Contacts of the strand formed by residues 952 - 957 (chain B) in PDB entry 4E5W
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 ILE 952 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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909B SER* 4.7 2.4 - - - -
910B LEU* 5.0 2.6 + - - +
919B ILE* 3.8 22.1 - - + +
922B LEU* 3.5 20.6 - - + +
923B LYS* 4.0 27.8 - - + -
926B ILE* 3.9 32.5 - - + -
943B ILE* 3.9 26.5 - - + -
944B CYS 3.3 11.7 - - - +
945B THR* 4.1 11.9 - - + -
946B GLU* 4.7 0.8 - - - +
950B ASN 4.5 2.2 - - - +
951B GLY* 1.3 73.5 - - - +
953B LYS* 1.3 72.6 + - - +
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Residues in contact with LYS 953 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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872B LYS* 4.2 35.3 - - - +
875B LEU* 4.5 5.8 - - + -
907B VAL* 3.9 24.0 - - + -
908B LYS 3.4 8.7 - - - +
909B SER* 3.7 26.6 + - - -
922B LEU* 4.8 0.2 - - - -
926B ILE* 4.3 4.3 - - - -
943B ILE* 3.3 11.6 - - - +
944B CYS* 2.9 50.5 + - + +
946B GLU* 5.2 12.3 + - + -
952B ILE* 1.3 78.3 - - - +
954B LEU* 1.3 59.7 + - - +
955B ILE* 4.4 0.7 - - + -
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Residues in contact with LEU 954 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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906B ALA 3.7 1.0 - - - +
907B VAL* 3.3 5.7 - - - -
908B LYS* 2.8 50.7 + - + +
922B LEU* 4.5 4.0 - - + +
925B GLU* 4.3 24.7 - - + +
926B ILE* 3.6 32.3 - - + +
929B LEU* 4.1 11.7 - - + -
940B TYR* 3.7 33.4 - - + -
942B GLY 4.1 1.3 - - - -
953B LYS* 1.3 71.4 - - - +
955B ILE* 1.3 71.1 + - - +
956B MET* 3.9 34.6 + - + +
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Residues in contact with ILE 955 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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870B PHE* 3.8 42.0 - - + -
875B LEU* 4.0 16.8 - - + -
905B VAL* 3.8 29.6 - - + -
906B ALA 3.6 1.8 - - - +
907B VAL* 3.7 33.2 - - + -
940B TYR 3.8 0.3 - - - -
941B LYS* 2.8 30.1 + - + -
942B GLY 2.8 32.7 + - - +
943B ILE* 4.0 7.4 - - - +
944B CYS* 4.3 9.6 - - + -
953B LYS 4.4 1.6 - - - +
954B LEU* 1.3 76.7 - - - +
956B MET* 1.3 60.8 + - - +
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Residues in contact with MET 956 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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889B VAL* 4.2 14.8 - - + -
905B VAL* 3.6 8.8 - - - +
906B ALA 2.8 39.9 + - - +
908B LYS* 4.1 27.1 - - + -
925B GLU* 5.9 0.7 - - - +
929B LEU* 3.8 32.5 - - + -
938B VAL* 4.1 9.6 - - + -
939B LYS 3.4 11.2 - - - +
941B LYS* 3.6 7.0 - - - +
954B LEU* 3.9 14.1 - - + -
955B ILE* 1.3 77.7 - - - +
957B GLU* 1.3 67.9 + - - +
1020B GLY 4.8 4.0 - - - +
1021B ASP* 6.0 2.2 - - - +
1022B PHE* 6.3 0.4 - - - -
1202B 0NT 3.8 27.8 - - + -
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Residues in contact with GLU 957 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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904B GLN 5.5 0.4 - - - -
905B VAL* 5.2 0.4 - - - +
906B ALA* 3.7 0.3 - - - +
938B VAL* 3.8 4.5 - - + +
939B LYS* 2.9 52.1 + - + +
941B LYS* 3.5 21.5 - - + +
956B MET* 1.3 74.1 - - - +
958B PHE* 1.3 60.1 + - - +
959B LEU* 3.6 17.3 + - + +
1012B GLU* 4.4 3.8 - - - +
1018B LYS* 2.8 37.8 + - - +
1202B 0NT 2.9 22.9 + - - -
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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