Contacts of the strand formed by residues 180 - 183 (chain B) in PDB entry 1EX0
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 THR 180 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52B LEU* 3.8 12.8 - - - +
74B LEU* 3.5 28.4 - - + +
76B VAL* 4.2 11.0 - - + -
82B PHE* 5.0 3.1 - - + -
103B TYR* 4.0 27.3 + - + -
156B LYS* 4.4 0.4 - - - -
157B PHE* 2.8 39.8 + - - +
159B MET* 4.7 0.3 - - - +
178B THR 2.7 16.9 + - - -
179B ASP* 1.3 70.7 + - - +
181B TYR* 1.3 75.8 + - - +
182B ILE* 3.6 7.6 + - + -
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Residues in contact with TYR 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B ASN* 3.5 19.9 + - - -
73B LYS* 3.8 23.6 - - + +
74B LEU 3.0 17.6 + - - -
75B ILE* 3.6 24.2 - - + -
76B VAL* 3.0 31.3 + - - +
155B GLY 3.4 7.0 - - - +
156B LYS* 3.3 45.0 + - + +
179B ASP 5.1 0.2 - - - -
180B THR* 1.3 75.3 - - - +
182B ILE* 1.3 60.8 + - - +
183B LEU* 4.4 4.9 - - + -
235B LEU* 3.3 26.2 - - + -
236B ASP* 2.6 38.0 + - - -
239B LEU* 3.8 14.6 - - + -
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Residues in contact with ILE 182 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B VAL* 3.3 16.4 - - + +
77B ARG 4.6 0.9 - - - -
78B ARG* 3.9 33.4 - - + +
82B PHE* 6.0 1.8 - - + -
103B TYR* 5.0 5.4 - - + -
130B TRP* 3.8 32.5 - - + -
148B SER* 4.7 4.3 - - - +
152B CYS* 4.1 9.9 - - + -
153B ILE 4.3 1.6 - - - +
154B VAL* 3.3 7.8 - - - +
155B GLY 2.8 31.7 + - - -
157B PHE* 3.7 35.9 - - + -
180B THR* 3.6 9.6 + - + +
181B TYR* 1.3 78.8 - - - +
183B LEU* 1.3 61.3 + - - +
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Residues in contact with LEU 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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66B THR* 4.6 2.5 - - + -
69B TYR* 3.4 33.4 - - + +
75B ILE* 3.6 29.6 - - + -
76B VAL 2.9 12.3 + - - +
77B ARG* 3.4 9.8 - - + +
78B ARG* 2.9 30.7 + - - +
154B VAL* 3.9 18.6 - - + -
155B GLY* 5.1 2.7 - - - +
181B TYR* 4.4 11.0 - - + -
182B ILE* 1.3 81.2 - - - +
184B PHE* 1.3 68.3 + - - +
235B LEU* 4.1 22.0 - - + -
239B LEU* 5.8 0.7 - - + -
327B CYS 3.8 6.1 - - - +
328B LEU* 3.4 11.2 - - + +
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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