Contacts of the helix formed by residues 207 - 213 (chain D) in PDB entry 2Q41
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 GLY 207 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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205D PRO 3.0 5.3 + - - -
206D ILE* 1.3 81.5 - - - +
208D PRO* 1.3 59.5 - - - +
209D ALA 2.8 4.6 + - - +
210D LYS* 2.6 38.8 + - - +
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Residues in contact with PRO 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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206D ILE* 4.4 5.2 - - + +
207D GLY* 1.3 81.9 - - - +
209D ALA* 1.3 57.0 + - - +
210D LYS 3.2 1.2 + - - -
211D GLU* 3.7 21.0 + - - +
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Residues in contact with ALA 209 (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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203D SER* 4.3 15.0 - - - +
204D ASP 3.8 20.6 - - - +
205D PRO* 4.5 1.3 - - + -
206D ILE* 5.1 2.9 - - + +
207D GLY 2.8 4.6 + - - -
208D PRO* 1.3 73.9 - - - +
210D LYS* 1.3 61.0 + - - +
211D GLU 2.9 6.1 - - - -
212D LEU* 3.1 27.0 + - + +
213D PHE* 3.0 18.9 - - - -
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Residues in contact with LYS 210 (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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205D PRO* 4.1 22.2 - - + +
207D GLY* 2.6 23.8 + - - +
209D ALA* 1.3 71.7 - - - +
211D GLU* 1.3 57.6 + - - +
212D LEU 3.2 0.4 - - - -
213D PHE* 3.0 28.7 + - + +
214D GLU* 3.1 41.3 + - - +
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Residues in contact with GLU 211 (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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182D ASP* 5.1 1.9 - - - +
184D VAL* 3.1 45.4 - - + +
188D LYS* 5.4 2.8 + - - -
208D PRO 3.7 16.4 + - - +
210D LYS* 1.3 74.5 - - - +
212D LEU* 1.3 57.3 + - + +
213D PHE 3.0 9.4 + - - -
214D GLU* 3.3 24.3 + - + +
216D PRO* 5.5 5.7 - - + +
217D PHE* 3.3 19.6 + - + +
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Residues in contact with LEU 212 (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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127D ILE* 4.6 16.2 - - + -
184D VAL* 3.9 21.5 - - + +
200D VAL* 4.3 10.3 - - + -
202D SER* 3.5 29.6 - - - +
209D ALA* 3.1 23.6 + - + +
211D GLU* 1.3 74.2 - - + +
213D PHE* 1.3 65.6 + - + +
214D GLU 3.6 0.4 - - - -
217D PHE* 3.4 57.4 - - + -
218D PHE* 3.7 9.2 - - - -
233D THR* 4.5 7.1 - - - +
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Residues in contact with PHE 213 (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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202D SER* 3.9 11.7 - - - -
203D SER 3.5 21.1 - - - -
205D PRO* 3.5 39.7 - - + -
209D ALA 3.0 29.6 - - - -
210D LYS* 3.0 20.3 + - + +
212D LEU* 1.3 82.2 - - + +
214D GLU* 1.3 63.1 + - + +
218D PHE* 3.0 23.2 - + - -
233D THR* 5.1 4.5 - - + -
234D GLN* 3.7 28.5 - - - -
235D ALA* 5.0 0.2 - - - -
236D GLU* 4.4 2.9 - - - -
244D ILE* 5.5 2.2 - - + -
248D ILE* 3.5 36.3 - - + +
251D ASN* 3.3 13.7 + - - -
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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