Contacts of the helix formed by residues 691 - 701 (chain A) in PDB entry 4YK6
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 ASN 691 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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647A ALA 5.2 0.4 + - - -
650A GLU* 3.4 23.6 + - - -
653A ARG* 3.3 41.8 - - - +
657A ARG* 3.3 12.3 + - - +
687A LEU 4.5 0.9 - - - +
689A ALA 3.1 2.4 + - - +
690A ARG* 1.3 81.0 + - - +
692A PRO* 1.3 71.8 - - - +
693A LYS* 3.1 5.9 + - - +
694A ASP* 2.9 27.6 + - + +
695A GLN* 2.9 29.5 + - - +
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Residues in contact with PRO 692 (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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690A ARG 4.2 3.6 - - - +
691A ASN* 1.3 88.2 - - - +
693A LYS* 1.3 63.1 + - - +
695A GLN* 3.6 13.9 - - - +
696A GLU* 3.0 26.3 + - - +
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Residues in contact with LYS 693 (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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650A GLU* 4.8 2.8 + - - +
654A GLN* 5.5 2.0 + - - -
657A ARG* 3.5 40.1 - - - +
691A ASN* 3.1 10.8 + - - +
692A PRO* 1.3 80.5 - - - +
694A ASP* 1.3 59.3 + - - +
696A GLU* 3.4 5.0 + - - +
697A ALA* 3.0 27.2 + - + +
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Residues in contact with ASP 694 (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 ARG* 2.8 44.1 + - - +
657A ARG* 2.8 33.4 + - - +
662A LEU* 3.7 26.7 - - + +
687A LEU* 4.1 7.3 - - - +
691A ASN* 2.9 14.5 + - - +
693A LYS* 1.3 76.3 - - - +
695A GLN* 1.3 61.0 + - - +
697A ALA* 3.6 7.1 - - - +
698A LEU* 2.9 37.1 + - + +
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Residues in contact with GLN 695 (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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687A LEU 5.2 0.2 + - - -
688A SER 2.9 31.6 + - - +
689A ALA* 4.1 0.2 - - - +
690A ARG* 3.3 22.6 - - - +
691A ASN 2.9 19.0 + - - +
692A PRO* 3.6 17.6 - - - +
694A ASP* 1.3 77.8 - - - +
696A GLU* 1.3 63.2 + - - +
698A LEU* 3.3 3.7 + - - +
699A TRP* 3.0 29.7 + - - -
728A ASN* 4.5 0.8 + - - +
729A LEU* 3.9 17.2 - - + +
732A ASN* 3.2 50.0 - - + +
734A PRO* 4.9 0.7 - - + -
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Residues in contact with GLU 696 (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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692A PRO 3.0 17.5 + - - +
693A LYS* 3.7 4.9 - - - +
695A GLN* 1.3 76.0 - - - +
697A ALA* 1.3 57.5 + - - +
699A TRP* 3.2 2.1 + - - +
700A ASP* 2.9 44.5 + - - +
734A PRO* 3.9 28.4 - - + +
735A ALA 5.4 0.5 + - - -
736A LYS* 3.0 35.9 + - - +
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Residues in contact with ALA 697 (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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662A LEU* 4.2 12.6 - - + -
693A LYS* 3.0 18.5 + - + +
694A ASP* 3.6 11.7 - - - +
695A GLN 3.3 0.2 - - - -
696A GLU* 1.3 75.8 - - - +
698A LEU* 1.3 56.6 + - - +
700A ASP* 3.2 9.0 + - - +
701A MET* 2.9 40.9 + - + +
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Residues in contact with LEU 698 (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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662A LEU* 4.1 21.3 - - + -
666A LEU* 4.1 8.3 - - + -
684A LEU* 4.0 25.6 - - + -
687A LEU 4.9 0.9 - - - -
688A SER* 4.1 31.9 - - - +
694A ASP 2.9 22.0 + - - +
695A GLN 3.7 4.3 - - - +
697A ALA* 1.3 75.7 - - - +
699A TRP* 1.3 64.2 + - - +
701A MET* 3.2 23.7 + - + -
702A GLY 3.3 0.2 + - - -
703A ALA* 3.0 47.6 + - + +
707A LEU* 6.1 1.6 - - + -
729A LEU* 4.0 14.6 - - + -
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Residues in contact with TRP 699 (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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695A GLN* 3.0 25.2 + - - +
696A GLU 3.5 7.9 - - - +
698A LEU* 1.3 74.8 - - - +
700A ASP* 1.3 62.4 + - - +
702A GLY* 3.1 15.6 + - - -
703A ALA 4.9 1.8 - - - +
704A VAL* 4.1 24.1 + - + +
729A LEU* 2.9 46.7 + - + +
730A MET* 4.1 25.8 - - + -
732A ASN 3.6 3.0 + - - -
733A ARG* 3.8 31.9 - - + -
734A PRO* 3.5 25.1 - - + +
737A TYR* 3.6 46.4 + + + -
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Residues in contact with ASP 700 (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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696A GLU* 2.9 24.0 + - - +
697A ALA* 3.5 8.3 - - - +
699A TRP* 1.3 76.1 - - - +
701A MET* 1.3 61.5 + - + +
702A GLY 3.4 0.9 + - - -
736A LYS* 2.9 36.6 + - - -
737A TYR* 2.7 30.1 + - - -
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Residues in contact with MET 701 (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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662A LEU* 3.6 29.4 - - + -
663A GLN* 3.5 40.6 - - - +
666A LEU* 3.6 14.4 - - + +
697A ALA* 2.9 37.5 + - + +
698A LEU* 3.2 14.5 + - + +
700A ASP* 1.3 79.2 - - + +
702A GLY* 1.3 59.4 + - - +
703A ALA 3.4 1.1 + - - -
706A MET* 3.4 18.5 - - - +
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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