Contacts of the strand formed by residues 978 - 983 (chain B) in PDB entry 5GJE
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 GLN 978 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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972B TYR* 3.4 8.7 - - - -
973B ASP* 3.0 31.0 + - + +
976B ASP* 3.7 22.8 - - + +
977B LYS* 1.3 83.3 - - - +
979B LEU* 1.3 59.8 + - - +
980B TYR* 3.6 12.7 + - + -
991B LYS* 2.9 48.6 + - + +
992B ALA 4.0 3.8 - - - +
993B GLN* 4.1 17.7 + - + +
998B GLN* 3.1 33.1 + - - +
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Residues in contact with LEU 979 (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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937B LEU* 3.7 24.5 - - + -
944B ILE* 3.7 35.0 - - + -
959B LEU* 3.6 29.8 - - + -
961B ILE* 4.2 13.2 - - + -
970B ILE* 4.6 6.3 - - + -
971B ASP 3.5 17.5 - - - +
972B TYR* 3.9 9.4 - - + -
978B GLN* 1.3 72.9 - - - +
980B TYR* 1.3 66.7 + - - +
981B TRP* 3.8 8.6 - - + -
991B LYS* 3.4 4.3 - - - -
992B ALA 2.7 39.7 + - - +
993B GLN* 4.4 0.4 - - - +
994B GLU* 4.9 6.5 - - + +
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Residues in contact with TYR 980 (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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970B ILE* 3.3 5.7 - - - +
971B ASP 2.9 34.0 + - - +
973B ASP* 3.6 26.5 + - + -
978B GLN* 3.6 15.6 + - + -
979B LEU* 1.3 79.9 - - - +
981B TRP* 1.3 63.7 + - - +
989B ILE* 4.8 2.0 - - + -
990B ARG 3.5 7.6 - - - +
991B LYS* 3.4 40.9 - - + +
1002B VAL* 4.4 7.9 - - + -
1019B LEU* 4.0 17.0 - - + -
1021B ILE* 3.5 20.0 - - + -
1028B ILE* 4.0 30.3 - - + -
1043B LEU* 3.3 33.4 - - + +
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Residues in contact with TRP 981 (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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944B ILE* 4.1 12.1 - - + -
961B ILE* 3.6 24.2 - - + -
963B SER* 3.7 24.5 + - - -
964B LEU* 3.3 32.7 - - + +
965B ARG 5.2 0.6 - - - +
967B VAL* 4.2 8.3 - - + -
969B ALA 3.2 13.7 - - - +
970B ILE* 4.0 11.7 - - + -
979B LEU* 3.8 22.7 - - + -
980B TYR* 1.3 77.1 - - - +
982B ILE* 1.3 77.0 + - - +
983B ASP* 4.0 13.7 + - - +
989B ILE* 3.4 6.3 - - - +
990B ARG* 2.9 61.4 + - + +
991B LYS 3.9 4.9 - - - -
992B ALA* 3.9 20.0 - - + -
1019B LEU* 4.7 2.2 - - - +
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Residues in contact with ILE 982 (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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967B VAL* 3.2 4.9 - - - -
968B ARG* 2.9 37.5 + - + -
969B ALA* 3.0 17.1 + - + +
981B TRP* 1.3 77.2 - - - +
983B ASP* 1.3 71.0 + - - +
984B SER* 4.4 1.1 - - - +
987B ASN* 6.1 0.2 - - - +
988B MET 3.5 5.8 - - - +
989B ILE* 4.1 15.3 - - + -
1016B PRO* 3.5 36.6 - - + +
1017B TYR 3.6 7.6 - - - +
1018B ASP* 3.5 41.7 - - - +
1019B LEU* 4.0 17.7 - - + +
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Residues in contact with ASP 983 (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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963B SER 4.6 2.6 - - - +
965B ARG* 3.8 15.3 + - - +
966B ASN* 3.4 19.7 + - - +
981B TRP* 4.0 14.0 + - - +
982B ILE* 1.3 71.8 - - - +
984B SER* 1.3 58.7 + - - +
985B ARG* 3.0 20.3 + - - +
986B GLN* 2.9 38.6 + - + -
987B ASN* 2.9 29.8 + - - -
988B MET* 2.9 31.4 + - + +
990B ARG* 5.9 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