Contacts of the helix formed by residues 590 - 594 (chain B) in PDB entry 6T2C
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 LEU 590 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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588B GLY 4.6 4.0 - - - +
589B LEU* 1.3 76.4 - - - +
591B VAL* 1.3 59.5 + - - +
592B ALA* 3.3 6.3 - - + +
593B ASP* 3.1 11.0 + - - +
594B GLY 3.3 0.2 + - - -
595B GLY 2.7 27.5 + - - -
608B GLU* 3.7 31.2 - - + +
609B VAL* 4.5 20.0 - - + -
612B LYS* 3.6 13.7 - - + +
616B MET* 5.2 3.4 - - - -
620B TYR* 3.3 13.6 + - - +
624B LEU* 3.9 23.3 - - + -
662B THR* 4.7 7.4 - - - +
664B HIS* 3.6 28.5 - - + +
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Residues in contact with VAL 591 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523B MET* 4.0 13.9 - - + -
552B ILE* 4.9 7.2 - - + -
555B TYR* 3.6 27.8 - - + -
556B ARG* 4.0 24.6 + - + +
561B CYS* 3.3 12.6 - - - +
590B LEU* 1.3 74.3 - - - +
592B ALA* 1.3 55.1 + - - +
593B ASP 3.1 0.2 - - - -
594B GLY* 2.7 22.0 + - - -
595B GLY 4.0 11.2 - - - +
596B PRO 4.3 1.3 - - - +
597B ASN* 4.1 29.6 - - + +
598B PRO* 4.6 1.6 - - + -
599B TYR* 6.3 0.4 - - + -
608B GLU* 3.1 20.8 + - - +
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Residues in contact with ALA 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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519B GLU* 3.3 33.9 - - + +
555B TYR* 4.1 7.6 + - - +
561B CYS* 3.9 16.0 - - - +
572B ARG* 3.0 25.6 + - - -
576B ILE* 4.7 1.6 - - - +
590B LEU* 3.3 2.9 - - + +
591B VAL* 1.3 77.5 - - - +
593B ASP* 1.3 55.2 + - - +
594B GLY 3.3 1.1 + - - -
608B GLU* 5.6 0.2 + - - -
664B HIS* 3.5 28.4 - - + +
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Residues in contact with ASP 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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576B ILE* 4.3 16.2 - - - +
579B LEU* 3.4 36.7 - - + +
580B TRP* 5.5 2.4 + - - +
589B LEU* 4.2 9.6 - - + +
590B LEU 3.1 10.1 + - - +
591B VAL 3.1 1.0 - - - -
592B ALA* 1.3 75.7 - - - +
594B GLY* 1.3 60.4 + - - +
595B GLY 3.4 1.1 + - - -
620B TYR* 2.3 34.2 + - - +
664B HIS* 3.3 17.1 + - - -
97C THR* 4.5 6.3 - - - +
100C ASN* 2.6 34.8 + - - +
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Residues in contact with GLY 594 (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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556B ARG* 6.2 0.2 - - - -
561B CYS 4.2 1.4 + - - -
562B HIS 3.5 23.3 - - - -
563B ARG* 3.8 5.4 - - - +
564B GLY 3.4 7.8 + - - -
576B ILE* 4.4 7.0 - - - +
580B TRP* 3.3 26.5 - - - -
591B VAL 2.7 15.7 + - - -
592B ALA 3.3 1.6 - - - -
593B ASP* 1.3 79.4 - - - +
595B GLY* 1.3 60.8 + - - +
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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