Contacts of the helix formed by residues 199 - 208 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29D ARG* 5.7 5.1 - - - +
169D GLY* 4.7 3.3 - - - -
170D PHE* 3.3 58.6 + - + +
194D CYS* 4.4 9.9 - - + +
197D PHE* 2.8 43.8 + - + +
198D CYS* 1.3 70.4 - - - +
200D GLY* 1.3 62.2 + - - +
201D HIS 3.3 1.6 - - - -
202D GLU* 3.3 31.2 - - - +
203D MET 4.0 0.3 + - - -
248D VAL* 5.1 9.4 - - - +
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Residues in contact with GLY 200 (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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169D GLY* 3.9 18.4 + - - -
191D VAL* 3.5 15.4 - - - +
192D ALA 4.5 0.7 - - - -
193D GLU* 4.2 18.7 - - - +
194D CYS 4.5 1.4 - - - +
198D CYS 3.4 1.2 - - - -
199D GLN* 1.3 77.1 - - - +
201D HIS* 1.3 62.9 + - - +
202D GLU 3.4 0.4 - - - -
203D MET* 3.5 2.6 + - - -
204D ALA* 2.9 29.1 + - - +
216D VAL* 5.4 1.1 - - - +
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Residues in contact with HIS 201 (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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193D GLU* 2.4 38.1 + - + -
198D CYS* 3.5 24.9 + - + +
199D GLN 3.3 1.4 - - - -
200D GLY* 1.3 76.1 - - - +
202D GLU* 1.3 66.3 + - - +
204D ALA* 3.2 4.8 + - - +
205D VAL* 2.9 34.3 + - - +
216D VAL* 4.1 7.8 - - + +
463E LEU 3.2 24.7 + - - -
464E GLN* 4.2 5.8 - - - -
465E CYS* 4.3 6.0 + - - -
472E ALA* 3.9 19.5 + - + +
473E LEU* 3.5 34.1 + - + +
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Residues in contact with GLU 202 (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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170D PHE* 4.7 15.9 - - + -
198D CYS 3.6 11.3 - - - +
199D GLN* 3.3 41.4 - - - +
201D HIS* 1.3 76.2 - - - +
203D MET* 1.3 59.7 + - - +
205D VAL* 3.3 9.6 - - + +
206D ASN* 2.8 44.0 + - - +
470E HIS* 4.4 32.7 + - + +
472E ALA* 4.1 5.0 - - - +
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Residues in contact with MET 203 (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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167D THR* 3.7 19.3 - - + -
169D GLY 3.4 22.0 - - - +
170D PHE* 3.6 32.1 - - + -
171D SER 4.6 0.7 - - - +
174D VAL* 3.7 27.6 - - + -
175D GLU* 4.5 13.9 - - + +
178D LEU* 4.1 8.3 - - + -
191D VAL* 4.2 11.0 - - + -
200D GLY 3.5 11.1 + - - +
201D HIS 3.3 0.4 - - - -
202D GLU* 1.3 82.0 - - - +
204D ALA* 1.3 56.3 + - - +
206D ASN* 3.3 6.2 + - - +
207D LEU* 2.9 55.1 + - + +
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Residues in contact with ALA 204 (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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191D VAL* 4.4 7.2 - - + +
200D GLY 2.9 18.8 + - - +
201D HIS* 3.2 7.8 + - - +
203D MET* 1.3 78.2 - - - +
205D VAL* 1.3 59.0 + - + +
207D LEU* 3.4 1.2 + - - +
208D SER* 2.9 31.9 + - - -
214D THR* 3.8 18.7 - - + +
216D VAL* 3.7 30.3 - - + -
473E LEU* 5.1 1.6 - - + -
482E LEU* 4.4 3.6 - - + -
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Residues in contact with VAL 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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201D HIS 2.9 16.0 + - - +
202D GLU* 3.3 20.9 - - + +
204D ALA* 1.3 76.6 - - - +
206D ASN* 1.3 61.2 + - - +
208D SER* 4.1 6.1 - - - -
209D LYS* 3.3 34.4 + - - +
470E HIS* 5.9 2.2 - - - +
472E ALA* 3.4 37.0 - - + +
473E LEU* 4.0 12.8 - - + -
479E HIS* 4.3 14.7 - - + +
482E LEU* 4.4 10.5 - - + -
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Residues in contact with ASN 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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170D PHE* 5.0 5.5 - - - -
175D GLU* 3.3 28.2 + - - +
179D LYS* 5.5 3.6 + - - -
202D GLU* 2.8 32.9 + - - +
203D MET* 3.8 4.6 - - - +
204D ALA 3.2 0.4 - - - -
205D VAL* 1.3 83.3 - - - +
207D LEU* 1.3 63.7 + - - +
208D SER 3.4 0.4 - - - -
209D LYS* 3.7 27.7 + - - +
210D ALA* 4.0 5.9 + - - +
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Residues in contact with LEU 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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175D GLU* 3.8 33.7 - - + +
178D LEU* 3.8 29.8 - - + -
179D LYS* 4.6 6.7 - - + +
189D VAL* 4.3 6.1 - - + -
191D VAL* 4.0 15.7 - - + -
203D MET* 2.9 39.1 + - + +
204D ALA 4.0 0.9 - - - +
206D ASN* 1.3 75.3 - - - +
208D SER* 1.3 59.6 + - - +
209D LYS 3.2 0.7 - - - -
210D ALA* 3.2 15.3 + - + +
211D GLY 3.3 8.0 + - - -
212D ILE* 3.5 33.0 + - + +
214D THR* 3.5 15.5 - - - +
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Residues in contact with SER 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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204D ALA 2.9 18.4 + - - -
205D VAL* 4.5 5.2 - - - -
206D ASN 3.4 0.2 - - - -
207D LEU* 1.3 75.1 - - - +
209D LYS* 1.3 64.2 + - - +
210D ALA 3.2 0.2 - - - -
211D GLY* 3.3 13.9 + - - +
212D ILE 4.8 0.4 - - - +
214D THR* 3.9 3.6 + - - -
479E HIS* 3.3 29.6 + - - +
480E ALA 5.7 0.2 + - - -
481E SER* 3.5 31.1 + - - -
482E LEU* 3.6 13.9 - - - +
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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