Contacts of the strand formed by residues 182 - 187 (chain B) in PDB entry 5UNG
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 182 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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117B CYS* 3.9 20.0 - - - +
118B LYS* 3.0 34.2 + - - +
121B GLY* 5.1 0.2 - - - -
178B THR* 3.1 33.0 + - + +
181B PHE* 1.4 73.8 - - - +
183B ASP* 1.3 57.0 + - - +
195B CYS* 2.8 38.6 + - - -
196B ILE* 3.4 9.4 - - - +
197B MET* 3.5 28.1 - - - +
215B LYS* 5.8 0.2 - - - +
1201B 8ES 3.1 79.5 + - + +
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Residues in contact with ASP 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114B PRO* 3.5 23.2 - - - +
117B CYS* 3.5 12.4 - - - -
118B LYS* 4.3 11.6 - - - +
181B PHE 3.4 1.5 + - - +
182B ARG* 1.3 74.9 - - - +
184B VAL* 1.3 71.1 + - - +
185B ARG* 3.3 32.2 + - - +
196B ILE* 3.0 29.9 + - - +
198B ALA* 4.2 15.7 - - + -
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Residues in contact with VAL 184 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B TRP* 3.6 37.5 - - + +
113B GLY* 3.7 13.7 - - - +
114B PRO* 3.8 19.4 - - + +
117B CYS* 3.8 7.2 - - + -
183B ASP* 1.3 84.8 + - - +
185B ARG* 1.3 64.2 + - - +
186B THR* 6.1 0.2 - - + -
193B ASN* 3.9 36.6 - - + +
194B ALA 3.5 9.4 - - - +
195B CYS* 4.1 4.0 - - - +
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Residues in contact with ARG 185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183B ASP* 3.3 28.3 + - - +
184B VAL* 1.3 75.7 + - - +
186B THR* 1.3 66.6 + - - +
187B ILE* 3.5 7.3 + - - +
193B ASN* 4.7 0.9 - - - -
194B ALA 3.0 27.9 + - - +
196B ILE* 3.8 29.2 - - + -
198B ALA* 3.5 27.7 + - + +
199B PHE 5.3 3.0 + - - -
201B PRO* 5.7 5.3 - - - +
1099B ASN* 5.4 14.1 - - - +
1103B GLN* 5.3 5.8 - - - +
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Residues in contact with THR 186 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185B ARG* 1.3 72.4 - - - +
187B ILE* 1.3 63.5 + - - +
188B GLU* 3.5 4.9 + - - +
192B VAL 3.6 5.4 - - - -
193B ASN* 3.5 34.3 - - - +
1096B THR* 5.0 12.8 - - - +
1099B ASN* 5.5 3.8 - - - +
1103B GLN* 4.2 9.9 + - - -
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Residues in contact with ILE 187 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185B ARG 3.9 10.3 - - - +
186B THR* 1.3 69.9 - - - +
188B GLU* 1.3 59.1 + - - +
189B TYR* 3.6 24.5 - - + +
190B LEU* 3.8 25.6 - - + -
191B GLY* 2.9 30.8 + - - -
192B VAL* 2.8 29.3 + - + +
194B ALA* 3.9 24.0 - - + -
196B ILE* 4.6 14.6 - - + -
1103B GLN* 3.4 36.3 - - + +
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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