Contacts of the strand formed by residues 178 - 182 (chain B) in PDB entry 3L82
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 178 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175B ASN* 6.2 2.9 - - - -
176B GLU* 3.6 15.7 - - + +
177B PRO* 1.3 73.1 - - - +
179B PHE* 1.3 70.6 + - - +
212B ARG* 3.6 37.6 + - - +
214B ILE* 3.4 26.5 - - - +
219B SER* 3.4 15.6 + - - +
232B ASN* 2.9 40.9 - - + +
234B LEU* 3.4 21.2 - - + +
285B VAL* 4.2 22.7 - - - +
286B VAL* 2.9 25.1 - - + +
287B ASP* 2.9 23.3 + - - +
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Residues in contact with PHE 179 (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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177B PRO* 4.0 12.6 - - + -
178B ARG* 1.3 83.8 - - - +
180B ALA* 1.3 59.7 + - - +
231B PHE* 4.0 32.3 - + + -
232B ASN 2.9 15.8 + - - +
233B ILE* 3.5 6.9 - - + +
234B LEU* 2.8 30.3 + - - +
286B VAL* 3.1 9.0 - - - -
287B ASP 4.6 0.9 - - - -
288B GLY* 3.6 25.4 - - - +
290B ILE* 3.9 29.6 - - + -
374B ILE* 5.2 2.7 - - + -
377B ILE* 3.8 39.0 - - + -
378B LEU* 4.0 17.0 - - + -
381B VAL* 4.1 15.0 - - + -
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Residues in contact with ALA 180 (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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179B PHE* 1.3 72.8 - - - +
181B MSE 1.3 59.2 + - - +
182B PHE* 4.3 3.4 - - + -
234B LEU* 3.6 8.1 - - - +
236B LEU* 4.6 4.7 - - + -
282B VAL* 4.1 23.1 - - + -
286B VAL* 3.3 6.6 - - + +
288B GLY 3.1 6.9 + - - -
289B PHE* 3.6 13.3 - - + -
290B ILE* 2.8 28.2 + - - +
313B MSE 4.3 21.8 - - + -
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Residues in contact with MSE 181 (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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180B ALA* 1.3 73.9 - - - +
182B PHE* 1.3 64.5 + - - +
186B LEU* 4.0 12.3 - - + +
193B LEU* 5.2 3.4 - - + -
194B VAL* 4.3 16.6 - - + -
197B LEU* 4.3 20.9 - - + -
233B ILE* 3.9 26.0 - - + -
234B LEU 3.0 9.5 + - - +
235B ILE* 3.7 32.4 - - + -
236B LEU* 3.1 27.2 + - - +
290B ILE* 3.3 25.4 - - + +
292B VAL* 3.8 26.2 - - + -
328B LEU* 4.9 6.3 - - - -
370B PHE* 5.2 4.5 - - - -
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Residues in contact with PHE 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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180B ALA* 4.3 3.4 - - + -
181B MSE 1.3 80.6 - - - +
183B GLY* 1.3 61.8 + - - +
186B LEU* 3.6 13.5 - - - -
236B LEU* 3.9 20.2 - - + +
238B SER 6.2 0.2 - - - +
239B THR 4.9 9.0 - - - +
289B PHE* 4.3 16.8 - + + -
290B ILE 3.1 18.1 + - - +
291B TYR* 3.4 35.5 - + + -
292B VAL* 2.9 23.6 + - - +
309B HIS* 4.9 5.8 - - + -
310B ILE* 4.6 17.9 - - + -
313B MSE 3.8 52.5 - - + -
314B THR* 6.5 0.4 - - - -
325B LEU* 5.6 1.1 - - + -
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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