Contacts of the strand formed by residues 204 - 208 (chain B) in PDB entry 4OE4
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 PHE 204 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106B VAL* 3.7 23.6 - - + +
109B ALA* 4.6 11.4 - - + -
110B LYS* 5.6 4.3 - - + +
113B LYS* 5.2 1.3 - - - +
203B GLY* 1.3 73.5 - - - -
205B VAL* 1.3 64.3 + - - +
206B TYR* 4.5 0.9 - - + -
230B THR* 3.9 20.9 - - - +
232B VAL* 3.6 34.5 - - + -
274B VAL* 3.6 31.0 - - + -
277B ASP* 3.6 14.8 - - + -
279B ASP* 2.9 32.3 + - + +
280B PHE* 3.4 34.5 - + - -
281B GLY 2.8 27.2 + - - -
282B ALA 3.2 4.8 + - - +
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Residues in contact with VAL 205 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201B LEU* 4.6 3.6 - - + -
203B GLY 4.8 0.4 - - - +
204B PHE* 1.3 77.1 - - - +
206B TYR* 1.3 71.4 + - - +
207B ALA* 4.5 1.1 - - - +
224B PRO* 3.9 17.0 - - + -
229B ASN* 3.8 33.2 - - + +
230B THR 3.1 10.1 + - - +
231B VAL* 3.2 12.9 - - + +
232B VAL* 2.9 26.5 + - - +
282B ALA* 3.5 17.0 - - + +
284B HIS* 4.1 10.5 - - + -
552B PHE* 4.1 25.6 - - + -
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Residues in contact with TYR 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204B PHE 4.0 0.8 + - - -
205B VAL* 1.3 72.3 - - - +
207B ALA* 1.3 60.8 + - - +
208B VAL* 3.4 28.2 - - + +
232B VAL* 3.3 25.1 - - + -
234B LYS* 4.0 22.0 - - + +
263B ILE* 5.3 1.1 - - + -
270B VAL* 3.8 8.7 - - + +
271B THR* 2.8 44.4 + - + -
274B VAL* 3.6 37.2 - - + -
275B LEU* 4.5 5.6 - - + -
280B PHE* 3.6 24.2 - + + -
282B ALA 2.8 8.1 + - - -
283B LEU* 3.6 15.9 - - + +
284B HIS 2.8 26.7 + - - -
295B LEU* 4.9 2.5 - - + -
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Residues in contact with ALA 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205B VAL* 3.9 1.5 + - + -
206B TYR* 1.3 73.1 - - - +
208B VAL* 1.3 61.9 + - - +
209B SER 4.0 0.7 - - - -
220B LEU* 4.0 19.1 - - + +
221B ILE* 3.9 18.8 - - + -
231B VAL* 3.8 21.8 - - + -
232B VAL 2.8 10.5 + - - +
233B TRP* 3.4 6.3 - - + -
234B LYS 3.0 26.7 + - - -
284B HIS* 3.4 9.4 - - + +
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Residues in contact with VAL 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B TYR* 3.4 46.0 + - + +
207B ALA* 1.3 72.3 - - - +
209B SER* 1.3 59.9 + - - +
220B LEU* 3.5 4.0 - - - +
234B LYS* 3.9 10.5 - - - -
271B THR* 5.0 1.8 - - - +
283B LEU* 4.1 9.0 - - + -
284B HIS 2.9 9.7 + - - +
285B PHE* 3.5 19.6 - - + -
286B THR 3.3 25.5 + - - +
295B LEU* 4.7 4.3 - - + -
1000B NAD 3.3 40.2 - - - +
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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
------------------------------------------------------------
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