Contacts of the helix formed by residues 208 - 215 (chain C) in PDB entry 4OGB
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 SER 208 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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204C HIS* 5.5 0.7 - - - -
207C VAL* 1.3 78.1 - - - +
209C ASN* 1.3 65.6 + - - +
210C GLN* 3.5 8.9 + - - +
211C PHE* 3.2 23.2 + - - +
212C LEU* 3.2 13.5 + - - +
229C LEU* 4.1 2.9 - - - -
343C GLN* 3.0 29.2 + - - -
355C SER* 5.0 1.0 + - - -
502C 2SR 6.3 3.1 - - - -
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Residues in contact with ASN 209 (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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208C SER* 1.3 72.7 - - - +
210C GLN* 1.3 57.8 + - - +
212C LEU* 3.2 7.6 + - - +
213C ILE* 2.9 41.2 + - + +
227C SER* 4.1 4.6 - - - +
228C VAL* 3.4 15.5 - - + +
229C LEU* 2.6 42.7 + - - +
230C GLU* 3.0 30.3 + - - -
272C ASP* 4.2 9.9 + - - -
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Residues in contact with GLN 210 (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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208C SER* 3.2 8.5 + - - +
209C ASN* 1.3 75.5 - - - +
211C PHE* 1.3 61.2 + - - +
213C ILE* 3.8 26.9 - - - +
214C ASN* 2.8 69.2 + - - +
355C SER* 5.9 3.1 - - - +
258D GLN* 4.5 2.8 - - - +
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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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514A EDO 4.1 10.1 - - - -
207C VAL* 3.5 28.3 - - + -
208C SER* 3.2 21.9 + - - +
210C GLN* 1.3 77.6 - - - +
212C LEU* 1.3 65.1 + - + +
214C ASN* 3.4 5.1 + - - +
215C THR* 3.1 43.6 + - + +
343C GLN* 3.7 13.9 - - + +
346C ARG* 4.0 38.1 - - + -
347C GLU* 3.7 36.3 - - + -
350C ARG* 4.0 22.4 - - - -
352C MET* 4.0 16.4 - - + -
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Residues in contact with LEU 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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514A EDO 4.1 21.8 - - - +
205C PRO* 4.4 9.0 - - + -
207C VAL* 3.9 18.8 - - + +
208C SER 3.2 11.4 + - - +
209C ASN* 3.2 8.8 + - - +
211C PHE* 1.3 75.4 - - + +
213C ILE* 1.3 62.2 + - - +
215C THR* 3.4 3.9 + - - -
217C SER* 2.9 47.7 + - - +
219C LEU* 4.4 10.5 - - + -
220C ALA* 3.6 2.7 - - - +
228C VAL* 4.3 17.9 - - + -
229C LEU* 3.6 39.5 - - + -
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Residues in contact with ILE 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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209C ASN* 2.9 29.5 + - + +
210C GLN* 3.6 32.3 - - - +
212C LEU* 1.3 77.0 - - - +
214C ASN* 1.3 65.1 + - - +
216C ASN* 3.1 21.1 + - - +
220C ALA* 3.9 10.0 - - + +
225C ASP* 3.5 59.6 - - + +
228C VAL* 4.3 5.6 - - + -
254D LYS* 4.5 0.9 + - - -
258D GLN* 4.6 7.2 + - - +
261D ARG* 5.6 0.4 - - - +
507D PEG 4.7 9.2 - - - +
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Residues in contact with ASN 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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244A GLU* 3.7 5.2 - - - +
210C GLN* 2.8 50.6 + - - +
211C PHE* 3.9 1.0 - - - +
213C ILE* 1.3 72.3 - - - +
215C THR* 1.3 58.4 + - - +
216C ASN 3.2 0.7 - - - -
347C GLU* 6.0 0.2 + - - -
352C MET* 3.7 27.8 - - + +
254D LYS* 2.8 27.3 + - - -
258D GLN* 2.9 28.7 + - - +
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Residues in contact with THR 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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243A GLU* 3.1 18.7 - - - +
244A GLU* 2.8 28.6 + - + -
514A EDO 4.0 12.2 - - - +
211C PHE* 3.1 34.2 + - + +
212C LEU* 3.4 11.6 + - - -
213C ILE 3.3 0.2 - - - -
214C ASN* 1.3 77.3 - - - +
216C ASN* 1.3 64.0 + - - +
217C SER 3.7 4.0 + - - -
350C ARG* 3.9 23.1 - - - +
352C MET* 4.2 14.8 - - + -
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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