Contacts of the strand formed by residues 690 - 698 (chain A) in PDB entry 2DGV
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 690 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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660A PRO 5.7 0.4 - - - -
661A PHE* 3.3 61.9 + - - -
663A PHE 5.6 1.1 + - - -
683A ILE* 5.1 8.0 - - - +
684A LYS 4.2 3.4 - - - -
685A MET* 3.5 23.2 - - - +
689A LYS* 1.3 74.4 - - - +
691A LYS* 1.3 61.7 + - - +
692A GLY* 3.5 4.7 - - - -
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Residues in contact with LYS 691 (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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658A ASN* 5.3 1.4 + - - -
661A PHE* 6.0 0.7 - - - -
684A LYS* 3.4 15.8 + - + +
685A MET 4.6 1.6 - - - -
686A GLU* 3.3 45.5 + - + +
689A LYS* 4.1 9.0 - - - +
690A SER* 1.3 77.3 - - - +
692A GLY* 1.3 62.7 + - - +
693A CYS* 3.4 26.9 + - - +
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Residues in contact with GLY 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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657A ARG 3.3 1.6 - - - -
658A ASN* 3.0 11.3 + - - -
659A LEU* 2.7 58.2 + - - +
660A PRO 5.4 1.1 - - - -
661A PHE* 5.8 1.5 - - - -
683A ILE* 5.1 5.1 - - - +
684A LYS 4.6 1.2 + - - -
690A SER* 3.5 6.5 - - - +
691A LYS* 1.3 80.4 - - - +
693A CYS* 1.3 58.5 + - - +
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Residues in contact with CYS 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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655A PHE* 4.1 12.3 - - + -
656A VAL 3.1 15.5 - - - +
657A ARG* 4.0 13.7 - - + -
659A LEU* 4.3 1.8 - - - -
683A ILE* 4.0 3.5 - - - +
684A LYS* 3.0 48.0 + - - +
691A LYS* 3.4 30.1 - - - +
692A GLY* 1.3 79.9 - - - +
694A GLY* 1.3 58.5 + - - +
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Residues in contact with GLY 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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655A PHE* 3.7 3.6 - - - -
656A VAL* 2.9 32.7 + - - +
659A LEU* 3.8 13.6 - - - +
668A LEU* 4.5 2.9 - - - -
682A ASP 3.4 15.3 - - - -
683A ILE* 4.5 1.8 - - - -
684A LYS* 4.3 5.6 - - - -
693A CYS* 1.3 74.6 - - - +
695A VAL* 1.3 69.1 + - - +
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Residues in contact with VAL 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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653A GLN* 3.9 18.4 - - - +
654A ILE 3.4 12.6 - - - +
655A PHE* 3.4 28.9 - - + +
656A VAL* 4.9 0.7 - - - -
668A LEU* 3.6 4.5 - - - +
680A TYR* 3.3 41.3 - - + +
681A ALA* 3.5 17.8 - - - -
682A ASP* 3.5 7.7 + - + +
684A LYS* 3.9 17.0 - - - +
694A GLY* 1.3 81.0 - - - +
696A VAL* 1.3 69.8 + - - +
726A ASP* 4.9 0.2 - - - +
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Residues in contact with VAL 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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652A CYS 3.8 1.7 - - - +
653A GLN* 3.5 3.2 - - - -
654A ILE* 3.0 44.2 + - + +
656A VAL* 4.7 1.6 - - + -
668A LEU* 3.7 31.9 - - + +
672A PHE* 3.7 18.6 - - + -
678A VAL* 3.4 38.4 - - + -
680A TYR* 3.4 3.8 - - - +
681A ALA* 4.9 2.0 - - + -
695A VAL* 1.3 83.0 - - - +
697A LYS* 1.3 61.6 + - - +
698A PHE* 3.6 16.8 - - + -
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Residues in contact with LYS 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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652A CYS* 3.8 23.1 - - - -
653A GLN* 4.1 23.3 - - + +
678A VAL* 3.4 7.1 - - - +
679A LEU* 2.8 42.3 + - + +
680A TYR* 2.9 40.2 + - + +
696A VAL* 1.3 74.3 - - - +
698A PHE* 1.3 70.5 + - - +
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Residues in contact with PHE 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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652A CYS* 3.2 34.1 + - - +
654A ILE* 4.1 8.5 - - + -
672A PHE* 3.5 20.2 - - + -
675A CYS* 4.3 0.4 - - + -
676A GLY 4.0 9.9 - - - -
677A HIS 3.7 9.6 - - - +
678A VAL* 3.5 22.4 - - + -
679A LEU* 3.7 11.2 - - - +
696A VAL* 3.6 29.4 - - + -
697A LYS* 1.3 81.3 - - - +
699A GLU* 1.3 65.7 + - - +
700A SER 3.5 16.4 - - - +
703A VAL* 3.4 26.5 - - + -
704A ALA* 3.9 9.9 - - - -
707A ALA* 3.5 28.5 - - + -
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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