Contacts of the strand formed by residues 985 - 990 (chain A) in PDB entry 1B0P
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 ASN 985 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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956A SER* 3.9 7.3 + - - +
957A VAL 2.9 28.1 + - - +
958A TRP* 3.2 49.3 - - + +
959A ILE* 2.9 25.7 + - - +
983A ASP* 4.5 4.0 + - - -
984A VAL* 1.3 76.5 - - - +
986A VAL* 1.3 62.1 + - - +
1056A ALA 3.3 10.7 - - - +
1057A GLU* 3.6 10.9 + - - +
1063A SER* 3.6 11.0 + - - -
1238A CA 2.7 27.7 - - - -
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Residues in contact with VAL 986 (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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958A TRP* 4.7 1.5 - - - -
959A ILE* 3.3 23.1 - - + +
965A TRP* 4.0 9.0 - - + -
974A LEU* 3.7 21.5 - - + -
977A VAL* 6.0 0.2 - - + -
978A LEU* 3.5 23.1 - - + -
984A VAL* 5.0 1.8 - - + -
985A ASN* 1.3 76.0 - - - +
987A PHE* 1.3 60.1 + - - +
988A VAL* 3.6 15.3 - - + -
1063A SER* 3.0 20.3 + - - +
1064A LEU* 3.5 21.5 + - + -
1065A VAL* 3.0 29.8 + - - +
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Residues in contact with PHE 987 (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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820A TYR* 3.3 37.2 - + + -
821A VAL* 4.5 4.3 - - + -
824A ILE* 3.8 25.1 - - + -
958A TRP* 3.7 21.3 - + + -
959A ILE 2.9 8.5 + - - -
960A PHE* 3.5 15.8 - + + +
961A GLY 3.1 24.1 + - - +
985A ASN 3.9 0.4 + - - -
986A VAL* 1.3 72.3 - - - +
988A VAL* 1.3 62.2 + - - +
989A MET* 3.5 32.9 + - + +
1049A PHE* 4.3 9.0 - + - -
1053A LEU* 5.0 1.1 - - + -
1065A VAL* 3.6 31.2 - - + -
1067A ALA* 3.8 18.8 - - + -
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Residues in contact with VAL 988 (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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961A GLY 3.1 3.6 - - - +
962A GLY 3.6 25.6 - - - +
963A ASP* 4.1 6.5 - - - +
965A TRP* 4.3 3.1 - - + -
966A ALA* 3.7 24.7 - - + -
967A TYR* 4.5 5.6 - - + -
986A VAL* 3.6 24.5 - - + -
987A PHE* 1.3 72.8 - - - +
989A MET* 1.3 65.9 + - - +
990A ASP* 3.4 1.1 + - + +
1025A LEU* 4.9 0.9 - - + -
1064A LEU* 3.7 17.0 - - + -
1065A VAL 3.0 8.7 + - - +
1066A ILE* 3.4 16.0 - - + -
1067A ALA* 2.9 28.6 + - - +
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Residues in contact with MET 989 (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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817A GLU* 3.1 62.3 - - + +
820A TYR* 5.1 2.7 - - + -
821A VAL* 3.5 23.3 - - + -
841A SER* 3.4 25.8 - - - +
844A TRP* 3.6 4.5 - - + -
960A PHE* 5.2 3.6 - - - -
961A GLY 3.0 14.9 + - - +
962A GLY* 3.4 20.1 - - - -
963A ASP* 3.4 2.9 + - - +
987A PHE* 3.5 35.6 + - + +
988A VAL* 1.3 71.4 - - - +
990A ASP* 1.3 59.7 + - - +
991A THR* 3.5 4.2 + - - +
1067A ALA* 3.9 4.9 - - - +
1069A ALA* 4.2 6.7 - - + -
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Residues in contact with ASP 990 (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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963A ASP* 3.5 16.8 - - + +
967A TYR* 2.8 20.9 + - - -
988A VAL* 3.4 2.0 + - + -
989A MET* 1.3 70.7 - - - +
991A THR* 1.3 57.7 + - - +
992A GLU* 2.8 41.0 + - - +
1004A ALA* 3.8 0.2 - - - +
1022A LYS* 2.7 26.1 + - - -
1066A ILE* 3.8 10.3 - - + -
1067A ALA 2.7 18.5 + - - +
1068A TYR* 3.8 5.4 - - - -
1069A ALA* 2.9 24.8 + - - +
1096A TRP* 3.4 16.4 - - + -
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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