Contacts of the strand formed by residues 178 - 182 (chain B) in PDB entry 6UPQ
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 178 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150B CYS* 3.5 9.4 - - + +
152B TYR* 4.2 12.1 - - + -
169B MET* 3.5 55.4 - - + +
172B LEU* 3.9 9.6 - - + -
173B ASP* 3.5 21.8 - - + +
176B VAL* 3.2 24.7 + - + +
177B ASN* 1.3 69.7 - - - +
179B ILE* 1.3 62.6 + - - +
180B PRO* 3.6 17.6 - - + +
209B VAL* 4.7 2.2 - - + -
210B GLN 4.2 10.2 + - - +
211B ILE* 3.6 5.7 - - + +
212B TYR* 3.0 29.6 + - - +
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Residues in contact with ILE 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B ALA* 4.5 5.2 - - + -
150B CYS 2.7 10.3 + - - +
151B LEU* 3.5 24.1 - - + -
152B TYR 3.1 19.2 + - - -
177B ASN 4.2 6.3 - - - +
178B ILE* 1.3 77.0 - - - +
180B PRO* 1.3 64.0 - - + +
181B ILE* 3.5 6.1 + - + +
212B TYR* 4.3 14.4 - - + +
214B PHE* 3.8 26.9 - - + -
234B PHE* 4.2 30.7 - - + -
273B LEU* 4.3 2.5 - - + -
277B LEU* 3.9 30.1 - - + -
285B LEU* 4.5 6.7 - - + -
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Residues in contact with PRO 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152B TYR* 3.6 10.1 - - + +
154B ILE* 4.0 20.0 - - + -
169B MET* 4.5 11.4 - - - -
178B ILE* 3.6 14.7 - - + +
179B ILE* 1.3 87.5 - - + +
181B ILE* 1.3 64.6 + - - +
201B MET* 5.3 0.9 - - - -
204B LEU* 4.1 19.1 - - + -
211B ILE* 4.1 27.1 - - + -
232B LEU* 6.4 0.2 - - + -
233B PRO* 3.2 24.0 - - + +
234B PHE* 3.8 5.5 + - - -
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Residues in contact with ILE 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B LEU* 3.6 31.6 - - + -
151B LEU* 4.2 12.6 - - + -
152B TYR 3.0 16.8 + - - +
153B PHE* 3.8 31.0 - - + -
154B ILE* 2.8 36.2 + - - +
179B ILE* 3.8 19.3 - - + +
180B PRO* 1.3 80.7 - - - +
182B ILE* 1.3 57.9 + - - +
233B PRO* 4.3 0.7 - - - -
234B PHE* 3.3 27.1 - - + +
236B VAL* 4.0 11.7 - - + -
273B LEU* 4.4 6.5 - - + -
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Residues in contact with ILE 182 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B ILE* 3.6 7.4 - - + +
156B PRO* 4.1 3.8 - - + -
181B ILE* 1.3 71.2 - - - +
183B ALA* 1.3 71.3 + - - +
185B ALA* 3.7 6.5 - - + +
188B ILE* 3.5 26.2 - - + -
193B LEU* 4.4 2.7 - - + -
196B PHE* 3.9 18.2 - - + -
197B LYS* 3.8 28.9 - - + -
200B ILE* 3.7 30.1 - - + -
233B PRO* 3.9 14.4 - - + +
234B PHE 2.8 12.2 + - - +
235B ALA* 4.1 10.1 - - + -
236B VAL* 3.1 27.1 + - - +
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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