Contacts of the strand formed by residues 91 - 96 (chain J) in PDB entry 3Q3G
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 91 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42J TYR 3.8 0.5 - - - +
43J GLN* 3.5 1.9 - - - -
44J GLN* 2.7 43.4 + - + +
90J ALA* 1.3 74.2 - - - +
92J TYR* 1.3 62.9 + - - +
93J TYR* 3.6 29.9 + - + +
107J GLY* 4.1 0.9 - - - -
108J THR 3.4 13.5 - - - +
109J LYS* 3.7 29.4 - - + -
709J GOL 3.6 37.9 - - - +
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Residues in contact with TYR 92 (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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6J GLN* 2.7 24.1 + - - -
21J MET* 3.7 27.1 - - - -
41J TRP* 4.6 3.8 - + + -
42J TYR 3.3 6.3 - - - +
43J GLN* 3.1 32.1 + - + -
53J LEU* 3.6 14.8 - - + -
68J PHE* 3.4 32.1 - + - -
79J LEU* 3.7 21.3 - - + -
81J ILE* 4.0 3.3 - - + +
88J ASP* 2.5 33.7 + - - +
90J ALA* 3.8 11.4 - - + -
91J VAL* 1.3 73.6 - - - +
93J TYR* 1.3 55.3 + - - +
107J GLY* 3.2 1.2 - - - -
108J THR 2.9 31.0 + - - +
110J LEU* 3.7 16.2 - - + -
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Residues in contact with TYR 93 (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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6J GLN* 3.5 2.7 - - - -
41J TRP* 3.3 6.2 - - - -
42J TYR* 2.7 47.7 + - + +
44J GLN* 3.4 29.9 + - + -
91J VAL* 3.6 24.4 - - + +
92J TYR* 1.3 75.1 - - - +
94J CYS* 1.3 63.6 - - - +
104J PHE* 4.6 5.2 - - + -
105J GLY 3.3 21.8 - - - -
106J ALA 3.6 19.3 - - - -
107J GLY* 3.7 6.5 - - - -
709J GOL 2.9 20.8 + - - -
41K GLN* 3.5 8.5 + - - -
45K GLN 3.4 13.3 + - - -
46K GLY* 3.9 12.3 - - - -
47K LEU* 3.8 28.7 - - + -
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Residues in contact with CYS 94 (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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4J MET* 3.8 13.6 - - - +
6J GLN* 3.3 22.2 + - - -
23J CYS* 2.1 53.6 - - + -
39J LEU* 4.5 2.2 - - + -
40J ALA 3.2 9.9 - - - +
41J TRP* 3.9 16.8 - - + -
93J TYR* 1.3 74.9 - - - +
95J GLN* 1.3 60.8 + - - +
104J PHE* 3.4 5.3 - - - +
105J GLY 2.9 25.6 + - - -
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Residues in contact with GLN 95 (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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4J MET* 3.9 6.7 - - - -
39J LEU* 3.4 4.7 - - - +
40J ALA* 2.8 39.4 + - - +
42J TYR* 2.6 39.4 + - + -
94J CYS* 1.3 76.2 - - - +
96J GLN* 1.3 78.3 + - - +
97J TYR* 3.8 18.5 + - - +
102J LEU* 3.9 7.6 - - - +
103J THR 3.3 16.4 - - - +
104J PHE* 3.6 25.1 - - + -
111K MET* 3.4 29.0 - - - +
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Residues in contact with GLN 96 (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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2J ILE* 3.7 25.1 - - + +
4J MET* 3.7 18.6 - - + +
29J LEU* 3.7 22.9 - - + -
38J TYR 3.3 5.2 - - - +
95J GLN* 1.3 85.2 - - - +
97J TYR* 1.3 59.4 + - - +
98J TYR* 2.9 28.2 + - - +
99J SER* 3.0 18.1 + - - -
101J PRO 2.9 27.9 + - - -
102J LEU* 3.9 2.6 - - - -
103J THR* 3.0 41.6 + - - +
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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