Contacts of the helix formed by residues 221 - 237 (chain A) in PDB entry 2VL7
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 ALA 221 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210A ILE* 3.8 25.1 - - + -
214A GLU* 3.2 16.5 + - + +
219A ILE* 3.7 4.9 + - + +
220A ASP* 1.3 72.3 - - - +
222A LYS* 1.3 62.6 + - - +
223A LYS 3.3 2.9 - - - -
224A VAL* 3.2 11.3 + - + -
225A LYS* 3.1 23.7 + - - +
260A GLU* 3.4 12.3 - - + +
264A VAL* 4.4 17.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 222 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214A GLU* 4.3 2.4 + - - -
220A ASP* 3.4 27.3 + - - +
221A ALA* 1.3 76.8 - - - +
223A LYS* 1.3 67.1 + - + +
225A LYS* 3.3 6.9 + - - +
226A ASP* 2.5 72.7 + - - +
260A GLU* 3.9 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 223 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221A ALA 3.3 0.6 - - - -
222A LYS* 1.3 81.5 - - + +
224A VAL* 1.3 57.9 + - - +
226A ASP* 3.7 6.8 + - - +
227A TYR* 3.1 21.3 + - - +
254A ASP* 4.9 4.9 - - - +
256A GLU* 2.9 41.6 + - + +
257A THR* 3.4 33.9 + - - +
260A GLU* 3.5 24.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 224 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210A ILE* 3.5 23.3 - - + -
221A ALA* 3.2 9.9 + - + +
223A LYS* 1.3 75.0 - - - +
225A LYS* 1.3 59.8 + - - +
227A TYR* 3.1 4.3 + - + +
228A ILE* 2.9 36.8 + - + +
257A THR* 3.8 12.3 - - + +
260A GLU* 3.4 36.1 - - + +
261A LEU* 3.4 39.0 - - + +
264A VAL* 4.5 5.8 - - + -
284A LEU* 5.4 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 225 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A LEU* 4.0 32.9 - - + +
210A ILE* 3.6 32.1 - - + -
211A GLU* 2.7 26.9 + - - +
214A GLU* 2.7 33.2 + - - +
221A ALA 3.1 12.7 + - - +
222A LYS* 3.3 6.7 + - - +
224A VAL* 1.3 75.3 - - - +
226A ASP* 1.3 60.7 + - - +
228A ILE* 3.2 2.4 + - - +
229A ASN* 2.9 40.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 226 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222A LYS* 2.5 58.5 + - - +
223A LYS* 3.9 6.5 - - - +
225A LYS* 1.3 76.6 - - - +
227A TYR* 1.3 61.4 + - - +
229A ASN* 3.5 10.3 + - - +
230A LEU* 2.9 28.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 227 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223A LYS 3.1 16.7 + - - +
224A VAL* 3.1 7.6 + - + +
226A ASP* 1.3 75.3 - - - +
228A ILE* 1.3 69.9 + - + +
230A LEU* 3.1 15.2 + - + +
231A LEU* 2.8 55.1 + - + +
250A MET* 3.8 5.2 - - - +
251A PRO* 2.7 33.4 + - + -
252A LEU* 3.4 26.7 - - - +
253A PRO* 3.6 29.2 - - + +
257A THR* 3.7 16.6 - - + -
261A LEU* 6.0 1.3 - - + -
284A LEU* 4.6 15.9 - - + -
288A VAL* 4.6 2.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 228 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A LEU* 3.8 31.0 - - + +
206A ALA* 3.9 22.4 - - + -
207A LEU* 3.7 21.5 - - + -
210A ILE* 3.8 27.8 - - + -
224A VAL* 2.9 21.6 + - + +
225A LYS 3.6 4.3 - - - +
227A TYR* 1.3 81.4 - - + +
229A ASN* 1.3 51.9 + - - +
231A LEU* 3.1 6.7 + - - +
232A ILE* 2.8 37.1 + - + +
281A LEU* 4.4 1.3 - - + -
284A LEU* 4.0 25.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 229 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A LEU* 3.6 25.6 - - - +
225A LYS* 2.9 28.7 + - - +
226A ASP* 3.9 9.1 + - - +
228A ILE* 1.3 72.7 - - - +
230A LEU* 1.3 64.0 + - - +
232A ILE* 3.6 12.1 - - - +
233A ASP* 3.1 23.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 230 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A ASP 2.9 18.9 + - - +
227A TYR* 3.4 14.8 - - + +
229A ASN* 1.3 77.3 - - - +
231A LEU* 1.3 57.1 + - - +
233A ASP* 3.4 6.2 + - - +
234A TYR* 3.1 24.2 + - + +
251A PRO* 3.5 38.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 231 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A ILE* 4.5 7.2 - - + -
203A LEU* 3.8 30.7 - - + -
227A TYR* 2.8 42.8 + - + +
228A ILE* 3.4 9.2 - - - +
230A LEU* 1.3 75.5 - - - +
232A ILE* 1.3 60.2 + - - +
234A TYR* 3.3 6.3 + - + +
235A MET* 2.9 36.4 + - - +
250A MET* 3.6 28.9 - - + -
251A PRO* 3.9 18.4 - - + +
284A LEU* 4.1 9.4 - - + -
301A LEU* 4.0 11.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 232 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200A ARG* 5.1 16.8 - - + +
203A LEU* 3.9 26.0 - - + -
204A GLU* 4.4 17.5 - - + +
207A LEU* 3.9 19.1 - - + -
228A ILE* 2.8 25.2 + - + +
229A ASN* 3.6 26.2 - - - +
230A LEU 3.3 0.2 - - - -
231A LEU* 1.3 72.7 - - - +
233A ASP* 1.3 65.4 + - - +
235A MET* 3.2 6.6 + - - +
236A SER* 3.0 23.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 233 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A ASN 3.1 17.4 + - - +
230A LEU* 3.7 7.4 - - - +
232A ILE* 1.3 77.2 - - - +
234A TYR* 1.3 63.8 + - - +
236A SER* 2.5 27.1 + - - -
237A LYS* 3.2 39.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 234 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230A LEU* 3.1 15.4 + - + +
231A LEU* 3.5 11.9 - - + +
232A ILE 3.3 0.2 - - - -
233A ASP* 1.3 77.9 + - - +
235A MET* 1.3 71.6 + - + +
237A LYS* 3.3 22.7 + - + +
238A LEU* 3.9 18.7 + - + +
247A LEU* 3.7 22.0 - - - +
249A LEU* 3.4 18.6 + - + -
250A MET* 4.2 5.5 - - + -
251A PRO* 3.7 39.7 - - + -
301A LEU* 4.3 19.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 235 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A ILE* 3.2 29.6 - - - +
199A SER 4.6 0.2 - - - -
200A ARG* 3.8 22.7 - - + +
203A LEU* 3.7 29.2 - - - -
231A LEU* 2.9 16.8 + - - +
232A ILE* 3.2 5.4 + - - +
234A TYR* 1.3 73.7 - - + +
236A SER* 1.3 61.0 + - - +
237A LYS 3.1 5.4 - - - -
238A LEU* 3.2 29.0 + - + +
299A GLY* 3.3 29.7 - - - +
300A SER* 3.8 2.0 - - - -
301A LEU* 3.8 35.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 236 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232A ILE* 3.0 13.8 + - - -
233A ASP* 2.5 31.6 + - - -
235A MET* 1.3 75.5 - - - +
237A LYS* 1.3 63.3 + - - +
238A LEU 3.4 3.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 237 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A ASP* 3.2 42.3 + - - +
234A TYR* 3.3 12.0 + - + +
235A MET 3.1 1.2 - - - -
236A SER* 1.3 79.0 - - - +
238A LEU* 1.3 65.1 + - - +
239A ILE* 3.5 9.2 + - - +
----------------------------------------------------------
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