Contacts of the strand formed by residues 85 - 88 (chain J) in PDB entry 5GJQ
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 VAL 85 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76J VAL* 4.6 7.2 - - + -
78J ARG 4.6 0.7 - - - -
79J ALA* 4.0 19.7 - - + +
84J LYS* 1.3 67.8 - - - +
86J LEU* 1.3 59.7 + - - +
87J VAL* 3.9 8.7 - - + -
96J VAL* 3.2 0.8 - - - -
97J VAL* 2.4 66.7 + - + +
98J ASP 3.9 0.9 - - - +
99J VAL* 2.9 32.5 - - + -
105J ILE* 5.1 1.6 - - + -
108J VAL* 3.6 31.6 - - + -
123J LEU* 3.6 22.2 - - + -
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Residues in contact with LEU 86 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109I VAL* 4.0 19.3 - - + -
163I LEU* 5.7 7.0 - - + -
76J VAL* 3.6 2.1 - - - +
77J VAL* 2.8 64.8 + - + -
78J ARG* 2.8 37.1 + - - +
80J MET* 3.5 18.6 - - + -
84J LYS 3.6 2.0 + - - -
85J VAL* 1.3 69.4 - - - +
87J VAL* 1.3 73.6 + - - +
94J LYS* 4.6 6.7 - - + -
96J VAL* 2.3 43.7 - - + +
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Residues in contact with VAL 87 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74J GLY* 4.2 7.4 - - - -
75J GLU 3.2 25.6 - - - +
76J VAL* 3.7 20.4 - - + +
77J VAL* 3.6 5.8 - - - +
85J VAL* 3.9 21.1 - - + +
86J LEU* 1.3 89.5 - - - +
88J LYS* 1.3 66.6 + - - +
89J VAL* 4.0 6.5 - - + +
94J LYS* 2.9 3.4 - - - +
95J PHE* 2.3 52.6 + - + +
97J VAL* 4.5 10.3 - - + -
114J VAL* 6.0 1.1 - - + -
116J LEU* 6.1 5.2 - - + -
123J LEU* 5.4 5.6 - - + -
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Residues in contact with LYS 88 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126I SER* 5.9 1.1 - - - -
75J GLU* 2.8 51.3 + - - +
77J VAL* 3.7 8.4 - - + +
87J VAL* 1.3 74.3 - - - +
89J VAL* 1.3 72.9 + - - +
90J HIS* 3.9 12.0 + - - +
92J GLU 3.5 21.3 + - - -
93J GLY* 3.2 23.6 - - - +
94J LYS* 3.3 23.6 - - + +
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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