Contacts of the helix formed by residues 210 - 224 (chain Y) in PDB entry 1VQN
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 210 (chain Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13130 A 2.9 19.6 + - - -
13140 U 4.0 14.6 - - - -
13150 G 4.0 0.2 - - - -
13160 G 3.8 16.4 - - - -
208Y LYS 3.3 2.6 + - - -
209Y VAL* 1.3 72.9 - - - +
211Y ALA* 1.3 59.9 + - - -
212Y ARG 3.3 3.3 + - - -
213Y LYS 3.4 2.3 + - - -
214Y ARG* 2.8 31.7 + - - +
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Residues in contact with ALA 211 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13150 G 3.4 30.6 + - - +
13160 G 3.1 15.9 + - - +
100Y ARG* 5.2 0.9 + - - -
210Y GLY* 1.3 68.7 - - - -
212Y ARG* 1.3 66.5 + - - +
214Y ARG* 3.5 11.8 - - - +
215Y GLU* 2.9 24.4 + - - +
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Residues in contact with ARG 212 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3120 U 5.7 1.2 + - - -
3130 U 6.1 1.0 - - - -
3190 A 4.7 13.3 + - - -
3200 G 3.3 47.3 + - - -
13140 U 4.8 11.7 + - - +
13150 G 3.0 90.9 + - + +
211Y ALA* 1.3 80.2 - - - +
213Y LYS* 1.3 65.1 + - - +
215Y GLU* 3.3 17.3 + - - +
216Y ARG* 3.4 38.7 + - - +
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Residues in contact with LYS 213 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13120 G 2.6 39.5 + - - +
13130 A 2.7 43.4 + - - +
13140 U 5.8 0.4 + - - -
188Y HIS 4.1 10.8 - - - +
189Y ASN* 4.5 6.1 - - + -
190Y VAL* 5.5 3.6 - - + +
209Y VAL* 4.0 5.2 - - + -
210Y GLY 3.4 2.0 + - - -
212Y ARG* 1.3 79.2 - - - +
214Y ARG* 1.3 65.0 + - - +
216Y ARG* 3.4 15.5 + - + +
217Y ILE* 3.0 40.9 + - + +
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Residues in contact with ARG 214 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13350 C 4.0 8.8 + - - -
100Y ARG* 5.4 0.2 - - - +
205Y ILE* 3.5 26.8 + - + +
206Y ALA 4.9 1.8 + - - -
209Y VAL* 3.7 29.8 - - + +
210Y GLY 2.8 23.0 + - - +
211Y ALA* 3.5 10.1 - - - +
213Y LYS* 1.3 76.9 - - - +
215Y GLU* 1.3 54.4 + - - +
217Y ILE* 3.1 7.6 + - - +
218Y GLU* 2.7 47.3 + - - +
230Y ASN* 2.6 46.4 + - - +
231Y PRO* 3.6 3.0 + - - +
232Y THR* 3.2 35.1 + - - +
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Residues in contact with GLU 215 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13150 G 3.3 27.7 + - - +
100Y ARG* 3.5 37.3 + - - +
211Y ALA 2.9 12.8 + - - +
212Y ARG* 3.4 11.5 - - - +
214Y ARG* 1.3 77.3 - - - +
216Y ARG* 1.3 66.8 + - + +
218Y GLU* 3.3 1.2 + - - +
219Y GLU* 3.1 33.0 + - + +
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Residues in contact with ARG 216 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3200 G 4.2 11.1 + - - -
3210 A 4.9 16.6 + - - -
190Y VAL* 4.3 15.0 - - + +
212Y ARG* 3.4 38.9 + - - +
213Y LYS* 3.4 16.7 + - + +
214Y ARG 3.3 0.4 - - - -
215Y GLU* 1.3 80.0 - - + +
217Y ILE* 1.3 62.0 + - - +
219Y GLU* 3.5 16.8 - - - +
220Y GLU* 3.2 25.3 + - - +
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Residues in contact with ILE 217 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187Y VAL* 4.2 13.2 - - + -
188Y HIS 3.9 7.9 - - - +
189Y ASN* 3.4 31.2 - - - +
190Y VAL* 3.7 24.5 - - + +
193Y LEU* 3.5 22.0 - - + +
205Y ILE* 3.9 25.8 - - + -
209Y VAL* 4.4 11.0 - - + -
213Y LYS* 3.0 22.6 + - + +
214Y ARG* 3.5 6.5 - - - +
216Y ARG* 1.3 75.6 - - - +
218Y GLU* 1.3 59.5 + - - +
220Y GLU 3.5 0.2 + - - -
221Y ALA* 3.0 27.6 + - + +
228Y VAL* 5.6 0.9 - - + -
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Residues in contact with GLU 218 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100Y ARG* 2.6 53.4 + - + +
101Y GLY* 5.4 2.9 + - - -
205Y ILE* 4.1 16.6 - - + -
214Y ARG* 2.7 29.8 + - - +
215Y GLU 3.3 4.0 + - - +
217Y ILE* 1.3 73.9 - - - +
219Y GLU* 1.3 61.5 + - - +
221Y ALA* 3.3 5.2 + - - +
222Y GLU* 3.2 24.0 + - - +
228Y VAL* 4.7 12.8 - - + +
231Y PRO* 3.4 8.5 - - - +
232Y THR* 2.6 42.8 + - - -
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Residues in contact with GLU 219 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100Y ARG* 5.9 0.2 - - - +
215Y GLU* 3.1 20.6 + - + +
216Y ARG* 3.5 26.0 - - - +
218Y GLU* 1.3 76.6 - - - +
220Y GLU* 1.3 68.7 + - + +
222Y GLU* 3.7 9.1 + - - +
223Y ASP* 3.0 35.4 + - - +
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Residues in contact with GLU 220 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190Y VAL* 3.9 26.6 - - + +
193Y LEU* 3.9 15.6 - - + +
216Y ARG 3.2 18.9 + - - +
219Y GLU* 1.3 82.2 - - + +
221Y ALA* 1.3 61.5 + - - +
223Y ASP* 3.7 10.7 + - - +
224Y ALA* 3.2 22.6 + - + +
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Residues in contact with ALA 221 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193Y LEU* 3.7 21.5 - - + +
203Y VAL* 4.8 0.2 - - + -
217Y ILE 3.0 19.1 + - - +
218Y GLU 3.8 2.0 - - - +
219Y GLU 3.3 0.2 - - - -
220Y GLU* 1.3 76.1 - - - +
222Y GLU* 1.3 64.3 + - - +
224Y ALA* 3.0 10.2 + - - -
226Y ILE* 2.8 38.1 + - + +
228Y VAL* 3.7 27.4 - - + -
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Residues in contact with GLU 222 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100Y ARG* 5.2 1.9 - - - +
101Y GLY* 3.5 37.4 + - - +
102Y LEU* 4.0 22.7 - - + +
218Y GLU 3.2 14.7 + - - +
219Y GLU* 3.9 9.1 - - - +
221Y ALA* 1.3 78.2 - - - +
223Y ASP* 1.3 60.2 + - - +
225Y GLY* 2.7 26.5 + - - -
226Y ILE 4.0 7.2 + - - -
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Residues in contact with ASP 223 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219Y GLU* 3.0 24.5 + - - +
220Y GLU* 4.0 11.2 - - - +
222Y GLU* 1.3 83.3 - - - +
224Y ALA* 1.3 58.4 + - - +
225Y GLY 3.2 1.4 + - - -
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Residues in contact with ALA 224 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193Y LEU* 5.8 2.7 - - + +
196Y VAL 5.4 0.9 - - - +
198Y GLY* 5.0 3.5 + - - -
220Y GLU* 3.2 17.6 + - + +
221Y ALA* 3.0 6.4 + - - +
222Y GLU 3.0 1.2 - - - -
223Y ASP* 1.3 76.0 - - - +
225Y GLY* 1.3 62.1 + - - +
226Y ILE* 3.3 23.3 + - + +
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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