Contacts of the strand formed by residues 172 - 176 (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 LYS 172 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A LYS* 5.8 3.0 - - - +
12A ARG* 2.9 31.7 - - - +
14A SER* 3.5 7.4 - - - +
16A ILE* 3.8 20.8 - - + +
29A ASP* 2.8 26.6 + - - -
33A ASP* 3.3 26.3 + - - -
34A CYS* 4.1 6.5 - - - -
135A VAL* 3.2 25.1 - - + +
136A GLN 2.7 29.6 + - - -
170A PRO* 3.1 3.3 - - - +
171A THR* 1.3 93.2 - - + +
173A ILE* 1.3 63.9 + - - +
174A TYR* 3.8 22.7 - - + +
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Residues in contact with ILE 173 (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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9A ILE* 5.0 5.6 - - + -
14A SER* 2.6 24.1 + - - +
15A ILE* 3.4 26.5 - - + -
16A ILE 2.9 25.7 + - - -
136A GLN* 3.3 9.9 - - + +
138A PRO* 4.5 1.1 - - + -
148A SER* 3.7 36.8 - - - +
149A ILE* 4.2 14.6 - - + -
170A PRO* 3.5 26.9 - - + -
172A LYS* 1.3 80.0 - - - +
174A TYR* 1.3 61.0 + - - +
175A ILE* 3.5 18.1 + - + +
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Residues in contact with TYR 174 (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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16A ILE* 3.6 35.2 - - + -
21A LEU* 4.4 7.6 - - + -
25A TYR* 3.9 19.5 - + - -
26A VAL* 3.9 42.2 - - + -
29A ASP* 2.7 30.5 + - + +
30A LEU* 3.9 20.5 + - + +
135A VAL* 4.3 5.6 - - + -
136A GLN 2.6 15.9 + - - +
137A VAL* 3.5 21.3 - - + +
138A PRO* 3.5 18.2 - - - +
172A LYS* 3.8 28.6 - - + +
173A ILE* 1.3 68.5 - - - +
175A ILE* 1.3 61.8 + - - +
176A ASP* 3.4 5.7 + - + +
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Residues in contact with ILE 175 (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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15A ILE* 4.1 20.2 - - + -
16A ILE 2.8 8.8 + - - -
17A ALA* 3.5 24.0 - - + -
18A ASP 3.1 22.3 + - - -
21A LEU* 4.1 1.8 - - - -
138A PRO* 3.7 20.4 - - + -
144A MET* 3.4 43.3 - - + +
149A ILE* 5.2 2.0 - - + -
173A ILE* 3.9 16.2 - - + +
174A TYR* 1.3 69.8 - - - +
176A ASP* 1.3 56.2 + - - +
177A LEU* 3.2 23.3 + - + +
243A ILE* 5.6 1.1 - - + -
244A LEU* 4.5 7.0 - - + -
247A ALA* 5.6 2.9 - - + -
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Residues in contact with ASP 176 (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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18A ASP 3.3 4.5 - - - -
20A GLY* 2.9 13.2 + - - -
21A LEU* 3.1 17.3 + - + +
22A TRP* 2.9 36.8 + - + +
23A ARG* 5.3 1.2 - - - +
26A VAL* 6.3 0.4 - - + -
137A VAL* 5.4 1.3 - - + -
138A PRO 4.9 1.0 + - - -
144A MET* 3.3 8.0 - - - +
174A TYR* 3.4 6.6 + - + +
175A ILE* 1.3 71.0 - - - +
177A LEU* 1.3 55.8 + - - +
178A GLU* 2.8 41.5 + - - +
179A PHE* 3.1 43.1 + - + -
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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