Contacts of the strand formed by residues 130 - 139 (chain V) in PDB entry 1UW9
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 LEU 130 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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303O ARG* 2.8 44.3 + - - +
42V MET* 5.2 0.2 - - + -
43V THR 3.7 11.9 - - - +
45V GLN* 3.9 2.8 + - - +
53V CYS* 3.9 17.0 - - - +
56V ALA* 6.5 0.4 - - + -
57V VAL* 3.9 26.5 - - + -
124V VAL 3.6 23.3 - - - +
125V PHE 4.0 5.4 - - - +
127V PHE* 3.1 14.9 - - + +
128V LYS 3.1 2.5 - - - +
129V ALA* 1.3 81.2 - - + +
131V ARG* 1.3 62.6 + - - +
132V ALA* 4.0 19.3 - - - +
133V LEU* 4.0 18.4 - - + -
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Residues in contact with ARG 131 (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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303O ARG* 4.7 2.9 - - - +
304O GLN* 3.0 18.4 + - - +
470O ASP* 2.9 31.5 + - - +
472O ILE* 3.5 42.5 - - + +
43V THR* 2.7 23.4 + - + +
44V PRO 3.9 12.8 - - - +
45V GLN* 3.1 43.6 + - - +
46V PRO* 4.1 12.6 - - - +
95V ASN* 4.7 6.5 - - - +
130V LEU* 1.3 74.8 - - - +
132V ALA* 1.3 57.2 + - + +
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Residues in contact with ALA 132 (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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304O GLN* 3.7 9.4 - - - +
41V ARG 4.5 0.2 - - - -
42V MET* 3.9 0.3 - - - -
43V THR* 3.0 42.9 + - + +
130V LEU* 3.6 8.5 - - - +
131V ARG* 1.3 82.1 - - + +
133V LEU* 1.3 63.0 + - - +
306V ASN* 3.4 32.8 - - + +
307V HIS* 3.6 8.5 - - - +
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Residues in contact with LEU 133 (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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40V PHE* 3.8 27.1 - - + -
41V ARG 3.3 14.6 - - - +
42V MET* 3.8 25.6 - - + -
57V VAL* 4.3 13.2 - - + -
124V VAL* 3.7 40.6 - - + +
125V PHE* 3.1 36.7 - - + -
130V LEU* 4.0 12.3 - - + -
132V ALA* 1.3 75.2 - - - +
134V ARG* 1.3 61.6 + - - +
306V ASN 3.8 2.0 - - - -
307V HIS* 3.1 9.6 + - - -
308V GLY 2.9 18.9 + - - -
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Residues in contact with ARG 134 (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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40V PHE* 3.4 3.0 - - - -
41V ARG* 2.7 46.2 + - + +
125V PHE* 4.4 0.9 - - - -
133V LEU* 1.3 77.2 - - - +
135V LEU* 1.3 63.7 + - - +
136V GLU* 3.0 38.4 + - - -
302V ASP 3.0 25.5 + - - -
304V GLN 3.2 18.6 + - - -
305V ARG* 3.4 25.1 + - - +
306V ASN 3.9 4.5 - - - +
307V HIS* 3.7 11.1 + - - +
308V GLY 3.1 25.8 - - - +
309V ILE 4.1 2.0 - - - +
310V HIS* 3.4 28.9 - - - +
473V ASP* 2.8 28.7 + - - -
474V LYS 5.1 1.6 + - - -
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Residues in contact with LEU 135 (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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38V ALA* 3.8 20.9 - - + -
39V ALA 3.7 10.3 - - - +
40V PHE* 4.1 16.2 - - + -
117V PHE* 5.8 1.6 - - + -
120V ILE* 4.1 3.6 - - + -
121V VAL* 3.7 22.7 - - + -
125V PHE* 4.0 17.5 - - + -
134V ARG* 1.3 69.8 - - - +
136V GLU* 1.3 59.6 + - - +
137V ASP 3.5 20.0 - - - +
138V LEU* 3.9 13.2 - - + -
308V GLY 2.9 11.1 + - - +
309V ILE* 3.4 9.2 - - + +
310V HIS 2.9 26.5 + - - -
313V VAL* 3.8 32.0 - - + +
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Residues in contact with GLU 136 (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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39V ALA* 2.8 13.3 + - + +
41V ARG* 2.9 45.5 + - + +
98V ILE* 4.9 1.3 - - + -
134V ARG* 3.0 42.5 + - - +
135V LEU* 1.3 73.9 - - - +
137V ASP* 1.3 61.1 + - - +
310V HIS* 3.8 5.1 - - - +
312V ARG* 2.8 55.3 + - - +
313V VAL* 3.6 3.1 - - - +
363V TYR* 3.6 32.8 + - + +
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Residues in contact with ASP 137 (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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38V ALA* 3.5 3.5 - - - -
39V ALA* 3.0 25.3 + - + -
135V LEU* 3.5 2.8 - - - +
136V GLU* 1.3 81.2 - - - +
138V LEU* 1.3 75.8 + - - +
312V ARG* 4.0 12.3 - - - +
313V VAL* 3.5 8.2 - - - +
316V LYS* 3.2 27.5 + - - +
348V LEU* 5.1 0.3 - - - +
362V ILE* 3.9 7.1 - - - +
363V TYR* 3.0 45.3 + - + -
364V PHE* 3.4 20.4 + - + +
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Residues in contact with LEU 138 (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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36V ILE* 4.7 1.6 - - + -
37V LEU 3.1 15.7 - - - +
38V ALA* 3.7 17.3 - - + -
116V MET* 3.7 35.9 - - + -
117V PHE* 4.8 2.9 - - + -
120V ILE* 3.8 20.4 - - + -
135V LEU* 3.9 18.6 - - + -
137V ASP* 1.3 86.7 + - - +
139V ARG* 1.3 56.7 + - - +
140V ILE* 3.6 13.1 + - + -
313V VAL* 3.8 24.0 - - + +
316V LYS* 2.6 39.3 + - + +
364V PHE* 3.7 4.5 - - - -
366V GLN* 3.5 0.9 - - - +
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Residues in contact with ARG 139 (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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31V VAL* 4.8 4.6 - - - +
32V ARG 3.0 23.8 + - - -
33V ASP* 4.0 18.3 + - - +
35V ASP 2.8 30.3 + - - +
36V ILE* 3.4 4.0 - - - +
37V LEU* 2.7 60.4 + - + +
138V LEU* 1.3 71.2 - - - +
140V ILE* 1.3 71.2 + - - +
141V PRO* 3.3 17.1 - - - +
142V PRO* 5.5 2.2 - - - +
364V PHE* 3.5 25.6 - - + -
365V THR 3.5 24.3 + - - +
366V GLN* 3.9 4.0 - - - +
367V ASP 6.0 0.7 - - - +
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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