Contacts of the strand formed by residues 204 - 208 (chain D) in PDB entry 1O97
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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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258C ILE* 3.6 41.5 - - + -
261C PHE* 3.9 24.0 - + + -
202D VAL* 3.8 6.1 - - + +
203D ASP* 1.3 82.0 - - + +
205D ILE* 1.3 75.9 + - - +
206D MET* 4.5 3.6 - - + -
228D ALA* 3.6 24.5 - - + -
229D GLY 3.8 21.7 - - - +
230D ALA* 3.7 18.6 - - + -
231D THR* 3.0 25.4 + - - -
262D LEU* 3.6 31.4 - - + -
264D VAL* 4.1 15.9 - - + -
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Residues in contact with ILE 205 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200D THR* 4.0 9.0 - - - +
202D VAL* 5.0 5.2 - - + +
204D PHE* 1.3 82.9 - - - +
206D MET* 1.3 74.2 + - - +
207D SER 4.1 0.4 - - - +
230D ALA* 4.3 0.2 - - - -
231D THR* 3.4 7.9 - - - +
233D CYS* 3.7 32.3 - - + -
257D VAL* 3.5 41.3 - - + -
260D CYS* 3.9 17.3 - - + -
262D LEU 3.0 8.6 + - - +
263D TYR* 3.4 27.1 - - + -
264D VAL* 2.8 29.8 + - - +
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Residues in contact with MET 206 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254C ILE* 5.6 0.7 - - + -
258C ILE* 4.4 14.6 - - + -
204D PHE* 4.5 2.2 - - + -
205D ILE* 1.3 78.2 - - - +
207D SER* 1.3 58.8 + - - +
221D PHE 5.4 0.9 - - - +
224D LEU* 3.9 31.6 - - + -
225D ALA* 3.9 30.7 - - + -
228D ALA* 4.0 16.6 - - + -
230D ALA* 3.9 14.8 - - + +
231D THR 3.0 8.9 + - - +
232D LEU* 3.4 11.0 - - + +
233D CYS 3.1 20.4 + - - -
264D VAL* 3.5 25.6 - - + -
266D MET* 3.9 12.6 - - + -
314D LEU* 4.3 14.4 - - + -
318D LEU* 5.9 0.2 - - + -
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Residues in contact with SER 207 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205D ILE* 4.1 2.4 - - - +
206D MET* 1.3 75.0 - - - +
208D ILE* 1.3 62.6 + - - +
233D CYS* 3.1 7.5 - - - +
234D CYS* 3.3 25.6 + - - -
263D TYR* 2.9 43.1 + - - -
264D VAL 2.8 9.7 + - - +
266D MET* 2.9 31.1 + - - +
268D ILE* 3.5 11.3 - - - +
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Residues in contact with ILE 208 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207D SER* 1.3 79.2 - - - +
209D GLY* 1.3 59.5 + - - +
212D ILE* 3.8 35.7 - - + -
218D VAL* 4.3 17.0 - - + -
221D PHE* 3.6 39.0 - - + -
232D LEU* 4.3 11.2 - - + -
233D CYS 2.9 18.0 + - - +
234D CYS* 3.1 10.8 - - + +
235D SER 3.0 22.2 + - - -
238D ILE* 3.6 9.3 - - + +
244D LEU* 3.7 24.7 - - + -
266D MET* 3.5 9.6 - - + +
268D ILE* 3.8 3.6 - - - -
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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