Contacts of the strand formed by residues 86 - 92 (chain V) in PDB entry 4UJ3
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 GLY 86 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13V LYS 3.3 6.5 + - - +
14V VAL* 3.1 12.6 - - - -
15V VAL* 2.9 25.1 + - - +
84V ALA* 3.5 2.0 - - - +
85V VAL* 1.3 81.2 - - - +
87V ALA* 1.3 61.4 + - - +
117V ILE* 3.9 4.5 - - - +
118V VAL 3.4 10.1 - - - -
168V ILE* 4.4 1.6 - - - -
172V ILE* 3.5 15.7 - - - -
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Residues in contact with ALA 87 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14V VAL* 4.1 0.7 - - - -
15V VAL* 3.2 22.4 - - + +
17V ILE* 5.2 3.6 - - + -
86V GLY* 1.3 74.4 - - - +
88V LEU* 1.3 64.5 + - - +
89V LEU 3.7 1.1 + - - +
109V LEU* 4.1 28.3 - - + -
117V ILE* 4.2 9.6 - - + -
118V VAL 2.9 9.0 + - - +
119V ILE* 3.7 3.9 - - + +
120V MET 3.1 24.3 + - - -
168V ILE* 3.6 5.8 - - - +
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Residues in contact with LEU 88 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14V VAL* 4.1 11.0 - - + -
15V VAL 2.8 9.3 + - - -
16V LEU* 3.3 27.8 - - + -
17V ILE* 3.1 27.2 + - - +
27V LEU* 5.8 3.4 - - + -
87V ALA* 1.3 70.3 - - - +
89V LEU* 1.3 61.4 + - - +
90V VAL* 3.4 10.6 + - + +
120V MET* 3.2 39.0 - - + -
122V VAL* 4.2 6.3 - - + -
164V ALA* 5.2 1.6 - - + +
165V PHE* 3.3 43.5 - - + -
168V ILE* 3.5 21.8 - - + -
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Residues in contact with LEU 89 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17V ILE* 3.5 18.2 - - + +
87V ALA 3.7 2.4 + - - +
88V LEU* 1.3 70.7 - - - +
90V VAL* 1.3 65.6 + - - +
102V VAL* 4.0 25.4 - - + +
105V TRP* 3.7 44.0 - - + -
106V LEU* 3.9 33.7 - - + +
109V LEU* 4.8 2.5 - - + -
119V ILE* 4.5 13.7 - - + -
120V MET 2.8 13.1 + - - +
121V LEU* 3.4 14.4 - - + +
122V VAL 2.8 25.5 + - - -
148V LEU* 5.5 1.3 - - + -
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Residues in contact with VAL 90 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16V LEU* 4.6 3.1 - - + -
17V ILE 2.9 10.5 + - - +
18V GLY* 3.5 18.7 - - - -
19V ASP 4.0 2.3 + - - -
22V VAL* 3.6 29.1 - - + +
24V LYS* 4.3 10.3 - - + +
27V LEU* 3.9 24.9 - - + -
88V LEU* 3.6 20.4 - - + +
89V LEU* 1.3 82.4 - - - +
91V TYR* 1.3 73.5 + - - +
98V THR 4.8 1.7 - - - +
102V VAL* 5.3 0.2 - - - +
105V TRP* 5.4 0.9 - - - -
122V VAL* 3.5 15.9 - - + +
124V ASN* 4.1 15.5 - - + -
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Residues in contact with TYR 91 (chain V).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22V VAL* 3.9 9.4 - - - +
90V VAL* 1.3 79.4 - - - +
92V ASP* 1.3 68.1 + - - +
93V ILE* 3.7 23.3 - - + +
98V THR* 3.6 23.3 - - - +
99V TYR* 3.8 34.8 - + + -
102V VAL* 4.0 4.3 - - + -
121V LEU* 4.1 23.1 - - + -
122V VAL 3.0 22.6 + - - +
123V GLY* 3.5 19.5 - - - -
124V ASN* 3.1 25.3 + - - +
134V VAL* 3.7 25.0 - - + +
139V ALA* 3.4 19.8 - - - +
150V PHE* 3.7 10.4 - + - -
152V GLU* 3.9 6.8 + - - -
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Residues in contact with ASP 92 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21V GLY 4.3 1.1 - - - +
22V VAL* 3.7 18.2 - - + +
91V TYR* 1.3 78.4 - - - +
93V ILE* 1.3 66.0 + - - +
94V ALA* 2.7 33.2 + - - +
95V LYS* 3.0 41.9 + - + +
98V THR* 2.8 19.6 + - + +
124V ASN 4.1 2.0 - - - -
125V LYS* 3.0 44.2 + - - +
128V LEU* 5.6 0.2 - - - +
134V VAL* 4.5 0.9 - - - +
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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