Contacts of the strand formed by residues 130 - 139 (chain O) 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 O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42O MET* 5.3 0.4 - - + -
43O THR 3.7 11.4 - - - +
45O GLN* 3.9 6.1 + - - +
53O CYS* 3.9 18.2 - - - -
56O ALA* 6.5 0.4 - - + -
57O VAL* 3.9 26.5 - - + -
124O VAL 3.6 23.8 - - - +
125O PHE 4.0 5.4 - - - +
127O PHE* 3.1 14.2 - - + +
128O LYS 3.1 2.8 - - - +
129O ALA* 1.3 80.1 - - + +
131O ARG* 1.3 55.6 + - - +
132O ALA* 4.0 19.3 - - - +
133O LEU* 4.0 17.9 - - + -
303V ARG* 2.8 48.9 + - - +
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Residues in contact with ARG 131 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43O THR* 2.7 20.9 + - + +
44O PRO 3.9 16.8 - - - +
45O GLN* 3.1 36.2 + - + +
46O PRO* 4.1 11.9 - - - +
95O ASN* 4.7 7.0 - - - +
130O LEU* 1.3 75.6 - - - +
132O ALA* 1.3 62.5 + - + +
303V ARG* 4.7 2.7 - - - +
304V GLN* 3.0 18.0 + - - +
470V ASP* 2.9 31.7 + - - +
472V ILE* 3.4 41.3 - - + +
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Residues in contact with ALA 132 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42O MET* 3.9 0.7 - - - -
43O THR* 2.9 43.5 + - + +
130O LEU* 3.6 8.8 - - - +
131O ARG* 1.3 81.1 - - + +
133O LEU* 1.3 63.8 + - - +
306O ASN* 3.4 32.5 - - + +
307O HIS* 3.6 8.5 - - - +
304V GLN* 3.7 8.7 - - - +
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Residues in contact with LEU 133 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40O PHE* 3.8 32.3 - - + -
41O ARG 3.3 14.4 - - - +
42O MET* 3.9 18.4 - - + -
57O VAL* 4.3 16.2 - - + -
124O VAL* 3.7 39.9 - - + +
125O PHE* 3.1 34.9 - - + -
130O LEU* 4.0 13.0 - - + -
132O ALA* 1.3 75.0 - - - +
134O ARG* 1.3 62.4 + - - +
306O ASN 3.6 2.0 + - - -
307O HIS* 3.1 9.4 + - - +
308O GLY 2.9 18.4 + - - -
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Residues in contact with ARG 134 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40O PHE* 3.5 3.7 - - - -
41O ARG* 2.7 47.5 + - + +
125O PHE* 4.4 0.7 - - - -
133O LEU* 1.3 75.7 - - - +
135O LEU* 1.3 64.3 + - - +
136O GLU* 3.0 39.3 + - - -
302O ASP* 3.0 24.2 + - - +
304O GLN 3.2 19.6 + - - -
305O ARG* 3.4 22.1 + - - +
306O ASN 3.8 12.6 - - - +
307O HIS 3.6 2.7 + - - -
308O GLY 3.1 25.1 - - - +
309O ILE 4.0 1.8 - - - +
310O HIS* 3.4 27.0 - - - +
473O ASP* 2.7 29.1 + - - -
474O LYS 5.1 1.8 + - - -
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Residues in contact with LEU 135 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38O ALA* 3.8 21.1 - - + -
39O ALA 3.7 9.9 - - - +
40O PHE* 4.0 15.7 - - + -
117O PHE* 5.8 1.8 - - + -
120O ILE* 4.1 4.3 - - + -
121O VAL* 3.7 22.2 - - + -
125O PHE* 4.0 15.1 - - + -
134O ARG* 1.3 70.2 - - - +
136O GLU* 1.3 60.0 + - - +
137O ASP 3.5 20.4 - - - +
138O LEU* 3.9 14.1 - - + -
308O GLY 2.8 12.8 + - - +
309O ILE* 3.4 9.1 - - + +
310O HIS 2.9 27.5 + - - -
313O VAL* 3.8 32.4 - - + +
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Residues in contact with GLU 136 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39O ALA* 2.8 14.0 + - + +
41O ARG* 2.8 45.3 + - + +
98O ILE* 5.0 1.1 - - + -
134O ARG* 3.0 44.3 + - - +
135O LEU* 1.3 73.9 - - - +
137O ASP* 1.3 61.0 + - - +
310O HIS* 3.8 4.6 - - - +
312O ARG* 2.8 55.0 + - - +
313O VAL* 3.5 4.0 - - - +
363O TYR* 3.7 32.9 + - + +
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Residues in contact with ASP 137 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38O ALA* 3.5 1.0 - - - -
39O ALA* 3.0 24.2 + - + -
135O LEU* 3.5 9.0 - - - +
136O GLU* 1.3 78.7 - - - +
138O LEU* 1.3 70.7 + - - +
312O ARG* 4.0 15.1 - - - +
313O VAL* 3.5 7.0 - - - +
316O LYS* 3.2 27.5 + - - +
348O LEU* 5.2 0.7 - - - +
362O ILE* 3.8 6.2 - - - +
363O TYR* 2.9 46.7 + - + -
364O PHE* 3.4 20.4 + - + +
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Residues in contact with LEU 138 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36O ILE* 4.7 1.3 - - + -
37O LEU 3.1 16.4 - - - +
38O ALA* 3.7 17.0 - - + -
116O MET* 3.7 35.4 - - + -
117O PHE* 4.9 3.1 - - + -
120O ILE* 3.8 20.2 - - + -
135O LEU* 3.9 19.7 - - + -
137O ASP* 1.3 84.9 + - - +
139O ARG* 1.3 57.3 + - - +
140O ILE* 3.6 13.8 + - + -
313O VAL* 3.8 23.3 - - + +
316O LYS* 2.5 40.1 + - + +
364O PHE* 3.7 4.7 - - - -
366O GLN* 3.5 1.6 - - - +
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Residues in contact with ARG 139 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31O VAL* 4.8 4.8 - - - +
32O ARG 3.0 24.0 + - - -
33O ASP* 4.0 19.8 + - - +
35O ASP 2.9 29.3 + - - +
36O ILE* 3.5 3.8 - - - +
37O LEU* 2.8 60.2 + - + +
138O LEU* 1.3 70.0 - - - +
140O ILE* 1.3 74.6 + - - +
141O PRO* 3.3 16.5 - - - +
142O PRO* 5.5 2.0 - - - +
364O PHE* 3.5 24.0 - - + -
365O THR 3.5 24.5 + - - +
366O GLN* 3.9 3.1 - - - +
367O 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