Contacts of the strand formed by residues 988 - 992 (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 MET 988 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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963B SER 5.3 1.1 - - - +
981B TRP 3.8 0.3 - - - +
982B ILE* 3.5 3.6 - - - +
983B ASP* 2.9 40.9 + - + +
986B GLN* 3.2 47.1 - - + +
987B ASN* 1.3 76.1 - - - +
989B ILE* 1.3 60.6 + - - +
990B ARG* 3.4 30.4 + - + +
1001B THR* 3.7 24.0 - - + -
1003B VAL 3.0 19.3 - - - +
1004B VAL* 4.1 14.1 - - + -
1016B PRO* 4.5 5.7 - - - +
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Residues in contact with ILE 989 (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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980B TYR* 4.8 2.2 - - + -
981B TRP 3.4 10.1 - - - +
982B ILE* 4.1 13.9 - - + -
988B MET* 1.3 77.0 - - - +
990B ARG* 1.3 65.8 + - - +
1001B THR* 3.9 1.4 - - - +
1002B VAL* 2.9 36.2 + - + +
1003B VAL* 3.2 31.1 + - + +
1016B PRO* 4.2 11.2 - - + -
1019B LEU* 3.8 28.7 - - + -
1028B ILE* 4.6 11.9 - - + -
1030B TRP* 3.9 38.4 - - + -
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Residues in contact with ARG 990 (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* 3.3 37.4 + - - -
980B TYR* 3.5 6.8 - - - +
981B TRP* 2.9 57.5 + - + +
983B ASP* 6.1 0.2 - - + -
988B MET* 3.4 34.9 + - + +
989B ILE* 1.3 76.3 - - - +
991B LYS* 1.3 59.8 + - - +
999B GLY* 3.1 16.2 - - - -
1000B PHE* 3.1 30.7 - - - +
1001B THR* 3.0 37.2 + - - +
1002B VAL* 4.3 1.1 - - - -
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Residues in contact with LYS 991 (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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978B GLN* 2.9 39.3 + - + +
979B LEU 3.4 9.4 - - - +
980B TYR* 3.4 40.2 - - + +
981B TRP* 3.9 3.6 - - - -
990B ARG* 1.3 80.4 + - - +
992B ALA* 1.3 68.7 + - - +
998B GLN* 2.9 27.9 + - - +
999B GLY* 3.0 1.6 - - - -
1000B PHE* 2.8 59.0 + - + +
1002B VAL* 4.2 4.0 - - + -
1043B LEU 5.0 5.6 - - - +
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Residues in contact with ALA 992 (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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961B ILE* 4.4 8.7 - - + -
963B SER* 5.5 1.1 - - - +
978B GLN* 4.4 3.6 - - - -
979B LEU* 2.7 44.1 + - - +
981B TRP* 3.9 17.7 - - + -
990B ARG* 5.5 0.2 - - - +
991B LYS* 1.3 80.8 - - - +
993B GLN* 1.3 63.2 + - - +
996B GLY 4.2 8.3 - - - +
997B SER 3.9 13.7 - - - +
998B GLN 4.0 6.3 - - - -
999B GLY* 4.0 6.5 - - - -
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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