Contacts of the helix formed by residues 209 - 221 (chain B) in PDB entry 2QVH
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 209 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53B ALA* 3.4 10.1 - - - +
56B GLU* 3.3 11.7 - - - -
204B VAL* 2.9 28.5 + - - +
207B LEU 4.6 0.9 - - - +
208B GLY* 1.3 79.2 - - - +
210B VAL* 1.3 60.4 + - - -
211B ARG 3.5 2.0 - - - -
212B ALA 3.5 1.4 + - - -
213B ALA* 3.0 29.8 + - - +
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Residues in contact with VAL 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56B GLU* 2.6 13.1 + - - +
62B TRP* 3.4 30.3 - - + +
63B PRO* 3.8 20.6 - - + -
204B VAL* 4.3 7.9 - - + -
209B GLY* 1.3 69.6 - - - -
211B ARG* 1.3 58.8 - - - +
213B ALA* 3.2 3.1 + - - +
214B LEU* 2.9 41.9 + - + +
238B ALA 3.5 24.5 - - - +
241B ALA 4.4 4.0 - - - +
242B LEU* 3.7 34.5 - - + +
245B ALA* 4.9 1.3 - - + -
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Residues in contact with ARG 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56B GLU* 3.1 24.2 + - - +
60B LEU* 4.4 17.8 + - - +
61B GLY 2.9 30.1 + - - -
62B TRP 3.9 12.9 + - - -
63B PRO* 3.7 25.5 - - + +
210B VAL* 1.3 74.8 - - - +
212B ALA* 1.3 63.1 + - - +
214B LEU* 3.3 9.6 + - + +
215B ARG* 3.0 48.6 + - - +
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Residues in contact with ALA 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56B GLU* 4.8 0.2 + - - -
207B LEU* 3.3 24.9 - - - +
208B GLY* 3.7 16.6 + - - +
209B GLY 3.5 2.7 + - - +
210B VAL 3.3 0.6 - - - -
211B ARG* 1.3 78.9 - - - +
213B ALA* 1.3 62.6 + - - +
215B ARG* 3.3 25.4 + - - +
216B LEU* 3.0 22.9 + - - +
310B TRP* 6.4 1.6 - - + -
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Residues in contact with ALA 213 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202B LEU* 4.0 6.9 - - + +
204B VAL* 5.3 2.0 - - - -
207B LEU* 4.2 27.3 + - + -
209B GLY 3.0 19.4 + - - +
210B VAL 3.2 2.4 + - - +
212B ALA* 1.3 74.7 - - - +
214B LEU* 1.3 59.2 + - - +
216B LEU* 3.3 4.2 + - - +
217B ALA* 2.9 29.3 + - - +
242B LEU* 3.6 32.5 - - + -
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Residues in contact with LEU 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63B PRO* 3.9 29.6 - - + -
210B VAL* 2.9 26.6 + - + +
211B ARG* 3.6 7.0 - - + +
213B ALA* 1.3 75.8 - - - +
215B ARG* 1.3 63.5 + - + +
217B ALA* 3.3 6.4 + - - +
218B GLU* 3.1 22.9 + - - +
242B LEU* 3.7 11.0 - - + -
245B ALA* 4.0 28.7 - - + +
246B LEU* 3.6 28.3 - - + -
247B PRO* 5.2 2.0 - - + -
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Residues in contact with ARG 215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211B ARG* 3.0 39.5 + - - +
212B ALA* 3.4 31.5 - - - +
213B ALA 3.2 0.2 - - - -
214B LEU* 1.3 77.4 - - - +
216B LEU* 1.3 61.9 + - - +
218B GLU* 3.3 9.8 + - - +
219B GLU* 3.1 37.1 + - - +
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Residues in contact with LEU 216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182B ILE* 3.7 28.7 - - + -
188B PRO* 4.1 20.4 - - + -
189B LEU* 3.9 17.0 - - + -
202B LEU* 4.5 5.6 - - + -
207B LEU* 4.0 24.0 - - + -
212B ALA 3.0 15.4 + - - +
213B ALA* 3.7 5.2 - - - +
215B ARG* 1.3 73.8 - - - +
217B ALA* 1.3 65.1 + - - +
219B GLU* 3.3 8.2 + - + +
220B CYS* 2.9 44.4 + - - +
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Residues in contact with ALA 217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200B VAL* 6.0 0.2 - - - -
202B LEU* 4.0 20.6 - - + +
213B ALA 2.9 17.5 + - - +
214B LEU 3.4 7.2 - - - +
216B LEU* 1.3 79.6 - - - +
218B GLU* 1.3 62.3 + - - +
220B CYS* 3.7 4.4 + - - +
221B GLY* 3.5 13.9 + - - -
222B LEU 4.5 7.6 - - - +
224B VAL* 4.2 16.3 - - + +
246B LEU* 4.0 17.5 - - + -
247B PRO* 6.2 0.7 - - + -
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Residues in contact with GLU 218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214B LEU 3.1 10.8 + - - +
215B ARG* 3.7 10.4 - - - +
216B LEU 3.2 0.2 - - - -
217B ALA* 1.3 81.3 - - - +
219B GLU* 1.3 65.9 + - + +
221B GLY* 3.3 12.8 + - - -
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Residues in contact with GLU 219 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189B LEU* 3.6 29.4 - - + +
192B ARG* 2.9 27.6 + - - +
215B ARG* 3.1 28.3 + - - +
216B LEU* 3.8 9.7 + - - +
218B GLU* 1.3 83.2 - - + +
220B CYS* 1.3 63.5 + - - +
221B GLY* 3.1 1.7 + - - -
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Residues in contact with CYS 220 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182B ILE* 4.5 20.0 - - - -
188B PRO 4.7 3.8 - - - -
189B LEU* 3.7 20.2 - - - -
191B VAL* 5.8 0.2 - - - -
192B ARG* 3.4 32.1 - - + +
200B VAL* 4.2 24.2 - - + -
216B LEU* 2.9 34.1 + - - +
217B ALA* 4.1 4.5 - - - +
219B GLU* 1.3 77.0 - - - +
221B GLY* 1.3 64.8 + - - +
222B LEU* 3.1 11.6 + - + +
224B VAL* 5.9 0.2 - - + -
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Residues in contact with GLY 221 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192B ARG* 5.5 0.4 - - - -
217B ALA 3.5 4.6 + - - -
218B GLU 3.3 12.3 + - - -
219B GLU 3.1 5.5 - - - -
220B CYS* 1.3 78.1 - - - +
222B LEU* 1.3 63.7 + - - +
223B PRO* 4.8 0.7 - - - +
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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