.4 - - - +
597B ASP* 1.3 83.8 - - - +
599B CYS* 1.3 61.0 + - - +
600B ASP 3.7 0.4 - - - -
604B TYR* 3.6 15.8 - + + -
605B ASN 2.9 23.0 + - - -
606B ILE* 3.0 32.1 + - + +
633B ILE* 3.9 19.3 - - + -
637B VAL* 3.8 15.0 - - + -
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Residues in contact with CYS 599 (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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686A SER 5.7 0.3 - - - +
687A ILE* 4.5 8.6 - - + +
594B GLY 3.4 17.9 - - - -
595B VAL 3.0 15.8 + - - +
598B TYR* 1.3 81.7 - - - +
600B ASP* 1.3 68.3 + - - +
601B ASN* 3.2 9.5 + - - -
605B ASN* 4.6 4.4 + - - +
606B ILE* 4.3 1.8 - - - +
607B LEU* 3.7 45.7 - - + +
630B LEU* 3.7 14.6 - - + -
633B ILE* 3.7 19.5 - - - -
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Residues in contact with ASP 600 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
686A SER* 4.2 8.3 + - - +
692A HIS* 3.4 22.4 + - + -
595B VAL 3.4 1.0 + - - -
596B ARG* 2.9 66.9 + - - +
598B TYR 3.7 0.2 - - - -
599B CYS* 1.3 77.2 - - - +
601B ASN* 1.3 65.6 + - - +
602B SER* 4.0 5.1 - - - +
603B ARG* 3.0 33.6 + - + +
605B ASN* 3.5 11.6 + - - -
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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