Contacts of the helix formed by residues 596 - 604 (chain A) in PDB entry 6T8O
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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472A LYS* 4.1 3.6 + - - -
499A PRO* 3.2 30.3 - - + +
500A LYS* 4.7 17.5 - - + -
594A VAL* 4.1 1.3 - - - -
595A ASP* 1.3 84.6 - - + +
597A PHE* 1.3 61.6 + - - +
598A ALA* 3.2 9.8 + - - +
599A ASP* 3.6 25.3 + - - +
600A MET* 3.9 5.4 + - - +
629A ALA 3.3 1.1 - - - -
630A THR* 3.4 15.5 - - - -
631A GLN* 2.9 35.5 + - - +
617F GLN* 2.8 32.6 + - - +
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Residues in contact with PHE 597 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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463A LEU* 4.2 15.7 - - + -
464A VAL 5.2 0.2 - - - -
594A VAL* 3.7 17.8 - - + +
596A GLU* 1.3 72.0 - - - +
598A ALA* 1.3 59.9 + - - +
599A ASP 3.4 0.4 - - - -
600A MET* 3.8 14.3 - - + +
601A MET* 2.9 54.2 + - + +
612A ILE* 6.2 3.4 - - + -
628A LEU* 3.8 39.7 - - + -
629A ALA 3.2 26.8 + - - -
630A THR* 3.6 20.6 - - + -
637A VAL* 3.6 26.9 - - + -
638A ILE* 4.0 17.5 - - + -
642A ILE* 5.2 7.9 - - + -
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Residues in contact with ALA 598 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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596A GLU* 3.2 14.7 - - - +
597A PHE* 1.3 77.3 - - - +
599A ASP* 1.3 59.2 + - - +
601A MET* 3.5 1.1 + - - +
602A MET* 2.9 21.0 + - - +
630A THR* 3.3 22.8 + - - +
632A ARG* 2.9 44.8 + - + +
637A VAL* 3.7 14.8 - - + +
617F GLN* 4.2 2.7 - - - +
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Residues in contact with ASP 599 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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499A PRO* 4.8 3.7 - - + +
500A LYS* 4.9 10.6 + - - +
521A MET* 3.9 21.1 - - + +
596A GLU* 3.6 27.9 + - - +
597A PHE 3.4 0.2 - - - -
598A ALA* 1.3 77.3 - - - +
600A MET* 1.3 58.6 + - - +
602A MET* 3.3 26.6 + - - +
603A ILE* 2.9 40.2 + - + +
614F ARG* 4.4 8.3 + - - +
617F GLN* 3.6 15.9 + - - +
618F LYS* 5.1 10.4 + - - +
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Residues in contact with MET 600 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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497A ILE* 3.7 30.3 - - + -
499A PRO* 5.2 5.4 - - + -
521A MET* 3.9 29.1 - - + +
524A ALA* 3.7 16.2 - - + -
525A ALA 5.4 0.7 - - - -
528A LEU* 4.3 14.8 - - + -
594A VAL* 4.5 13.5 - - + -
596A GLU 3.9 4.1 + - - +
597A PHE* 3.5 18.0 + - - +
598A ALA 3.3 0.2 - - - -
599A ASP* 1.3 78.9 - - - +
601A MET* 1.3 59.4 + - - +
604A VAL* 3.0 42.7 + - + +
608A VAL* 3.7 31.2 - - + -
612A ILE* 6.2 0.2 - - - -
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Residues in contact with MET 601 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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597A PHE* 2.9 46.5 + - + +
598A ALA* 3.8 2.9 - - - +
600A MET* 1.3 77.3 - - + +
602A MET* 1.3 58.5 + - - +
604A VAL* 5.2 0.4 - - - -
605A GLY* 3.3 26.8 + - - +
608A VAL* 4.2 21.1 - - + -
609A GLU* 3.4 45.8 - - + +
612A ILE* 5.6 4.9 - - - -
632A ARG* 5.5 0.2 - - - -
636A ASP 4.9 9.6 - - - +
637A VAL* 3.3 27.8 - - + +
639A THR* 5.3 0.7 - - + -
642A ILE* 5.1 4.9 - - + -
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Residues in contact with MET 602 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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598A ALA 2.9 12.7 + - - +
599A ASP* 3.3 28.7 - - - +
601A MET* 1.3 78.1 - - - +
603A ILE* 1.3 71.6 + - + +
605A GLY* 4.8 1.9 + - - -
632A ARG* 3.0 40.2 - - - +
636A ASP 5.8 2.2 - - - +
610F GLU* 5.9 2.5 - - - +
614F ARG* 3.7 36.1 - - + +
617F GLN* 4.6 6.3 - - - +
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Residues in contact with ILE 603 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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521A MET* 4.0 30.5 - - + -
522A LYS* 6.2 3.8 - - - +
599A ASP* 2.9 23.8 + - + +
600A MET* 4.2 2.0 - - - +
602A MET* 1.3 88.3 - - + +
604A VAL* 1.3 68.2 + - + +
605A GLY 3.6 0.4 - - - -
614F ARG* 3.8 28.5 - - - +
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Residues in contact with VAL 604 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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521A MET* 4.9 13.2 - - + +
522A LYS* 4.2 29.2 - - + +
525A ALA* 5.6 0.2 - - + -
600A MET* 3.0 26.4 + - + +
603A ILE* 1.3 83.4 - - + +
605A GLY* 1.3 60.6 + - - +
607A LYS* 3.6 32.1 - - - +
608A VAL* 3.6 31.4 - - + -
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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