Contacts of the strand formed by residues 693 - 701 (chain A) in PDB entry 2YA6
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 LYS 693 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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689A MET* 3.5 4.8 - - - -
690A HIS 2.8 35.5 + - - +
691A GLU 4.3 12.9 + - - +
692A GLY* 1.3 78.3 - - - +
694A GLU* 1.3 60.1 + - - +
695A TYR* 3.2 36.5 - - + +
715A ARG* 4.0 32.3 - - - +
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Residues in contact with GLU 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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638A LEU* 3.4 5.0 - - - +
639A ASN* 2.5 48.3 + - - +
640A ASN 5.0 1.0 + - - -
687A HIS* 2.7 16.6 + - - +
689A MET* 3.1 24.9 - - + -
692A GLY 4.2 0.6 + - - -
693A LYS* 1.3 73.6 - - - +
695A TYR* 1.3 59.6 + - - +
715A ARG* 3.3 15.9 - - - +
716A VAL* 2.9 57.4 + - + +
717A GLU 5.2 0.7 - - - +
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Residues in contact with TYR 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 HIS* 3.8 7.1 - - - -
688A THR* 2.9 39.7 + - + +
690A HIS* 3.6 20.9 + - + -
693A LYS* 3.2 63.3 - - + +
694A GLU* 1.3 71.4 - - - +
696A ILE* 1.3 67.4 + - - +
713A LEU* 4.0 21.5 - - + -
714A ALA 3.2 22.7 - - - +
715A ARG* 3.6 21.2 + - - -
716A VAL* 3.9 4.0 - - - -
725A LEU* 3.9 18.1 - - + +
771A TRP* 3.6 24.5 - + - -
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Residues in contact with ILE 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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636A VAL* 3.9 21.8 - - + -
638A LEU* 3.8 26.7 - - + -
644A LYS* 4.7 2.0 - - + -
646A PHE* 3.8 37.0 - - + -
685A ALA* 4.1 9.0 - - + -
686A ILE 3.3 10.8 - - - +
687A HIS* 4.5 1.6 - - + -
688A THR 4.8 0.2 - - - +
695A TYR* 1.3 78.9 - - - +
697A ILE* 1.3 75.2 + - - +
698A LEU* 4.1 3.9 + - + +
712A HIS 3.9 0.2 - - - +
713A LEU* 3.8 2.7 - - - -
714A ALA* 3.0 37.0 + - + +
716A VAL* 3.9 5.3 - - + +
722A LEU* 3.9 15.9 - - + -
724A TRP* 4.2 4.6 - - + -
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Residues in contact with ILE 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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685A ALA* 3.1 3.1 - - - +
686A ILE* 2.8 41.8 + - + -
688A THR* 3.6 24.9 - - + -
696A ILE* 1.3 77.8 - - - +
698A LEU* 1.3 60.9 + - - +
711A VAL* 3.4 30.3 - - + -
712A HIS 3.5 4.5 - - - +
713A LEU* 3.8 17.9 - - + -
740A LEU* 3.5 20.4 - - + +
748A TYR* 3.7 32.8 - - + -
769A PHE* 4.6 1.6 - - + -
774A LEU* 3.7 18.2 - - + -
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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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646A PHE* 3.3 42.2 - - + -
654A LEU* 3.9 18.2 - - + -
676A VAL* 4.4 6.5 - - + -
683A MET* 4.1 20.2 - - - -
684A SER 3.2 12.8 - - - +
685A ALA* 4.0 6.5 - - + -
696A ILE* 4.1 0.9 + - + -
697A ILE* 1.3 74.5 - - - +
699A SER* 1.3 63.3 + - - +
700A ASN* 4.1 14.4 - - - +
711A VAL* 3.6 1.4 - - - -
712A HIS* 2.7 57.3 + - + -
724A TRP* 3.9 16.2 - - + -
740A LEU* 4.1 2.0 - - - -
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Residues in contact with SER 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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683A MET* 3.4 1.6 - - - +
684A SER 2.9 21.3 + - - -
698A LEU* 1.3 75.5 - - - +
700A ASN* 1.3 65.6 + - - +
710A MET 2.9 17.7 + - - -
711A VAL* 4.3 6.8 - - - +
735A PHE* 3.6 9.7 - - - -
738A ASN* 3.0 31.0 + - - +
740A LEU* 3.9 8.9 - - - +
750A ILE* 3.3 27.2 - - - +
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Residues in contact with ASN 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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654A LEU* 5.6 0.6 - - - +
676A VAL* 4.2 6.3 - - - +
677A LYS 3.0 24.1 + - - +
678A ASP* 4.2 9.5 + - - +
679A VAL 5.3 0.6 - - - +
681A VAL* 4.8 6.0 + - + +
682A GLN 4.1 7.9 - - - +
683A MET* 3.8 23.3 - - + +
698A LEU* 4.1 9.1 - - - +
699A SER* 1.3 79.5 + - - +
701A ALA* 1.3 68.6 + - - +
710A MET* 3.0 25.6 + - - +
712A HIS* 2.8 31.5 + - - -
735A PHE* 3.6 7.2 - - - -
736A ALA 5.1 0.2 - - - -
738A ASN* 3.9 10.3 - - - +
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Residues in contact with ALA 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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677A LYS 4.1 7.4 - - - +
679A VAL* 3.9 22.3 + - + +
681A VAL* 4.2 9.8 - - + +
700A ASN* 1.3 89.6 + - - +
702A GLY* 1.3 61.7 + - - +
703A GLY 3.3 0.4 + - - -
705A LYS 3.8 9.0 - - - +
706A ARG* 4.1 1.1 - - - -
707A GLU 3.6 20.4 - - - +
708A ASN 4.0 0.2 - - - -
712A HIS* 5.2 0.2 + - - -
735A PHE* 3.7 30.7 - - + +
736A ALA 5.0 1.0 + - - -
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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