Contacts of the strand formed by residues 683 - 690 (chain A) in PDB entry 5M9O
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 683 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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681A SER 4.6 4.0 - - - +
682A TYR* 1.3 73.8 - - - +
684A PRO* 1.3 78.8 - - + +
685A VAL* 3.4 28.8 + - - +
700A ASP* 3.4 34.7 + - + +
702A GLU* 5.7 6.5 - - + -
796A TYR* 3.8 22.2 + - - -
827A LEU* 3.4 2.6 - - - -
828A LEU* 2.8 48.5 + - + +
830A VAL* 6.0 0.4 - - - +
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Residues in contact with PRO 684 (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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682A TYR 4.5 2.5 - - - +
683A LYS* 1.3 92.4 - - + +
685A VAL* 1.3 64.3 + - - +
700A ASP* 4.0 1.2 - - - -
701A VAL* 3.2 29.8 + - + +
702A GLU* 4.7 19.7 + - + +
825A GLN* 3.8 24.7 - - - +
826A CYS 3.5 6.7 - - - +
827A LEU* 4.0 13.0 - - + -
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Residues in contact with VAL 685 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
683A LYS* 3.4 32.5 - - - +
684A PRO* 1.3 81.0 - - - +
686A PHE* 1.3 59.8 + - - +
687A VAL* 4.6 1.8 - - + -
698A VAL* 3.8 33.2 - - + -
699A GLN 3.1 11.7 - - - +
700A ASP* 4.3 1.1 - - - +
701A VAL* 3.6 6.7 - - - +
825A GLN* 3.3 6.4 - - - +
826A CYS* 2.8 52.7 + - + +
828A LEU* 4.0 21.1 - - + -
842A LEU* 4.5 2.0 - - + -
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Residues in contact with PHE 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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685A VAL* 1.3 72.6 - - - +
687A VAL* 1.3 60.9 + - - +
688A THR* 3.6 26.0 + - + +
698A VAL* 3.2 3.3 - - - -
699A GLN* 2.8 55.8 + - + +
701A VAL* 3.9 9.4 - - + +
766A TYR* 6.3 0.9 - + - -
823A ASN* 3.4 44.6 - - - -
824A THR* 3.6 14.4 - - - -
825A GLN* 3.9 4.0 - - + -
111B 2MR 3.2 76.1 - - + +
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Residues in contact with VAL 687 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
685A VAL* 4.6 2.2 - - + -
686A PHE* 1.3 72.8 - - - +
688A THR* 1.3 60.0 + - - +
689A GLU 4.5 1.3 - - - +
690A ILE* 3.7 30.1 - - + -
696A PHE* 4.5 4.9 - - + -
697A TYR 3.6 11.9 - - - +
698A VAL* 4.1 13.9 - - + -
821A ILE* 3.4 28.9 - - + +
822A GLN* 4.5 1.3 - - - -
823A ASN* 2.7 35.0 + - - -
824A THR 3.1 12.1 + - - +
826A CYS* 3.9 27.4 - - + -
842A LEU* 4.5 4.0 - - + -
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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 PHE* 3.6 21.5 - - + +
687A VAL* 1.3 76.6 - - - +
689A GLU* 1.3 61.1 + - - +
697A TYR* 2.9 15.2 + - - +
698A VAL* 4.3 2.6 + - - -
699A GLN* 3.6 34.2 - - - +
766A TYR* 2.7 42.9 + - + -
793A ALA* 4.9 0.2 - - - +
822A GLN* 3.5 19.7 + - - +
823A ASN* 4.5 7.6 - - - +
113B 2MR 4.1 14.3 - - - -
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Residues in contact with GLU 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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687A VAL* 3.9 1.2 - - - +
688A THR* 1.3 83.3 + - - +
690A ILE* 1.3 84.0 + - - +
691A THR* 4.6 6.5 - - + +
696A PHE* 3.1 6.1 - - - +
697A TYR* 2.8 40.6 + - + +
766A TYR 3.6 15.9 - - - +
767A GLY 3.7 18.9 - - - +
768A ASN* 3.8 26.7 - - + +
769A ARG 4.8 1.4 + - - -
822A GLN* 4.3 10.5 + - - +
113B 2MR 5.7 0.3 - - - -
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Residues in contact with ILE 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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687A VAL* 3.7 19.7 - - + -
689A GLU* 1.3 88.9 + - - +
691A THR* 1.3 73.4 + - - +
692A ASP* 5.2 1.4 - - - +
694A LEU* 4.7 7.6 - - + -
695A HIS 3.6 9.9 - - - +
696A PHE* 3.6 20.9 - - + -
814A VAL* 4.1 11.0 - - + +
817A VAL* 3.6 28.7 - - + -
818A VAL* 3.6 42.4 - - + +
821A ILE* 3.9 4.7 - - + -
822A GLN* 4.6 11.1 - - + +
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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