Contacts of the helix formed by residues 595 - 604 (chain B) in PDB entry 1J1B
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 ASN 595 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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292A LYS* 5.8 0.7 - - - +
587B VAL* 4.4 12.6 - - - +
588B LEU 5.3 0.2 - - - +
589B GLN* 3.3 30.7 + - - +
594B LYS* 1.3 71.8 - - - +
596B ARG* 1.3 64.9 + - - +
597B GLU* 3.1 22.6 + - - +
598B LEU* 2.7 39.1 - - + +
599B GLN* 3.0 30.3 + - - +
617B TYR* 5.7 0.9 + - - +
628B LEU* 3.4 22.8 - - + +
630B LEU* 5.3 0.6 - - - +
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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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290A GLU* 3.8 15.6 + - - -
292A LYS* 4.5 38.6 - - - +
594B LYS 3.3 6.4 + - - -
595B ASN* 1.3 69.1 - - - +
597B GLU* 1.3 67.2 + - - +
599B GLN* 3.4 7.7 + - + +
600B ILE* 3.0 37.0 + - + +
680B ARG* 4.4 4.0 - - - +
701B PHE 6.0 0.2 - - - +
704B ALA 3.4 18.1 + - - +
705B LYS* 3.1 49.2 - - - +
706B GLN 5.6 0.2 - - - +
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Residues in contact with GLU 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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567B PHE* 5.8 1.7 - - - -
585B LYS* 2.7 40.8 + - - +
587B VAL* 4.7 9.0 - - - +
595B ASN* 3.1 13.6 + - - +
596B ARG* 1.3 78.5 - - - +
598B LEU* 1.3 57.2 + - - +
600B ILE* 3.3 4.2 + - - +
601B MET* 2.8 42.3 + - + +
630B LEU* 4.1 13.9 - - + +
700B ASP* 4.5 0.5 - - - -
701B PHE* 3.6 32.6 + - + +
702B GLY* 3.5 24.2 + - - -
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Residues in contact with LEU 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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595B ASN* 2.7 27.7 - - + +
597B GLU* 1.3 73.0 - - - +
599B GLN* 1.3 79.7 + - - +
601B MET* 3.2 3.8 + - - -
602B ARG* 2.9 51.7 + - + +
612B LEU* 3.8 5.2 - - + -
615B PHE* 3.8 41.7 - - + -
617B TYR* 4.0 9.4 - - - +
628B LEU* 3.9 18.2 - - + -
630B LEU* 3.7 23.6 - - + -
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Residues in contact with GLN 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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594B LYS* 4.1 25.7 - - + +
595B ASN 3.0 34.6 + - - +
596B ARG* 3.7 8.5 - - + +
598B LEU* 1.3 96.9 - - - +
600B ILE* 1.3 63.0 + - + +
602B ARG* 3.8 30.3 + - - +
603B LYS* 3.3 22.9 + - - +
617B TYR* 5.7 0.2 + - - -
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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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596B ARG* 3.0 30.9 + - + +
597B GLU* 3.7 3.4 - - - +
599B GLN* 1.3 74.4 - - + +
601B MET* 1.3 66.3 + - - +
602B ARG 3.1 2.7 + - - -
603B LYS* 3.1 22.1 + - - +
604B LEU* 3.2 32.6 - - + +
677B ILE* 4.2 29.4 - - + -
701B PHE* 4.0 19.1 - - + +
704B ALA* 3.6 36.8 - - + +
705B LYS* 4.1 7.0 - - - +
706B GLN 5.0 1.1 - - - +
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Residues in contact with MET 601 (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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546B GLN* 4.5 1.2 + - - -
597B GLU* 2.8 43.0 + - + +
598B LEU* 3.7 5.8 - - - +
600B ILE* 1.3 74.7 - - - +
602B ARG* 1.3 61.4 + - - +
604B LEU* 3.3 24.2 + - - +
609B ILE* 5.9 0.4 - - - -
610B VAL* 4.4 18.6 - - + +
612B LEU* 3.6 35.0 + - + +
630B LEU* 4.9 7.2 - - + -
632B LEU* 3.2 36.1 - - + -
700B ASP 5.7 1.3 - - - -
701B PHE* 3.6 34.1 - - + -
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Residues in contact with ARG 602 (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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543B THR* 4.5 6.7 - - - +
544B PRO 4.5 6.7 + - - -
545B GLY 3.8 21.3 + - - +
546B GLN* 2.8 25.3 + - - +
547B GLY 5.4 4.0 + - - -
549B ASP* 5.8 4.4 - - - +
598B LEU* 2.9 51.7 + - + +
599B GLN* 3.8 24.4 + - - +
600B ILE 3.1 0.2 + - - -
601B MET* 1.3 79.0 - - - +
603B LYS* 1.3 57.2 + - - +
604B LEU 3.4 0.2 - - - -
612B LEU* 3.9 5.4 - - + -
615B PHE* 3.7 29.4 - - + -
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Residues in contact with LYS 603 (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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546B GLN* 4.3 8.2 - - - +
599B GLN* 3.3 22.8 + - - +
600B ILE* 3.3 15.3 - - - +
602B ARG* 1.3 78.4 - - + +
604B LEU* 1.3 69.0 + - + +
605B ASP* 5.1 0.5 - - - +
671B TYR* 3.8 8.5 + - - -
675B PHE* 4.8 19.4 - - + -
677B ILE* 4.5 16.4 - - + -
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Residues in contact with LEU 604 (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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546B GLN* 3.2 15.6 + - - -
600B ILE* 3.2 27.1 - - + +
601B MET* 3.3 16.1 + - - +
602B ARG 3.4 0.2 - - - -
603B LYS* 1.3 89.2 - - + +
605B ASP* 1.3 62.0 + - - +
606B HIS 4.2 0.2 - - - -
609B ILE* 4.3 15.7 - - + -
611B ARG* 6.2 0.5 - - - -
671B TYR* 3.7 20.2 - - + -
672B ILE* 4.1 15.0 - - + -
675B PHE* 4.6 7.0 - - + -
677B ILE* 4.4 14.1 - - + -
701B PHE* 3.7 36.8 - - + -
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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