Contacts of the strand formed by residues 876 - 881 (chain A) in PDB entry 4D86
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 HIS 876 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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817A ASP 5.1 1.2 + - - -
818A VAL* 3.4 18.2 - - + +
819A VAL 4.4 0.7 + - - -
866A ILE* 3.7 27.1 - - + -
867A SER 3.1 26.5 - - - +
868A LYS* 4.2 7.8 - - + +
869A ALA* 3.8 3.8 - - - -
874A TYR* 3.4 14.0 - - - +
875A HIS* 1.3 92.7 + - + +
877A VAL* 1.3 67.9 + - - +
911A TYR* 4.1 24.7 + + - -
913A TYR* 3.0 26.8 + - - +
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Residues in contact with VAL 877 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
818A VAL* 4.3 0.2 - - - -
819A VAL* 3.8 17.7 - - + +
821A ASN* 3.8 11.7 - - + -
837A LEU* 4.2 8.3 - - + -
845A LEU* 4.4 5.2 - - + -
866A ILE* 3.4 2.5 - - - +
867A SER* 2.9 34.3 + - - +
869A ALA* 3.8 11.6 - - + +
872A LEU* 3.6 31.2 - - + -
874A TYR* 4.9 1.1 - - + -
876A HIS* 1.3 78.4 - - - +
878A ILE* 1.3 75.5 + - - +
879A HIS* 3.5 30.9 - - + +
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Residues in contact with ILE 878 (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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818A VAL* 3.9 23.3 - - + +
819A VAL 2.9 11.9 + - - +
820A VAL* 3.2 7.3 - - + -
821A ASN 2.7 32.6 + - - -
864A ALA* 4.5 0.4 - - + -
865A THR 3.3 11.0 - - - +
866A ILE* 4.0 19.1 - - + -
877A VAL* 1.3 76.0 - - - +
879A HIS* 1.3 58.5 + - - +
904A SER* 3.6 51.8 - - - +
907A LEU* 4.1 9.6 - - + -
908A ALA* 3.8 25.4 - - + +
913A TYR* 5.4 0.2 - - + -
916A ILE* 4.4 4.9 - - + -
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Residues in contact with HIS 879 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
821A ASN* 3.1 25.5 + - - +
823A SER* 4.0 4.3 - - - -
827A LEU* 3.7 23.3 - - + -
829A HIS* 3.5 26.5 - + - -
845A LEU* 3.9 7.9 - - + -
849A CYS* 3.3 14.4 - - - -
859A LEU* 4.8 2.4 - - - +
864A ALA* 3.1 6.8 - - - -
865A THR* 2.8 43.4 + - + +
867A SER* 2.8 32.2 + - - -
877A VAL* 3.5 31.2 - - + +
878A ILE* 1.3 71.9 - - - +
880A ALA* 1.3 60.7 + - - +
881A VAL* 4.1 0.8 + - - -
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Residues in contact with ALA 880 (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 VAL* 3.6 16.2 - - + -
821A ASN 2.9 8.9 + - - +
822A ALA* 3.7 1.7 - - - -
823A SER* 2.8 26.3 + - - +
863A ASN 3.6 4.5 - - - -
878A ILE 3.9 1.4 + - - -
879A HIS* 1.3 73.2 - - - +
881A VAL* 1.3 62.5 + - - +
882A GLY 3.8 1.6 + - - -
900A ALA* 4.2 11.4 - - + -
904A SER* 3.5 22.2 - - - +
921A ILE* 3.9 19.2 - - + +
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Residues in contact with VAL 881 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
823A SER* 3.9 7.4 - - - +
824A ASN* 3.4 42.6 - - - +
825A GLU* 4.0 11.4 - - - +
827A LEU* 4.5 1.3 - - + -
859A LEU* 3.7 30.1 - - + -
860A LEU 3.7 20.4 - - - +
861A PRO* 4.1 4.9 - - + -
862A GLY* 2.8 33.3 + - - -
863A ASN 2.9 15.7 + - - +
879A HIS 4.8 0.2 - - - +
880A ALA* 1.3 74.4 - - - +
882A GLY* 1.3 63.4 + - - +
900A ALA* 3.7 3.2 - - - +
926A PHE* 5.0 0.7 - - + -
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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