Contacts of the helix formed by residues 199 - 208 (chain C) in PDB entry 6O81
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 GLN 199 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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169C GLY* 4.5 4.4 - - - -
170C PHE* 3.2 59.4 + - + +
194C CYS* 4.7 4.0 - - + +
197C PHE* 2.7 21.2 + - + +
198C CYS* 1.3 70.7 - - - +
200C GLY* 1.3 62.1 + - - +
201C HIS 3.2 3.2 + - - -
202C GLU* 3.3 35.9 + - - +
203C MET 3.9 0.9 + - - -
248C VAL* 5.0 10.2 - - - +
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Residues in contact with GLY 200 (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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169C GLY* 3.9 17.8 + - - -
191C VAL* 3.3 25.1 - - - +
192C ALA 4.8 0.7 - - - -
193C GLU* 4.5 16.1 - - - +
194C CYS 4.7 1.2 - - - +
198C CYS* 3.4 2.0 - - - +
199C GLN* 1.3 76.1 - - - +
201C HIS* 1.3 61.9 + - - +
203C MET* 3.5 2.8 + - - +
204C ALA* 2.9 25.3 + - - +
216C VAL* 5.7 0.2 - - - -
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Residues in contact with HIS 201 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193C GLU* 2.5 36.5 + - + -
198C CYS* 3.9 27.5 + - + +
199C GLN 3.2 0.8 - - - -
200C GLY* 1.3 78.3 - - - +
202C GLU* 1.3 63.1 + - - +
204C ALA* 3.2 6.1 + - - +
205C VAL* 3.0 33.3 + - - +
216C VAL* 4.2 12.2 - - + +
463F LEU* 3.3 20.3 + - - +
464F GLN* 4.5 2.5 - - - -
465F CYS* 4.3 9.6 + - - -
472F ALA* 3.8 20.2 + - + +
473F LEU* 3.5 33.7 + - + +
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Residues in contact with GLU 202 (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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170C PHE* 4.3 20.4 - - + -
198C CYS 3.7 11.8 - - - +
199C GLN* 3.3 42.0 + - - +
201C HIS* 1.3 78.8 - - - +
203C MET* 1.3 58.2 + - - +
205C VAL* 3.3 10.4 - - + +
206C ASN* 2.8 43.6 + - - +
470F HIS* 5.0 25.2 + - + +
472F ALA* 4.3 5.9 - - + +
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Residues in contact with MET 203 (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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167C THR* 3.7 32.1 - - + -
169C GLY 3.7 18.8 - - - +
170C PHE* 3.6 29.2 - - + -
171C SER 4.8 0.2 - - - -
174C VAL* 3.8 17.3 - - + -
175C GLU* 4.1 21.1 - - + +
178C LEU* 4.1 7.2 - - + -
191C VAL* 4.8 9.0 - - + -
199C GLN 3.9 4.5 + - - +
200C GLY 3.5 8.0 + - - +
201C HIS 3.3 0.4 - - - -
202C GLU* 1.3 83.0 - - - +
204C ALA* 1.3 57.0 + - - +
206C ASN* 3.8 5.5 - - - +
207C LEU* 2.9 57.5 + - + +
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Residues in contact with ALA 204 (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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191C VAL* 4.4 13.0 - - + +
200C GLY 2.9 18.3 + - - +
201C HIS* 3.6 7.2 - - - +
203C MET* 1.3 77.9 - - - +
205C VAL* 1.3 58.6 + - + +
207C LEU* 4.7 0.2 - - - -
208C SER* 2.9 31.8 + - - -
214C THR* 3.5 13.6 - - - +
216C VAL* 3.7 30.5 - - + -
473F LEU* 5.1 1.1 - - + -
482F LEU* 4.4 5.2 - - + -
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Residues in contact with VAL 205 (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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201C HIS 3.0 15.3 + - - +
202C GLU* 3.3 20.6 - - + +
204C ALA* 1.3 77.2 - - - +
206C ASN* 1.3 63.4 + - - +
208C SER* 4.0 6.4 - - - -
209C LYS* 3.3 36.9 + - - +
470F HIS* 6.3 0.9 - - - +
472F ALA* 3.4 34.5 - - + +
473F LEU* 4.3 10.5 - - + -
479F HIS* 4.6 14.9 - - + +
482F LEU* 4.6 11.9 - - + -
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Residues in contact with ASN 206 (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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170C PHE* 4.8 4.9 - - - -
175C GLU* 3.4 34.6 + - - +
179C LYS* 4.5 11.2 + - - +
202C GLU* 2.8 34.2 + - - +
203C MET* 3.9 2.2 - - - +
204C ALA 3.2 0.2 - - - -
205C VAL* 1.3 81.8 - - - +
207C LEU* 1.3 64.8 + - - +
209C LYS* 3.8 28.1 + - - +
210C ALA* 4.0 6.6 + - - +
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Residues in contact with LEU 207 (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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175C GLU* 3.5 38.4 - - + +
178C LEU* 3.8 11.0 - - + -
179C LYS* 4.2 5.2 - - + -
189C VAL* 3.8 32.3 - - + -
191C VAL* 4.6 4.9 - - + -
203C MET* 2.9 43.0 + - + +
204C ALA* 4.1 2.2 - - - +
206C ASN* 1.3 75.0 - - - +
208C SER* 1.3 64.5 + - - +
209C LYS 3.2 0.4 - - - -
210C ALA* 3.2 10.9 + - - -
211C GLY 3.2 8.0 + - - -
212C ILE* 3.4 32.3 + - + +
214C THR* 4.5 10.8 - - + -
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Residues in contact with SER 208 (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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204C ALA 2.9 19.9 + - - -
205C VAL* 4.4 5.2 - - - -
206C ASN 3.4 0.2 - - - -
207C LEU* 1.3 74.2 - - - +
209C LYS* 1.3 63.4 + - - +
210C ALA 3.2 0.2 - - - -
211C GLY* 3.3 12.7 + - - +
212C ILE 4.8 0.9 - - - +
214C THR* 3.7 16.1 - - - +
479F HIS* 3.3 31.6 + - - +
480F ALA 5.8 0.2 + - - -
481F SER* 3.6 17.1 + - - -
482F LEU* 3.5 13.5 - - - +
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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