Contacts of the strand formed by residues 592 - 601 (chain A) in PDB entry 6TAV
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 GLN 592 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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590A ALA* 3.1 5.2 - - - +
591A PRO* 1.3 91.4 + - + +
593A SER* 1.3 67.2 + - - +
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Residues in contact with SER 593 (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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566A ASN* 4.1 16.6 - - - -
589A ALA* 3.9 8.0 - - - +
590A ALA* 3.2 30.6 + - - +
592A GLN* 1.3 78.0 + - - +
594A VAL* 1.3 65.4 + - - +
595A CYS* 4.0 9.7 + - - -
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Residues in contact with VAL 594 (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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157A PRO* 6.2 2.7 - - + -
185A GLY* 3.9 28.9 - - - +
187A LEU* 4.4 22.9 - - + -
593A SER* 1.3 75.6 - - - +
595A CYS* 1.3 69.5 + - - +
596A ALA* 4.4 0.7 + - - -
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Residues in contact with CYS 595 (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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566A ASN* 5.6 2.7 - - - -
568A VAL* 5.4 4.0 - - - -
587A VAL* 5.0 11.9 - - + -
589A ALA* 4.0 26.7 - - - -
593A SER* 4.0 13.4 + - - -
594A VAL* 1.3 84.7 - - - +
596A ALA* 1.3 62.1 + - - +
597A LEU* 3.6 21.5 + - + +
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Residues in contact with ALA 596 (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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132A GLN* 4.5 6.5 + - - +
147A ARG* 3.6 38.3 + - - +
187A LEU* 4.4 14.8 - - + +
189A GLN* 5.1 3.4 - - - +
594A VAL* 4.3 1.8 + - - +
595A CYS* 1.3 70.8 - - - +
597A LEU* 1.3 62.5 + - - +
598A ARG 4.3 0.3 + - - -
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Residues in contact with LEU 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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147A ARG* 3.2 22.3 + - - +
570A LEU* 6.2 2.2 - - + -
585A LEU* 5.1 24.0 - - + +
587A VAL* 4.3 24.5 - - + -
595A CYS* 3.6 22.6 + - + +
596A ALA* 1.3 77.8 - - - +
598A ARG* 1.3 61.8 + - - +
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Residues in contact with ARG 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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132A GLN* 3.8 32.7 - - - +
133A THR 3.5 18.8 + - - -
134A ASP* 2.7 38.7 + - + +
135A LYS* 4.3 0.6 - - - +
147A ARG* 4.3 5.2 - - - +
570A LEU* 5.8 3.8 - - - +
596A ALA 4.3 0.6 + - - -
597A LEU* 1.3 75.7 - - - +
599A ALA* 1.3 64.3 + - - +
600A VAL* 4.0 19.7 - - + +
605A LEU* 4.2 9.7 - - - +
610A ASP* 3.2 41.1 + - - +
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Residues in contact with ALA 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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572A PHE* 6.0 5.4 - - + -
585A LEU* 5.4 11.4 - - + -
598A ARG* 1.3 76.9 - - - +
600A VAL* 1.3 63.9 + - - +
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Residues in contact with VAL 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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134A ASP 4.5 2.9 - - - +
135A LYS* 4.3 18.4 - - + -
598A ARG* 4.0 23.8 - - + +
599A ALA* 1.3 75.5 - - - +
601A ASP* 1.3 69.5 + - - +
602A GLN* 3.4 3.3 + - - +
604A VAL* 3.3 28.0 - - + -
605A LEU* 4.5 19.2 - - + +
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Residues in contact with ASP 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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226A LEU* 4.1 10.0 - - + +
600A VAL* 1.3 77.8 - - + +
602A GLN* 1.3 76.0 + - - +
603A SER* 2.7 41.7 + - - +
604A VAL* 3.3 23.0 + - + +
605A LEU 3.5 2.4 + - - -
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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