Contacts of the strand formed by residues 133 - 138 (chain A) in PDB entry 1NUA
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 133 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33A ASP 5.0 0.6 + - - -
34A CYS* 3.5 20.2 - - - +
35A SER* 2.8 31.3 + - - +
36A SER* 3.5 2.6 - - - -
105A ARG 5.0 3.0 + - - +
106A ASP* 2.6 41.2 + - - +
107A THR 3.6 7.9 + - - +
108A VAL* 3.5 18.7 - - + +
109A VAL 3.1 18.4 + - - -
132A VAL* 1.3 82.5 - - - +
134A TYR* 1.3 60.6 + - - +
168A TRP* 5.1 0.9 - - - +
171A THR* 3.7 26.0 - - - +
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Residues in contact with TYR 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A VAL* 4.7 1.3 - - - -
109A VAL* 3.2 25.4 - - + +
111A ALA* 5.0 4.5 - - + -
121A THR* 5.0 2.0 - - + -
122A GLY* 3.5 26.2 - - - -
125A ALA* 3.8 9.2 - - + -
133A ARG* 1.3 78.8 - - - +
135A VAL* 1.3 71.1 + - - +
136A GLN* 4.0 19.5 + - + -
151A GLY* 4.6 1.7 - - - -
153A THR* 3.5 14.4 - - - +
168A TRP* 2.7 60.4 + + + -
169A GLN 3.7 9.6 + - - -
170A PRO* 3.4 23.3 - - + +
171A THR* 2.6 34.8 + - - +
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Residues in contact with VAL 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A VAL* 5.9 0.2 - - + -
30A LEU* 3.8 21.8 - - + -
34A CYS* 4.4 8.3 - - - -
108A VAL* 4.4 4.3 - - + -
109A VAL 2.9 7.1 + - - +
110A ILE* 3.5 38.4 - - + -
111A ALA* 3.1 27.9 + - - +
134A TYR* 1.3 81.9 - - - +
136A GLN* 1.3 63.3 + - - +
137A VAL* 4.7 1.1 - - + -
170A PRO* 4.4 0.2 - - - -
171A THR* 4.4 1.6 - - - -
172A LYS* 3.2 38.8 - - + +
174A TYR* 4.3 11.7 - - + -
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Residues in contact with GLN 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A ALA* 3.6 20.7 - - - +
113A GLY 5.5 1.2 - - - +
118A GLY* 3.6 29.4 + - - -
134A TYR* 4.0 15.4 + - + -
135A VAL* 1.3 75.6 - - - +
137A VAL* 1.3 60.0 + - - +
138A PRO* 3.4 5.3 - - + +
147A SER* 4.7 2.4 + - - -
148A SER* 3.5 46.7 + - - +
152A LYS 5.7 2.6 + - - -
153A THR* 5.8 1.2 - - - +
170A PRO* 3.9 17.7 - - + -
172A LYS 2.7 13.1 + - - +
173A ILE* 3.3 5.9 - - + -
174A TYR* 2.6 34.1 + - - +
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Residues in contact with VAL 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A TRP* 3.8 27.8 - - + -
26A VAL* 4.9 1.1 - - + -
110A ILE* 4.0 18.4 - - + -
111A ALA 3.0 19.5 + - - +
112A LEU* 3.4 26.1 - - + +
113A GLY 3.4 9.4 + - - -
135A VAL* 4.7 1.3 - - + -
136A GLN* 1.3 80.9 + - - +
138A PRO* 1.3 66.4 - - - +
139A THR 3.4 2.4 + - - -
174A TYR* 3.5 30.3 - - + +
176A ASP* 5.4 1.1 - - + -
179A PHE* 3.6 19.7 - - + -
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Residues in contact with PRO 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A GLY 3.3 8.7 - - - +
136A GLN* 3.4 11.9 - - + +
137A VAL* 1.3 86.6 - - - +
139A THR* 1.3 60.2 + - - +
140A THR 3.5 0.4 - - - -
143A ALA* 3.5 33.2 - - + +
144A MET* 3.5 19.2 - - + +
148A SER* 3.8 17.0 - - - +
173A ILE* 4.5 1.6 - - + -
174A TYR 3.5 12.0 - - - +
175A ILE* 3.7 26.2 - - + -
176A ASP 4.9 0.5 + - - -
179A PHE* 3.4 16.5 - - - -
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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