Contacts of the strand formed by residues 861 - 866 (chain A) in PDB entry 4AY6
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 861 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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832A ILE* 3.2 11.4 - - - +
834A TYR* 3.7 22.9 - - - -
855A LEU* 3.1 13.9 + - - +
858A VAL* 2.6 28.0 + - - -
859A PRO 3.2 3.2 - - - -
860A ASN* 1.3 77.7 - - - +
862A VAL* 1.3 69.0 + - - +
889A ARG* 2.9 37.5 + - - -
1024B ASP* 4.4 1.2 - - - +
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Residues in contact with VAL 862 (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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827A LEU* 4.8 2.0 - - + -
828A PRO* 3.8 35.2 - - + -
831A ALA* 4.4 2.7 - - + -
832A ILE 2.9 7.8 + - - +
833A VAL* 3.9 31.0 - - + -
834A TYR* 3.0 27.0 + - - +
855A LEU* 3.8 6.1 - - - -
860A ASN 5.7 0.2 - - - -
861A SER* 1.3 80.1 - - - +
863A LEU* 1.3 61.9 + - - +
888A ASN 4.1 15.0 - - - +
889A ARG* 3.3 15.7 - - - +
891A ILE* 4.4 12.8 - - + -
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Residues in contact with LEU 863 (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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834A TYR* 3.2 30.5 - - + +
835A CYS 4.6 4.7 - - - +
836A ASN* 4.9 0.7 - - + +
848A LEU* 4.9 2.7 - - + -
851A TRP* 3.6 39.0 - - + -
855A LEU* 3.8 18.5 - - + +
862A VAL* 1.3 75.2 - - - +
864A TRP* 1.3 60.2 + - - +
865A LEU* 3.9 29.8 - - + -
889A ARG 3.0 9.6 + - - +
890A ILE* 3.5 18.9 - - + +
891A ILE* 2.8 29.0 + - - +
912A LEU* 4.1 14.1 - - + -
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Residues in contact with TRP 864 (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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825A TYR* 3.8 32.1 - + + +
827A LEU* 3.7 34.8 - - + +
833A VAL* 4.0 16.6 - - + -
834A TYR 2.6 16.0 + - - +
835A CYS* 3.4 8.5 - - + +
836A ASN 3.0 28.1 + - - +
837A PHE* 3.6 28.8 - + - -
863A LEU* 1.3 71.6 - - - +
865A LEU* 1.3 68.9 + - - +
891A ILE* 3.4 24.1 - - + +
893A SER* 3.2 26.0 + - - -
904A ARG* 3.5 44.9 - - + -
907A LEU* 4.3 7.6 - - + -
908A ALA* 4.4 5.4 - - + -
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Residues in contact with LEU 865 (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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836A ASN* 3.4 33.9 - - + +
837A PHE* 5.2 0.4 - - - -
840A LEU* 4.8 5.6 - - + -
843A ILE* 4.8 15.5 - - + -
848A LEU* 5.8 0.4 - - + -
851A TRP* 4.4 8.7 - - + -
863A LEU* 3.9 31.2 - - + -
864A TRP* 1.3 81.8 - - - +
866A LEU* 1.3 73.3 + - - +
876A ILE* 4.5 12.6 - - + -
890A ILE* 3.9 15.9 - - + -
891A ILE 2.8 9.7 + - - +
892A PHE* 3.6 26.2 - - + -
893A SER 3.0 23.0 + - - -
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Residues in contact with LEU 866 (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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836A ASN 4.3 2.6 + - - -
837A PHE* 3.5 46.7 - - + +
838A ASN 4.7 3.5 + - - +
840A LEU* 3.4 23.6 - - - +
865A LEU* 1.3 86.4 - - - +
867A ARG* 1.3 61.7 + - - +
868A PHE* 3.0 24.3 + - + -
892A PHE* 3.9 6.8 - - - -
893A SER* 3.4 18.6 - - - +
894A PRO 4.0 2.0 - - - +
895A VAL* 4.9 4.7 - - + -
901A HIS* 4.7 0.2 - - - +
904A ARG* 3.1 24.5 - - - +
1200A 12V 3.6 30.3 - - + +
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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