Contacts of the strand formed by residues 181 - 185 (chain B) in PDB entry 1CL2
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 ILE 181 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97B PHE* 3.2 47.3 - - + -
149B LYS* 3.0 35.7 + - + +
150B ILE* 3.4 9.8 - - + +
151B VAL 3.2 19.4 + - - -
179B ASP 4.5 1.1 - - - +
180B ALA* 1.3 75.5 - - - +
182B ILE* 1.3 61.1 + - - +
183B MET* 3.7 28.9 + - + -
202B ASP* 3.5 9.4 - - + -
203B VAL* 4.6 1.3 - - + -
228B ARG* 4.1 12.8 - - - +
229B CYS* 4.1 22.9 - - - -
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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
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151B VAL* 3.4 23.1 - - + +
153B LEU* 3.9 27.4 - - + -
169B ILE* 6.1 0.9 - - + -
170B VAL* 4.2 28.7 - - + -
173B VAL* 4.2 21.8 - - + -
174B ARG* 3.8 33.4 - - - +
180B ALA* 4.8 0.9 - - + +
181B ILE* 1.3 72.5 - - - +
183B MET* 1.3 62.1 + - - +
200B GLY 4.4 1.1 - - - +
201B ILE* 3.4 14.7 - - + +
202B ASP* 2.8 46.4 + - - +
203B VAL 3.4 2.1 + - - -
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Residues in contact with MET 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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93B SER* 3.4 29.6 - - - +
94B ILE* 4.2 15.3 - - - -
97B PHE* 3.4 35.4 - - + -
150B ILE* 3.9 16.8 - - + -
151B VAL 2.9 8.6 + - - +
152B PHE* 3.9 17.3 - - + -
153B LEU* 2.8 28.6 + - - +
181B ILE* 3.8 18.2 - - + +
182B ILE* 1.3 79.3 - - - +
184B ILE* 1.3 62.9 + - - +
201B ILE* 4.1 1.8 - - - -
203B VAL* 3.5 19.5 - - + +
205B ILE* 4.2 9.9 - - + -
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Residues in contact with ILE 184 (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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152B PHE* 4.9 2.2 - - - -
153B LEU* 3.3 25.6 - - + +
154B GLU* 4.2 0.4 - - - +
155B SER* 4.2 23.3 - - - +
166B VAL* 4.7 3.8 - - + -
183B MET* 1.3 76.9 - - - +
185B ASP* 1.3 69.8 + - - +
186B ASN* 3.3 8.9 + - + +
194B PHE* 3.9 25.8 - - + -
196B ALA* 3.6 28.5 - - + -
201B ILE* 3.7 21.3 - - + -
203B VAL 3.1 11.4 + - - +
204B SER* 4.2 3.1 - - - -
205B ILE* 2.8 31.8 + - - +
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Residues in contact with ASP 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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90B VAL* 4.0 14.8 - - + +
111B TYR* 4.8 1.6 - - - +
114B SER* 4.8 1.2 + - - -
152B PHE* 4.1 13.3 - - + -
153B LEU 2.9 10.3 + - - +
154B GLU* 3.8 34.3 - - + +
155B SER 4.1 6.4 + - - +
184B ILE* 1.3 76.8 - - - +
186B ASN* 1.3 56.2 + - - +
187B THR* 2.8 31.5 + - - -
188B TRP 5.3 0.5 + - - -
205B ILE* 3.5 10.2 - - - +
207B ALA 5.7 0.2 - - - -
500B PPG 2.8 37.9 + - - +
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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