Contacts of the helix formed by residues 200 - 218 (chain A) in PDB entry 2VGL
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 HIS 200 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A ASP* 3.1 35.8 + - + +
163A SER* 5.2 1.3 - - - -
166A GLN* 3.5 20.1 + - - -
198A ASP* 2.7 20.0 + - - +
199A GLN* 1.3 70.9 - - + +
201A LEU* 1.3 62.7 + - - +
202A GLY* 3.2 31.9 - - - -
203A VAL* 2.8 33.7 + - + +
204A VAL* 3.0 11.1 + - - +
247A TYR* 3.5 6.4 + - - -
125S GLU* 3.6 3.8 + - - -
130S LYS* 2.8 38.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 201 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A GLN 3.6 7.4 + - - +
200A HIS* 1.3 74.0 - - - +
202A GLY* 1.3 56.0 + - - +
204A VAL* 2.9 11.9 + - + +
205A THR* 2.7 34.0 + - - +
232A ARG* 3.5 29.6 - - - +
236A ILE* 5.0 3.6 - - + -
244A LEU* 3.5 37.2 - - + -
247A TYR* 3.7 46.2 - - + -
254A ALA* 4.4 4.0 - - + -
257A LEU* 3.5 28.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 202 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A GLN* 3.4 28.9 - - - +
200A HIS* 3.1 4.6 + - - -
201A LEU* 1.3 77.1 - - - +
203A VAL* 1.3 59.1 + - - +
205A THR* 3.4 6.7 + - - -
206A ALA* 3.1 19.1 + - - +
247A TYR* 3.0 24.4 + - - -
124S ARG 4.5 4.5 - - - +
125S GLU* 3.8 4.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 203 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A ASP* 3.8 44.6 - - + +
165A LYS* 4.7 10.5 - - + +
166A GLN* 3.8 8.3 - - + +
195A LEU* 3.9 39.5 - - + -
198A ASP* 4.0 14.8 - - + +
200A HIS* 2.8 24.3 + - + +
202A GLY* 1.3 73.2 - - - -
204A VAL* 1.3 64.3 + - - +
206A ALA* 3.4 3.3 + - + +
207A ALA* 3.1 19.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 204 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A LEU 4.0 16.6 - - - +
196A LEU* 4.1 20.9 - - + +
198A ASP* 3.8 4.3 - - + +
200A HIS 3.0 13.2 + - - +
201A LEU* 2.9 16.7 + - + +
203A VAL* 1.3 78.3 - - - +
205A THR* 1.3 56.9 + - - +
207A ALA* 3.4 3.4 + - - +
208A THR* 2.6 37.0 + - - +
232A ARG* 3.5 32.3 - - + +
257A LEU* 3.6 24.5 - - + -
261A LEU* 4.8 5.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 205 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A LEU 2.7 21.5 + - - -
202A GLY* 3.7 7.2 - - - -
204A VAL* 1.3 73.3 - - - +
206A ALA* 1.3 64.9 + - - +
208A THR* 2.9 14.1 + - - -
209A SER* 3.1 11.6 + - - -
247A TYR* 5.8 1.9 - - - -
256A TRP 5.6 0.9 - - - -
257A LEU* 3.6 30.5 + - + +
260A LYS* 3.2 39.0 - - + +
123S ILE* 4.1 11.7 - - + +
124S ARG 4.2 9.9 - - - +
126S THR* 5.5 5.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 206 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A LYS 5.3 0.2 - - - -
166A GLN* 3.6 36.1 - - + +
169A ALA* 3.8 12.0 - - + +
170A LEU* 4.3 19.4 - - + +
202A GLY 3.1 14.8 + - - +
203A VAL* 3.8 4.5 - - + +
205A THR* 1.3 79.3 - - - +
207A ALA* 1.3 62.7 + - - +
209A SER* 3.3 5.2 + - - -
210A LEU* 3.2 20.4 + - - +
260A LYS* 5.3 0.4 - - - +
123S ILE 5.4 0.7 - - - -
124S ARG* 5.2 2.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 207 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A ALA* 4.4 6.0 - - + +
192A VAL* 4.3 11.4 - - + +
195A LEU* 3.9 30.7 - - + -
196A LEU* 4.5 5.6 - - + -
203A VAL 3.1 15.0 + - - +
204A VAL* 3.7 5.2 - - - +
206A ALA* 1.3 80.7 - - - +
208A THR* 1.3 56.9 + - - +
210A LEU* 3.3 6.6 + - - +
211A ILE* 3.0 39.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 208 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A LEU* 3.1 19.4 - - - +
204A VAL* 2.6 20.4 + - - +
205A THR* 2.9 10.4 + - - -
207A ALA* 1.3 73.0 - - - +
209A SER* 1.3 58.2 + - - +
211A ILE* 4.1 1.4 - - - +
212A THR* 2.6 38.7 + - - +
257A LEU* 4.1 1.3 - - - +
260A LYS* 3.5 41.7 - - + +
261A LEU* 3.8 12.6 - - + +
264A LEU* 3.8 21.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 209 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A LEU* 4.0 16.8 - - - -
173A LEU* 4.0 10.0 - - - +
177A ARG* 5.1 0.7 + - - -
205A THR 3.1 4.8 + - - -
206A ALA 3.3 8.7 + - - -
208A THR* 1.3 78.4 - - - +
210A LEU* 1.3 60.3 + - - +
212A THR* 3.7 5.0 - - - -
213A THR* 3.4 23.6 + - - -
260A LYS* 2.6 41.2 + - - +
122S GLU* 3.9 10.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 210 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A LEU* 3.9 28.7 - - + -
169A ALA* 3.7 14.6 - - + +
170A LEU* 5.9 0.2 - - - -
172A LEU* 4.0 16.8 - - + +
173A LEU* 3.6 43.5 - - + +
176A TYR* 5.4 1.6 - - + -
188A TRP* 5.0 0.2 - - + -
192A VAL* 3.9 20.4 - - + -
206A ALA 3.2 10.2 + - - +
207A ALA* 3.6 8.3 - - - +
208A THR 3.2 0.4 - - - -
209A SER* 1.3 76.5 - - - +
211A ILE* 1.3 62.2 + - - +
213A THR* 3.4 3.3 + - - -
214A LEU* 3.0 53.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 211 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A VAL* 3.7 38.4 - - + +
193A VAL* 4.1 9.0 - - + -
196A LEU* 4.1 23.6 - - + -
207A ALA* 3.0 26.9 + - + +
208A THR* 4.1 3.4 - - - +
210A LEU* 1.3 74.6 - - + +
212A THR* 1.3 56.5 + - - +
214A LEU* 3.0 7.4 + - - +
215A ALA* 2.6 34.4 + - + +
222A PHE* 3.9 32.5 - - + -
225A SER* 4.2 8.7 - - - +
264A LEU* 3.6 21.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 212 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208A THR* 2.6 25.4 + - - +
209A SER* 3.7 7.4 - - - -
211A ILE* 1.3 79.1 - - - +
213A THR* 1.3 67.3 + - - +
215A ALA* 3.3 8.3 + - - +
216A GLN* 3.3 19.7 + - - +
260A LYS 4.6 1.0 + - - -
263A ARG* 4.6 15.0 - - + +
264A LEU* 3.5 32.5 + - - +
267A CYS* 4.0 18.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 213 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A LEU* 2.9 36.3 - - + +
176A TYR* 3.9 28.2 + - + -
177A ARG* 3.3 28.5 + - + +
209A SER 3.4 6.3 + - - -
210A LEU 3.7 1.8 - - - -
211A ILE 3.4 0.2 - - - -
212A THR* 1.3 80.9 - - - +
214A LEU* 1.3 62.2 + - - +
216A GLN* 3.2 34.7 + - - +
217A LYS 4.4 0.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 214 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A TYR* 3.3 48.5 - - + -
183A VAL* 5.0 2.7 - - + -
185A MET* 4.3 4.9 - - + -
188A TRP* 4.0 23.8 - - + -
210A LEU* 3.0 38.7 + - + +
211A ILE* 3.5 4.9 - - - +
213A THR* 1.3 75.8 - - - +
215A ALA* 1.3 63.6 + - - +
216A GLN 3.1 0.7 + - - -
217A LYS 3.7 1.0 + - - -
218A ASN* 2.9 35.8 + - - +
222A PHE* 3.5 37.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 215 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211A ILE* 2.6 22.7 + - + +
212A THR* 3.3 6.0 + - - +
214A LEU* 1.3 71.8 - - - +
216A GLN* 1.3 64.2 - - - +
218A ASN 4.0 10.3 - - - -
219A PRO* 3.1 23.9 - - - +
222A PHE* 4.5 2.6 - - + -
264A LEU* 4.8 2.7 - - + -
267A CYS* 3.8 27.4 - - + +
268A TYR* 3.8 21.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 216 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212A THR* 3.3 17.7 + - - +
213A THR* 3.3 32.3 - - - +
214A LEU 3.1 1.4 + - - -
215A ALA* 1.3 78.6 - - - +
217A LYS* 1.3 65.3 + - + +
219A PRO* 4.3 6.8 - - - +
267A CYS* 5.0 9.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 217 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A TYR* 4.0 23.7 + - - +
180A PRO* 5.9 5.3 - - - +
213A THR 4.4 0.8 + - - -
214A LEU 3.7 2.0 + - - -
216A GLN* 1.3 80.1 - - + +
218A ASN* 1.3 66.0 + - - +
219A PRO* 3.5 10.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 218 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A TYR* 3.5 25.1 + - - -
185A MET* 3.4 34.3 - - - +
214A LEU* 2.9 22.7 + - - +
215A ALA* 3.4 3.7 + - - -
217A LYS* 1.3 83.8 - - - +
219A PRO* 1.3 68.6 - - - +
220A GLU 3.3 2.1 + - - -
221A GLU* 3.5 11.7 + - + -
222A PHE* 3.3 29.3 - - + -
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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