Contacts of the helix formed by residues 204 - 219 (chain B) in PDB entry 3QVL
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 ASP 204 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B ALA* 3.9 4.3 - - - +
99B ILE* 5.6 0.3 - - - +
182B LEU* 4.6 7.6 - - + -
184B SER 4.7 4.7 - - - +
188B ALA* 3.3 40.0 - - - +
191B ALA* 3.6 26.1 - - + +
202B VAL 3.9 0.2 + - - -
203B ILE* 1.3 75.6 - - - +
205B GLY* 1.3 60.9 + - - +
206B VAL* 3.0 23.6 + - - +
207B SER* 2.9 50.0 + - - +
208B ALA* 3.2 12.0 + - - +
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Residues in contact with GLY 205 (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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80B PHE* 6.2 0.9 - - - -
99B ILE* 3.2 37.1 - - - +
102B ALA* 3.9 0.3 - - - +
103B ALA* 3.7 13.2 - - - +
182B LEU 5.0 4.0 + - - -
184B SER 5.9 0.2 + - - -
203B ILE 3.9 0.6 + - - -
204B ASP* 1.3 73.3 + - - +
206B VAL* 1.3 55.9 + - - +
208B ALA* 3.7 4.0 - - - +
209B ALA* 2.8 36.6 + - - +
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Residues in contact with VAL 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B VAL* 4.5 6.3 - - + -
21B ILE* 3.5 50.3 - - + +
24B ALA* 4.3 3.1 - - + -
25B ALA* 4.1 16.2 - - + +
76B VAL* 4.7 0.9 - - - +
78B ALA* 4.3 1.8 - - + -
99B ILE* 3.6 20.1 - - + +
185B GLY* 4.3 11.9 - - - -
188B ALA* 4.0 12.3 - - + -
204B ASP* 3.0 17.7 + - - +
205B GLY* 1.3 77.3 - - - +
207B SER* 1.3 63.0 + - - +
209B ALA* 3.4 2.3 + - - +
210B VAL* 3.2 27.2 + - - +
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Residues in contact with SER 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B ALA* 4.1 8.3 - - - -
28B VAL* 3.6 36.5 - - - +
191B ALA* 5.5 0.7 - - - +
204B ASP* 2.9 35.2 + - - +
206B VAL* 1.3 75.6 - - - +
208B ALA* 1.3 61.2 + - - +
210B VAL* 3.5 5.8 + - - +
211B LYS* 3.2 28.0 + - - +
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Residues in contact with ALA 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B ALA* 3.8 16.2 - - + -
103B ALA* 4.2 1.8 - - - +
106B MET* 3.7 29.8 - - + -
203B ILE* 4.5 3.4 - - + -
204B ASP 3.2 15.8 + - - +
205B GLY* 3.7 5.2 - - - +
207B SER* 1.3 81.8 + - - +
209B ALA* 1.3 56.9 + - - +
211B LYS* 3.2 9.7 + - - +
212B MET* 3.0 31.0 + - - +
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Residues in contact with ALA 209 (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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76B VAL* 3.6 30.3 - - + -
97B ILE* 3.8 15.8 - - + +
98B GLY 4.1 4.7 - - - +
99B ILE* 4.2 1.1 - - + -
102B ALA* 3.4 16.5 - - + +
205B GLY 2.8 22.1 + - - +
206B VAL 3.8 0.9 - - - +
208B ALA* 1.3 69.7 - - - +
210B VAL* 1.3 65.3 + - - +
212B MET* 3.2 2.5 + - - +
213B VAL* 3.0 28.6 + - - +
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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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6B ILE* 3.8 8.4 - - + +
8B VAL* 4.1 16.6 - - + -
25B ALA* 3.7 41.5 - - + +
28B VAL* 4.5 6.3 - - + -
29B ALA* 4.4 5.8 - - - -
35B ILE* 4.1 13.5 - - + -
76B VAL* 4.3 8.1 - - + -
206B VAL* 3.2 15.0 + - + +
207B SER 3.6 8.1 - - - +
208B ALA 3.3 0.2 - - - -
209B ALA* 1.3 76.8 - - - +
211B LYS* 1.3 56.8 + - - +
213B VAL* 3.4 2.5 + - - +
214B GLU* 3.0 45.0 + - - +
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Residues in contact with LYS 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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28B VAL* 3.0 38.9 + - + +
30B ALA* 3.7 13.5 - - - +
106B MET* 6.1 0.7 - - - -
207B SER* 3.2 16.8 - - - +
208B ALA* 3.2 9.5 + - - +
210B VAL* 1.3 77.2 - - + +
212B MET* 1.3 65.5 + - + +
214B GLU* 2.8 26.5 + - - +
215B SER* 2.7 37.8 + - - +
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Residues in contact with MET 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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97B ILE* 4.1 19.7 - - + -
102B ALA* 4.3 14.1 - - + -
105B HIS* 5.7 3.8 - - + -
106B MET* 3.5 40.6 - - + -
109B MET* 5.8 1.3 - - - -
208B ALA 3.0 19.6 + - - +
209B ALA 3.2 8.0 + - - +
211B LYS* 1.3 88.2 - - + +
213B VAL* 1.3 60.2 + - - +
215B SER* 3.4 11.5 + - - +
216B LEU* 3.0 37.5 + - + +
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Residues in contact with VAL 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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6B ILE* 3.8 21.8 - - + -
74B GLY* 3.7 27.8 - - - -
75B HIS 3.6 24.2 - - - +
76B VAL* 3.9 9.2 - - + -
95B PRO* 4.4 6.7 - - + +
97B ILE* 3.7 14.8 - - + -
209B ALA 3.0 20.7 + - - +
210B VAL 3.8 3.8 - - - +
212B MET* 1.3 73.5 - - - +
214B GLU* 1.3 60.2 + - - +
216B LEU* 3.3 7.5 + - - +
217B VAL* 2.9 42.6 + - + +
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Residues in contact with GLU 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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4B VAL* 5.1 4.5 - - + -
6B ILE* 3.6 16.2 - - + -
29B ALA* 3.5 2.9 - - - -
30B ALA* 2.8 32.1 + - + +
33B THR* 2.8 27.4 + - - +
210B VAL* 3.0 23.3 + - - +
211B LYS* 2.8 38.9 + - - +
213B VAL* 1.3 76.1 - - - +
215B SER* 1.3 58.8 + - - +
217B VAL* 3.8 5.5 - - - +
218B ALA* 3.0 30.0 + - - +
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Residues in contact with SER 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 LYS* 2.7 24.9 + - - +
212B MET* 3.5 16.8 - - - +
213B VAL 3.2 0.2 - - - -
214B GLU* 1.3 76.1 - - - +
216B LEU* 1.3 57.1 + - - +
218B ALA* 3.3 6.2 + - - +
219B LEU* 2.9 43.0 + - - +
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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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95B PRO* 3.8 26.9 - - + -
97B ILE* 3.8 22.7 - - + -
212B MET* 3.0 22.4 + - + +
213B VAL 3.8 2.9 - - - +
215B SER* 1.3 75.6 - - - +
217B VAL* 1.3 61.5 + - - +
219B LEU* 3.3 10.3 + - + +
220B GLY 3.1 3.6 + - - -
221B LEU* 2.8 67.0 + - + +
222B ALA* 6.2 0.2 - - - -
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Residues in contact with VAL 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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4B VAL* 4.1 31.9 - - + -
73B ASP* 3.8 37.2 - - + +
95B PRO* 4.6 6.5 - - + -
213B VAL* 2.9 29.6 + - + +
214B GLU 3.8 3.6 - - - +
216B LEU* 1.3 75.2 - - - +
218B ALA* 1.3 62.0 + - - +
220B GLY* 3.1 13.4 + - - -
221B LEU 4.6 2.9 - - - +
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Residues in contact with ALA 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 GLU 3.0 18.8 + - - +
215B SER* 3.7 6.3 - - - +
217B VAL* 1.3 77.0 - - - +
219B LEU* 1.3 61.4 + - + +
220B GLY 3.2 0.8 + - - -
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Residues in contact with LEU 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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215B SER* 2.9 33.9 + - - +
216B LEU* 3.6 11.2 - - + +
217B VAL 3.2 0.4 - - - -
218B ALA* 1.3 76.5 - - + +
220B GLY* 1.3 61.5 + - - +
221B LEU* 3.6 31.5 + - + +
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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