Contacts of the helix formed by residues 596 - 604 (chain B) in PDB entry 6T8B
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 GLU 596 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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617A GLN* 3.8 21.2 - - - +
618A LYS* 5.4 2.0 - - - -
472B LYS* 5.5 0.3 - - - +
499B PRO* 3.2 26.6 - - + +
500B LYS* 4.5 24.4 - - + +
595B ASP* 1.3 91.1 + - - +
597B PHE* 1.3 65.4 + - - +
598B ALA* 3.2 2.8 - - - +
599B ASP* 3.6 28.2 + - + +
600B MET* 3.3 4.2 + - - +
629B ALA 3.0 10.9 + - - -
630B THR* 5.2 0.2 - - - +
631B GLN* 2.6 42.4 + - - +
801B AGS 5.1 2.8 + - - -
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Residues in contact with PHE 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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594B VAL* 3.6 24.7 - - + -
595B ASP 3.4 3.0 + - - -
596B GLU* 1.3 73.3 - - - +
598B ALA* 1.3 58.4 + - - +
600B MET* 3.3 17.8 - - - +
601B MET* 3.0 54.9 + - + +
612B ILE* 3.8 42.6 - - + -
628B LEU* 4.0 13.2 - - + -
629B ALA 2.8 10.8 + - - +
630B THR* 3.5 15.3 - - + -
637B VAL* 3.7 12.1 - - + -
638B ILE* 3.5 37.2 - - + -
642B ILE* 4.5 7.9 - - + -
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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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617A GLN* 3.6 28.0 - - - +
596B GLU* 3.2 7.5 - - - +
597B PHE* 1.3 79.4 - - - +
599B ASP* 1.3 58.7 + - - +
601B MET* 3.1 4.7 + - - +
602B MET* 2.9 31.6 + - - +
630B THR* 4.5 2.0 - - - +
631B GLN* 4.7 16.6 - - - +
637B VAL* 3.6 31.1 - - + +
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Residues in contact with ASP 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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614A ARG* 3.1 35.9 + - - +
617A GLN* 3.6 9.4 + - - +
618A LYS* 2.8 38.2 + - + +
499B PRO* 3.5 6.3 - - + +
596B GLU* 3.6 27.6 + - + +
598B ALA* 1.3 75.3 - - - +
600B MET* 1.3 65.1 + - - +
602B MET* 3.2 3.8 + - - -
603B ILE* 2.9 41.1 + - - +
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Residues in contact with MET 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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497B ILE* 3.4 37.9 - - + -
499B PRO* 3.9 2.9 - - + +
521B MET* 3.7 27.4 - - + -
524B ALA* 4.5 3.1 - - + -
528B LEU* 4.9 2.7 - - - -
594B VAL* 3.5 22.2 - - + -
595B ASP 4.8 3.6 - - - +
596B GLU 3.3 10.5 + - - +
597B PHE* 3.3 27.6 - - - +
599B ASP* 1.3 77.5 - - - +
601B MET* 1.3 60.6 + - - +
603B ILE* 3.1 1.2 + - - -
604B VAL* 2.9 35.4 + - + +
608B VAL* 3.8 33.2 - - + -
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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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597B PHE* 3.0 53.4 + - + +
598B ALA* 3.1 8.7 + - - +
600B MET* 1.3 75.6 - - - +
602B MET* 1.3 59.5 + - + +
603B ILE 3.4 0.2 - - - -
605B GLY* 3.4 41.1 + - - +
608B VAL* 4.6 7.4 - - - -
609B GLU* 3.6 47.6 - - + +
636B ASP 5.7 1.3 - - - +
637B VAL* 3.7 21.1 - - + +
642B ILE* 5.9 0.4 - - + -
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Residues in contact with MET 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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610A GLU* 3.3 57.2 - - + +
613A ALA* 3.6 15.3 - - + -
614A ARG* 3.6 23.4 + - + -
617A GLN* 3.4 37.2 - - - +
641A LEU* 4.6 8.1 - - + -
598B ALA* 2.9 15.3 + - - +
599B ASP* 3.2 7.6 + - - +
600B MET 3.1 0.4 - - - -
601B MET* 1.3 77.6 - - + +
603B ILE* 1.3 61.7 + - - +
605B GLY 5.0 0.2 - - - -
636B ASP 6.1 0.9 - - - +
637B VAL* 6.3 1.3 - - + -
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Residues in contact with ILE 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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536A GLU* 4.7 3.1 - - - +
614A ARG* 3.4 31.9 - - - +
618A LYS* 4.3 4.7 - - - +
521B MET* 3.8 39.7 - - + +
522B LYS* 5.1 14.4 + - - +
599B ASP* 2.9 35.9 + - - +
600B MET* 4.0 1.8 - - - +
602B MET* 1.3 81.6 - - - +
604B VAL* 1.3 67.2 + - + +
605B GLY 3.6 0.2 - - - -
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Residues in contact with VAL 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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521B MET* 3.1 46.7 - - + +
522B LYS* 5.8 6.1 - - + +
524B ALA* 4.8 3.1 - - + -
525B ALA* 4.9 5.8 - - + +
600B MET* 2.9 17.4 + - + +
601B MET* 5.6 0.2 - - - -
603B ILE* 1.3 75.5 - - - +
605B GLY* 1.3 62.0 + - - +
606B LYS 3.9 1.0 + - - -
607B LYS* 3.7 42.1 + - + +
608B VAL* 3.5 33.7 - - + +
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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