Contacts of the helix formed by residues 650 - 661 (chain X) in PDB entry 6AH0
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 650 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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646X MET* 6.2 0.7 - - - +
647X SER 2.9 13.5 + - - +
649X SER* 1.3 78.9 - - - +
651X LYS* 1.3 64.6 + - - +
652X ARG 3.3 1.2 + - - -
653X LYS* 3.6 3.8 + - - -
654X LYS* 3.2 18.0 + - - -
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Residues in contact with LYS 651 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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647X SER 3.9 3.8 + - - -
648X GLU* 3.3 13.9 + - - +
649X SER 3.3 0.2 - - - -
650X GLU* 1.3 78.1 - - - +
652X ARG* 1.3 57.4 + - - +
654X LYS* 3.3 1.5 + - - +
655X LEU* 2.9 26.9 + - - -
739X TYR 6.0 1.8 - - - -
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Residues in contact with ARG 652 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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648X GLU 5.0 0.6 + - - -
649X SER 4.5 3.8 + - - -
650X GLU 3.3 0.8 - - - -
651X LYS* 1.3 77.4 - - - +
653X LYS* 1.3 57.6 + - - +
655X LEU* 3.4 2.0 + - - +
656X LEU* 3.0 24.4 + - - -
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Residues in contact with LYS 653 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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649X SER 5.3 0.8 + - - -
650X GLU 3.6 5.1 + - - -
651X LYS 3.4 0.2 - - - -
652X ARG* 1.3 75.4 - - - +
654X LYS* 1.3 62.5 + - - +
656X LEU* 3.4 1.3 + - - +
657X ALA* 3.0 20.8 + - - -
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Residues in contact with LYS 654 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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650X GLU 3.2 15.3 + - - -
651X LYS* 3.8 2.7 - - - +
653X LYS* 1.3 71.9 - - - +
655X LEU* 1.3 66.9 + - - +
657X ALA* 3.3 2.8 + - - +
658X ILE* 3.0 19.4 + - - -
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Residues in contact with LEU 655 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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651X LYS 2.9 15.2 + - - -
652X ARG* 3.8 3.4 - - - +
654X LYS* 1.3 74.6 - - - +
656X LEU* 1.3 57.2 + - - +
658X ILE* 3.0 4.2 + - - +
659X LEU* 2.8 26.3 + - - -
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Residues in contact with LEU 656 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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652X ARG 3.0 14.2 + - - -
653X LYS* 3.8 3.4 - - - +
655X LEU* 1.3 73.3 - - - +
657X ALA* 1.3 57.0 + - - +
659X LEU* 3.2 2.2 + - - +
660X GLU* 2.8 28.8 + - - -
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Residues in contact with ALA 657 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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653X LYS 3.0 15.7 + - - -
654X LYS* 3.3 3.8 + - - +
655X LEU 3.3 0.2 - - - -
656X LEU* 1.3 75.5 - - - +
658X ILE* 1.3 63.0 + - - +
660X GLU* 3.4 2.6 + - - +
661X GLN* 3.3 14.6 + - - -
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Residues in contact with ILE 658 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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654X LYS 3.0 9.8 + - - -
655X LEU* 3.0 7.5 + - - +
657X ALA* 1.3 75.7 - - - +
659X LEU* 1.3 62.1 + - - +
661X GLN* 3.0 16.9 + - - +
662X GLY 3.8 5.5 + - - +
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Residues in contact with LEU 659 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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655X LEU 2.8 16.5 + - - -
656X LEU* 3.7 3.6 - - - +
658X ILE* 1.3 71.0 - - - +
660X GLU* 1.3 52.3 + - - +
662X GLY* 2.8 29.8 + - - -
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Residues in contact with GLU 660 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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656X LEU 2.8 19.0 + - - -
657X ALA* 3.4 3.6 + - - +
658X ILE 3.2 0.4 - - - -
659X LEU* 1.3 71.8 - - - +
661X GLN* 1.3 59.8 + - - +
662X GLY* 3.0 2.1 + - - -
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Residues in contact with GLN 661 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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657X ALA 3.3 8.0 + - - -
658X ILE 3.0 11.8 + - - -
660X GLU* 1.3 75.5 - - - +
662X GLY* 1.3 63.2 + - - +
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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