Contacts of the helix formed by residues 645 - 651 (chain A) in PDB entry 2XTA
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 ASP 645 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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644A GLY* 1.4 70.6 - - - +
646A ALA* 1.3 68.8 + - - +
648A PHE* 3.7 0.6 + - - +
649A ALA* 3.5 13.0 + - - +
675A VAL* 3.8 8.5 - - - +
676A VAL 3.7 4.2 + - - +
677A ASN* 3.3 36.8 - - - +
678A ASN* 2.9 26.9 + - - +
679A GLN* 3.5 5.4 - - - -
680A ILE 3.2 26.4 + - - +
686A PRO* 4.6 7.1 - - - +
690A ARG* 4.7 5.4 + - - +
695A CYS* 3.5 27.0 - - + +
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Residues in contact with ALA 646 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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645A ASP* 1.3 85.6 + - - +
647A ALA* 1.3 56.8 + - - +
649A ALA* 3.5 2.4 + - - +
650A GLY* 3.1 24.8 + - - -
680A ILE 4.8 0.7 - - - +
681A GLY* 3.9 28.0 - - - +
684A THR* 6.3 0.2 - - - -
689A SER* 4.0 30.0 - - - +
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Residues in contact with ALA 647 (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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606A LEU* 3.9 38.1 - - + -
607A GLU* 3.5 19.1 - - + +
644A GLY* 3.7 9.7 + - - +
645A ASP 3.4 0.2 - - - -
646A ALA* 1.3 76.7 - - - +
648A PHE* 1.4 63.4 + - - +
650A GLY* 4.5 0.7 - - - +
651A GLN* 3.1 35.5 + - + +
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Residues in contact with PHE 648 (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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607A GLU* 3.5 3.5 + - - -
643A HIS* 3.3 49.6 - + + -
644A GLY 3.0 19.7 + - - +
645A ASP* 4.1 4.3 - - - +
646A ALA 3.5 0.4 - - - -
647A ALA* 1.4 75.8 - - - +
649A ALA* 1.3 59.9 + - - +
651A GLN 4.6 1.0 - - - +
654A VAL* 3.6 41.3 - - + +
658A LEU* 4.7 7.4 - - + -
673A HIS* 4.3 11.2 - + - -
675A VAL* 4.0 15.9 - - + -
695A CYS 3.2 20.4 - - - +
696A THR* 3.7 22.9 - - + -
698A VAL* 3.7 22.9 - - + +
699A ALA* 4.8 4.5 - - + -
736A VAL* 4.6 10.5 - - + -
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Residues in contact with ALA 649 (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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645A ASP 3.5 12.4 + - - +
646A ALA* 3.5 4.8 + - - +
647A ALA 3.2 0.4 - - - -
648A PHE* 1.3 81.5 - - - +
650A GLY* 1.3 59.4 + - - +
651A GLN 3.7 1.4 - - - +
689A SER* 4.2 3.4 - - - +
690A ARG* 3.8 30.3 - - + -
692A SER* 5.8 0.7 - - - +
695A CYS* 3.9 17.5 - - - +
698A VAL* 5.5 1.6 - - - -
655B ALA 5.0 0.5 - - - +
656B GLU* 5.6 0.3 - - - -
659B ASN* 3.4 19.8 - - - +
701B MET* 3.8 16.6 - - + +
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Residues in contact with GLY 650 (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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646A ALA 3.1 16.8 + - - -
647A ALA* 5.2 0.2 - - - -
649A ALA* 1.3 79.2 - - - +
651A GLN* 1.3 65.9 + - - +
689A SER 4.7 1.5 + - - -
656B GLU* 3.4 26.6 - - - +
659B ASN* 3.9 13.7 - - - -
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Residues in contact with GLN 651 (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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606A LEU* 3.7 25.1 - - + +
607A GLU* 4.0 17.3 - - + -
647A ALA* 3.1 26.7 + - + +
648A PHE 4.6 1.0 - - - +
649A ALA 3.7 0.9 - - - +
650A GLY* 1.3 78.7 + - - +
652A GLY* 1.3 64.1 + - - +
653A VAL* 4.3 8.6 - - + +
654A VAL* 3.2 20.6 + - - +
655A ALA* 4.3 0.9 + - - +
953A PHE* 5.3 7.1 - - - -
655B ALA* 5.8 0.9 - - - +
656B GLU* 3.9 7.9 + - - +
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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