Contacts of the helix formed by residues 656 - 661 (chain A) in PDB entry 4XK8
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 PHE 656 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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614A PHE* 3.4 48.0 - + + -
617A SER* 3.7 17.7 - - - -
618A TRP* 3.7 44.2 - + + -
651A GLY 3.4 3.0 + - - -
652A TRP* 3.3 21.8 - + - +
654A ARG 3.3 0.2 - - - -
655A ASP* 1.3 79.9 - - - +
657A LEU* 1.3 85.7 + - + +
660A GLN* 2.9 68.1 + - - +
749A PHE* 3.8 16.4 - + - -
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Residues in contact with LEU 657 (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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614A PHE* 3.7 28.0 - - + -
652A TRP* 2.9 25.0 + - + +
653A LEU* 3.7 23.3 - - + +
656A PHE* 1.3 93.1 - - + +
658A TRP* 1.3 57.2 + - - +
661A ALA* 2.9 36.7 + - - +
749A PHE* 4.4 11.2 - - + -
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Residues in contact with TRP 658 (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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653A LEU* 3.1 19.4 + - + +
654A ARG* 3.3 24.4 + - + +
657A LEU* 1.3 79.0 - - - +
659A ALA* 1.3 87.9 + - + +
661A ALA* 3.6 9.7 + - - +
662A SER* 3.8 8.7 + - - -
665A ILE* 5.5 2.6 - - - +
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Residues in contact with ALA 659 (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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654A ARG 2.9 13.1 + - - +
655A ASP* 3.3 25.6 - - - +
657A LEU 3.4 0.4 - - - -
658A TRP* 1.3 91.3 - - + +
660A GLN* 1.3 58.6 + - + +
662A SER* 2.4 28.7 + - - -
663A GLN* 4.4 1.6 + - - +
753A ARG* 4.5 3.4 + - - -
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Residues in contact with GLN 660 (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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617A SER* 4.1 0.9 + - - -
618A TRP* 4.1 10.7 - - - +
621A GLN* 2.7 30.9 + - - +
638A THR* 4.1 17.5 - - + +
655A ASP 4.2 9.6 + - - +
656A PHE* 2.9 50.0 + - - +
659A ALA* 1.3 74.4 - - + +
661A ALA* 1.3 58.5 + - - +
662A SER 3.0 5.8 - - - -
663A GLN* 3.1 16.4 + - - +
664A VAL 4.7 0.7 + - - -
749A PHE* 3.4 21.2 - - + -
753A ARG* 3.4 39.7 + - - +
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Residues in contact with ALA 661 (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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657A LEU 2.9 19.9 + - - +
658A TRP* 4.1 5.8 - - - +
659A ALA 3.4 0.6 - - - -
660A GLN* 1.3 75.7 - - - +
662A SER* 1.3 63.3 + - - +
663A GLN 3.3 0.9 - - - -
664A VAL* 3.3 8.9 + - + +
665A ILE* 2.9 39.9 + - + +
679A PHE* 4.8 9.0 - - + -
749A PHE* 3.6 15.9 - - + -
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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