Contacts of the strand formed by residues 204 - 210 (chain L) in PDB entry 6R90
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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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160L THR* 3.9 9.0 - - - +
175L SER* 4.2 9.2 - - - -
176L SER 3.7 12.4 + - - +
179L GLY* 3.3 26.5 - - - -
180L THR* 3.6 9.4 - - - -
181L THR* 3.3 44.0 - - + -
195L ALA* 3.8 11.9 - - + -
196L SER* 3.4 36.1 - - - -
197L SER* 3.8 4.7 - - - -
203L TRP* 1.3 94.5 - - - +
205L CYS* 1.3 62.2 + - - +
218L THR* 4.4 4.3 - - + +
219L GLY 3.6 7.6 - - - +
220L ASP* 2.9 32.5 - - - -
226L ILE* 4.2 9.4 - - + -
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Residues in contact with CYS 205 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160L THR* 3.2 36.2 + - + +
175L SER* 4.0 2.1 + - - -
203L TRP* 4.0 9.9 - - - -
204L PHE* 1.3 79.2 - - - +
206L SER* 1.3 58.7 + - - +
219L GLY 2.6 9.7 + - - -
220L ASP 3.3 25.6 - - - +
221L ASN* 3.4 16.8 - - - -
244L LYS* 3.6 20.0 - - + -
245L VAL 3.5 19.1 - - - +
246L THR* 4.2 5.9 - - - +
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Residues in contact with SER 206 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161L GLY* 5.6 1.1 - - - -
175L SER* 4.2 3.9 - - - -
205L CYS* 1.3 75.0 - - - +
207L LEU* 1.3 58.9 + - - +
218L THR* 2.4 31.4 + - - -
219L GLY* 2.9 22.2 + - - -
245L VAL 3.1 10.3 + - - -
246L THR 2.7 36.8 + - - -
247L HIS* 3.1 5.3 + - - -
248L VAL* 3.8 19.3 - - - -
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Residues in contact with LEU 207 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161L GLY* 3.8 16.7 - - - +
162L LEU* 4.8 4.9 + - - +
163L LYS* 4.7 12.4 + - + +
173L TYR* 3.7 22.2 - - + +
174L ALA* 3.2 50.3 - - - +
175L SER* 3.6 10.1 - - - +
181L THR* 5.7 4.0 - - + -
206L SER* 1.3 79.0 - - - +
208L ASP* 1.3 75.2 + - - +
209L VAL* 4.7 3.6 - - + -
216L VAL* 5.5 2.0 - - + -
217L VAL 3.3 21.5 - - - +
218L THR* 4.0 10.1 - - - +
247L HIS* 5.3 5.5 + - - -
248L VAL* 4.1 7.7 - - - +
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Residues in contact with ASP 208 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163L LYS* 2.6 43.2 + - - +
207L LEU* 1.3 76.7 - - - +
209L VAL* 1.3 95.9 + - - +
217L VAL* 2.9 45.3 + - + +
248L VAL 3.9 18.7 - - - +
249L ALA* 4.7 11.6 - - - +
250L LEU* 3.8 10.6 + - + +
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Residues in contact with VAL 209 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163L LYS* 5.3 9.0 - - + +
164L PHE 5.3 5.4 - - - +
165L ASN* 5.8 0.4 - - - +
166L PRO* 4.9 15.2 - - + +
173L TYR* 3.9 39.3 - - + +
207L LEU* 4.7 3.4 - - + -
208L ASP* 1.3 101.6 + - - +
210L SER* 1.3 70.9 + - - +
215L MET 3.3 13.9 - - - +
216L VAL* 3.5 23.8 - - + -
250L LEU* 3.4 7.3 - - - +
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Residues in contact with SER 210 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166L PRO* 5.6 1.1 - - - -
209L VAL* 1.3 78.9 - - - +
211L ALA* 1.3 61.7 + - - +
212L SER* 3.7 5.5 + - - -
213L SER* 3.6 24.3 + - - -
214L ARG* 3.1 3.9 + - - -
215L MET* 2.9 35.5 + - - +
250L LEU* 3.4 28.0 - - - +
251L ASN 5.2 4.7 + - - -
255L ASP* 4.7 4.2 + - - +
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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
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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