Contacts of the strand formed by residues 684 - 690 (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 SER 684 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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557A THR 6.1 2.7 - - - -
634A THR* 3.8 9.6 - - - -
682A GLN* 4.7 1.1 - - - -
683A MET* 1.3 73.8 - - - +
685A ALA* 1.3 62.8 + - - +
686A ILE* 6.2 0.4 - - - -
698A LEU* 3.2 4.4 - - - +
699A SER 2.9 30.9 + - - -
738A ASN* 2.7 37.8 + - - -
739A SER* 3.7 8.5 - - - -
740A LEU* 3.0 26.3 + - - +
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Residues in contact with ALA 685 (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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557A THR 5.8 0.3 - - - +
559A ILE* 6.0 0.3 - - - +
634A THR* 3.2 27.8 + - + -
635A VAL 4.2 3.6 - - - +
636A VAL* 3.4 23.4 - - + +
646A PHE* 4.0 9.2 - - + -
684A SER* 1.3 77.2 - - - +
686A ILE* 1.3 68.0 + - - +
696A ILE* 4.1 5.2 - - + -
697A ILE 3.1 11.7 - - - +
698A LEU* 4.0 14.4 - - + -
740A LEU* 4.3 0.9 - - - +
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Residues in contact with ILE 686 (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* 4.2 7.9 - - - -
684A SER* 6.2 0.4 - - - -
685A ALA* 1.3 79.7 - - - +
687A HIS* 1.3 65.3 + - - +
696A ILE* 3.3 5.2 - - - +
697A ILE* 2.8 47.7 + - + +
740A LEU* 3.4 38.6 - - + +
741A GLN* 3.7 17.0 - - - +
742A GLU* 3.7 28.9 - - + +
748A TYR* 4.0 21.8 - - + -
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Residues in contact with HIS 687 (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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562A ARG* 3.0 37.8 + - - +
636A VAL* 3.7 21.1 - - + +
637A GLN 3.3 10.1 - - - +
638A LEU* 4.3 3.4 - - + -
639A ASN* 3.4 6.5 - - - -
686A ILE* 1.3 79.7 - - - +
688A THR* 1.3 63.8 + - - +
689A MET* 2.8 35.1 + - + +
694A GLU* 2.7 28.0 + - + +
695A TYR 3.8 11.9 - - - -
696A ILE* 4.7 3.4 - - + -
742A GLU* 4.1 13.3 - - - +
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Residues in contact with THR 688 (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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686A ILE* 5.1 1.1 - - - -
687A HIS* 1.3 78.4 - - - +
689A MET* 1.3 70.4 + - - +
695A TYR* 2.9 51.0 + - + +
697A ILE* 3.6 27.4 - - + +
742A GLU* 2.6 20.9 + - - -
748A TYR* 2.5 35.3 + - - +
771A TRP* 4.2 7.9 - - + -
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Residues in contact with MET 689 (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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639A ASN* 3.4 20.0 - - - +
687A HIS* 2.8 38.1 - - + +
688A THR* 1.3 102.9 + - - +
690A HIS* 1.3 63.4 + - - +
691A GLU 4.1 1.3 - - - +
692A GLY* 4.9 10.1 - - - +
693A LYS 3.5 4.3 - - - +
694A GLU* 3.1 31.6 - - + -
742A GLU* 4.0 4.8 + - - +
748A TYR* 4.4 3.1 + - - -
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Residues in contact with HIS 690 (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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689A MET* 1.3 75.6 + - - +
691A GLU* 1.3 100.9 + - + +
693A LYS* 2.8 28.0 + - - +
695A TYR* 3.6 9.9 + + + -
746A GLY* 5.9 5.2 - - - -
748A TYR* 5.3 0.2 + - - -
771A TRP* 3.2 82.9 - + + -
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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