Contacts of the strand formed by residues 191 - 195 (chain B) in PDB entry 3CFV
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 HIS 191 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184B TRP* 3.7 2.4 - - - -
185B ASN* 3.0 36.0 + - + -
188B LEU* 3.1 51.3 + - + +
189B SER 3.7 9.2 + - - -
190B GLY* 1.3 76.8 - - - +
192B LEU* 1.3 58.5 - - - +
203B LEU* 4.5 11.0 - - + -
204B TRP 3.3 13.2 - - - +
205B ASP* 3.3 31.0 + - + +
207B ASN* 5.2 0.9 - - - -
219B LYS* 4.5 14.2 - - - -
234B TRP* 3.3 18.9 + + + -
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Residues in contact with LEU 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B ALA* 3.6 22.4 - - + -
148B VAL* 4.3 6.3 - - + -
150B VAL* 4.8 0.9 - - + -
172B LEU* 3.8 24.7 - - + -
182B LEU* 3.5 28.0 - - + -
183B SER 3.4 17.9 - - - +
184B TRP* 3.5 44.4 - - + +
190B GLY 3.5 3.0 + - - +
191B HIS* 1.3 74.5 - - - +
193B LEU* 1.3 63.6 + - - +
203B LEU* 3.5 6.9 - - - +
204B TRP* 3.1 42.0 + - + +
206B ILE* 5.3 1.3 - - + -
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Residues in contact with LEU 193 (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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182B LEU* 3.3 11.5 - - - +
183B SER* 2.8 33.7 + - - +
192B LEU* 1.3 74.3 - - - +
194B SER* 1.3 60.0 + - - +
201B VAL* 3.9 16.8 - - + -
202B CYS 3.5 14.1 - - - +
203B LEU* 3.9 20.9 - - + -
222B PHE* 4.7 0.2 - - + -
232B VAL* 3.8 18.8 - - + -
234B TRP* 3.3 40.6 - - + +
242B PHE* 3.4 45.3 - - + -
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Residues in contact with SER 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B LYS* 2.6 39.1 + - - +
148B VAL* 3.6 5.6 - - - +
175B HIS* 3.0 9.3 + - - -
181B GLY 3.3 6.3 - - - -
182B LEU* 4.5 3.6 - - - -
193B LEU* 1.3 77.2 - - - +
195B ALA* 1.3 57.9 + - - +
201B VAL* 3.2 7.6 - - - +
202B CYS 3.0 31.6 + - - -
204B TRP* 3.3 25.6 - - - -
232B VAL* 4.1 4.0 - - - -
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Residues in contact with ALA 195 (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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142B LYS* 2.8 25.5 + - - -
179B GLY* 3.4 5.7 - - - -
180B TYR 3.8 1.7 + - - -
181B GLY* 3.0 27.5 + - - +
194B SER* 1.3 73.0 - - - +
196B SER* 1.3 62.1 + - - +
200B THR 3.9 5.4 - - - -
201B VAL* 4.2 4.0 - - + -
229B VAL* 3.5 33.9 - - + +
231B ASP 4.2 10.8 - - - +
232B VAL* 4.0 1.5 - - + +
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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