Contacts of the strand formed by residues 210 - 217 (chain C) in PDB entry 3OF6
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 210 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163C TRP 4.8 1.6 + - - -
164C VAL* 3.3 10.6 - - - +
165C ASN* 2.8 43.8 + - - +
166C GLY 5.8 0.6 + - - -
209C ASN* 1.3 72.6 - - - +
211C PHE* 1.3 64.4 + - - +
212C ARG* 3.7 18.8 - - + +
241C GLU* 3.0 52.7 + - + +
242C ALA 4.2 2.2 - - - -
243C TRP* 3.3 51.8 - + + -
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Residues in contact with PHE 211 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130C VAL* 5.4 1.4 - - - +
146C LEU* 3.6 27.1 - - + -
162C TRP* 4.9 6.3 - - + -
163C TRP 4.0 2.5 - - - -
164C VAL* 4.0 19.5 - - + -
197C LEU* 5.2 5.6 - - + -
199C VAL* 4.9 10.3 - - + -
203C PHE* 3.3 33.0 - + - -
204C TRP* 3.3 41.5 - + - -
209C ASN* 3.5 33.7 - - + -
210C HIS* 1.3 72.7 - - - +
212C ARG* 1.3 58.5 + - - +
240C ALA 4.1 0.5 - - - +
241C GLU* 3.3 1.6 - - - -
242C ALA* 2.7 52.0 + - - +
244C GLY* 3.7 7.9 - - - -
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Residues in contact with ARG 212 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162C TRP* 3.7 8.3 - - - -
163C TRP* 2.9 80.2 + - - +
166C GLY* 6.2 1.0 - - - -
210C HIS* 3.7 16.1 - - + +
211C PHE* 1.3 75.0 - - - +
213C CYS* 1.3 62.5 + - - +
214C GLN* 3.5 24.2 + - - +
239C SER* 3.2 33.0 + - - -
240C ALA 3.5 13.2 - - - +
241C GLU* 3.9 20.0 - - + -
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Residues in contact with CYS 213 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128C VAL* 3.7 3.2 - - + +
130C VAL* 3.6 13.4 - - + +
148C CYS* 2.0 55.6 - - + -
160C LEU* 3.8 26.2 - - - -
161C SER 4.1 1.8 - - - -
162C TRP* 3.9 13.4 - - + -
212C ARG* 1.3 70.8 - - - +
214C GLN* 1.3 62.2 + - - +
215C VAL* 4.5 0.4 - - - -
239C SER* 3.0 7.5 - - - -
240C ALA 2.9 29.9 + - - -
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Residues in contact with GLN 214 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159C GLU 5.7 0.2 + - - -
160C LEU* 3.2 5.5 - - - +
161C SER* 2.8 54.8 + - - +
163C TRP* 2.8 38.9 - - + +
212C ARG* 3.5 22.7 + - - +
213C CYS* 1.3 72.1 - - - +
215C VAL* 1.3 69.8 + - - +
216C GLN* 4.2 2.9 - - - +
237C ILE* 3.4 32.4 - - + +
239C SER* 3.2 14.4 - - - +
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Residues in contact with VAL 215 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126C PRO* 3.9 22.4 - - + -
128C VAL* 3.5 21.1 - - + -
148C CYS* 4.8 0.2 - - - -
150C ALA* 4.4 9.0 - - + -
158C VAL* 3.8 27.8 - - + -
159C GLU 3.5 5.2 - - - +
160C LEU* 3.9 24.7 - - + +
193C LEU* 6.0 0.7 - - + -
213C CYS* 4.5 5.2 - - - -
214C GLN* 1.3 82.0 - - - +
216C GLN* 1.3 59.8 + - - +
217C PHE* 3.3 3.3 + - - +
237C ILE* 3.3 7.0 - - - -
238C VAL 2.9 38.6 + - - +
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Residues in contact with GLN 216 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158C VAL* 3.1 5.8 - - - -
159C GLU* 2.8 51.0 + - + +
214C GLN* 4.2 4.3 - - + +
215C VAL* 1.3 68.9 - - - +
217C PHE* 1.3 84.1 + - - +
218C TYR* 3.3 33.7 - - + +
235C THR* 3.4 18.2 - - - +
236C GLN 3.2 8.7 + - - +
237C ILE* 3.0 31.4 - - + +
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Residues in contact with PHE 217 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123C VAL* 3.8 11.7 - - + -
124C PHE 3.2 27.4 - - - -
125C PRO* 4.1 8.5 - - + -
126C PRO* 3.4 36.1 - - + -
153C PHE* 4.4 0.9 - - + -
154C TYR 3.7 17.0 - - - -
155C PRO 3.9 14.4 - - - -
157C HIS 3.5 9.6 - - - -
158C VAL* 3.8 9.4 - - + -
215C VAL 3.3 2.9 + - - +
216C GLN* 1.3 83.1 + - - +
218C TYR* 1.3 69.9 + - - +
219C GLY* 3.5 22.7 - - - -
233C PRO 4.4 4.7 - - - -
234C VAL 3.4 19.7 - - - -
235C THR* 3.1 0.9 - - - +
236C GLN* 2.7 40.7 + - + +
237C ILE* 5.3 0.2 - - - -
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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