Contacts of the strand formed by residues 90 - 96 (chain U) 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 ARG 90 (chain U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40U LEU* 3.1 3.9 - - - -
41U GLY 2.9 34.7 + - - +
43U TRP 6.0 1.1 - - - +
44U GLN* 6.5 0.4 - - + -
79U TYR* 4.0 5.4 - - - +
83U LYS* 3.3 10.8 - - - +
87U ALA 4.4 4.5 - - - +
88U ARG* 3.9 12.1 - - - +
89U GLU* 1.3 77.3 - - - +
91U ILE* 1.3 69.3 + - - +
92U VAL* 3.3 2.8 + - + +
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Residues in contact with ILE 91 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38U VAL* 5.2 12.8 - - + -
39U LEU 3.8 6.3 - - - +
40U LEU* 4.0 20.9 - - + -
43U TRP* 5.7 0.3 - - - +
54U PHE* 5.2 6.3 - - + -
75U LEU* 6.0 3.8 - - + -
79U TYR* 1.3 97.4 + - + +
90U ARG* 1.3 75.8 - - - +
92U VAL* 1.3 59.5 - - - +
93U GLY* 4.8 1.1 - - - +
115U TYR* 4.0 20.4 - - + +
116U CYS* 2.0 40.0 - - + -
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Residues in contact with VAL 92 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39U LEU* 2.7 19.0 + - + +
40U LEU 4.3 0.9 - - - -
41U GLY* 3.8 25.4 - - - +
42U SER 4.3 1.6 - - - +
43U TRP* 4.1 27.1 - - + +
48U LEU* 4.4 7.2 - - + -
49U ASP 5.3 1.8 - - - +
50U VAL* 5.8 8.3 - - + -
90U ARG* 3.4 15.9 - - + +
91U ILE* 1.3 77.3 - - - +
93U GLY* 1.3 61.0 + - - +
112U MET* 5.5 1.2 - - - +
116U CYS* 3.0 26.2 - - - +
119U SER* 3.4 14.8 - - - +
120U VAL* 4.3 23.3 - - + +
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Residues in contact with GLY 93 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38U VAL* 3.3 5.3 - - - +
39U LEU* 2.5 41.5 + - - +
91U ILE* 5.6 0.7 - - - -
92U VAL* 1.3 84.8 - - - +
94U TRP* 1.3 61.2 + - - -
112U MET* 5.6 2.0 - - - -
119U SER* 4.6 1.1 - - - -
120U VAL* 3.2 22.0 - - - -
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Residues in contact with TRP 94 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36U VAL* 5.0 9.9 - - + -
37U GLY 3.2 16.8 - - - +
38U VAL* 3.8 11.4 - - + +
39U LEU* 4.3 3.6 - - - +
93U GLY* 1.3 74.8 - - - +
95U TYR* 1.3 71.4 + - - +
96U HIS* 4.0 13.5 - + + -
105U ASP* 4.0 6.1 - - - -
108U ILE* 3.6 31.8 + - + -
109U ASN* 2.1 52.5 + - - +
112U MET* 2.7 40.5 - - + +
119U SER* 5.7 1.0 - - - -
120U VAL 3.0 5.3 + - - +
121U LEU* 2.3 80.3 - - + +
122U VAL 3.5 2.1 + - - -
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Residues in contact with TYR 95 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19U VAL* 3.6 39.3 + - + +
22U HIS* 3.9 19.1 - + - +
35U VAL* 4.6 4.3 - - + -
36U VAL* 3.1 25.5 - - - +
37U GLY* 2.8 49.8 + - - +
38U VAL 3.8 9.0 - - - -
39U LEU* 3.9 18.2 - - + -
53U SER* 4.4 12.3 + - - -
54U PHE 4.6 0.7 - - - -
55U ALA* 4.3 8.3 + - - +
94U TRP* 1.3 78.7 - - - +
96U HIS* 1.3 68.0 + - - +
97U THR* 4.4 5.4 - - - -
121U LEU* 3.5 2.2 - - - -
122U VAL* 3.1 24.5 - - + +
123U ILE* 5.2 0.4 - - - -
124U ILE* 5.3 7.9 - - + +
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Residues in contact with HIS 96 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34U ARG* 3.3 31.4 - - - +
35U VAL 3.0 10.1 - - - +
36U VAL* 3.7 9.0 - - + -
94U TRP* 4.0 20.2 - + + -
95U TYR* 1.3 77.3 - - - +
97U THR* 1.3 58.3 + - - +
98U GLY* 3.0 19.8 + - - -
100U LYS 2.7 30.7 + - - -
101U LEU* 3.5 15.0 - - - -
102U HIS* 3.7 7.9 + - - -
105U ASP* 3.6 7.4 + - - -
121U LEU* 3.9 5.3 - - + +
122U VAL 3.7 2.6 + - - -
123U ILE* 3.4 36.7 - - + +
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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