Contacts of the helix formed by residues 214 - 226 (chain A) in PDB entry 2VWJ
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 PHE 214 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A ASP* 5.5 4.7 - - - -
142A ILE* 4.0 25.6 - - + -
144A THR* 4.0 27.4 - - + -
152A PHE* 4.4 13.1 - + - -
209A TYR 5.8 0.7 - - - +
210A ASN* 3.1 22.9 + - + +
213A ASN* 1.3 76.5 - - - +
215A ALA* 1.3 78.6 + - + +
216A PHE 3.4 2.0 - - - -
217A ALA* 2.9 19.5 + - - +
218A TYR* 3.0 31.1 + + - +
----------------------------------------------------------
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
----------------------------------------------------------
140A PHE* 4.4 21.5 - - + +
141A ASP* 5.2 7.4 - - - +
142A ILE* 4.1 23.1 - - + +
208A THR* 5.4 2.0 - - + -
210A ASN 5.1 0.2 - - - -
211A GLY* 4.1 16.2 + - - -
214A PHE* 1.3 83.8 - - + +
216A PHE* 1.3 63.4 + - - +
218A TYR* 3.2 2.1 + - - +
219A LEU* 2.9 31.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 216 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A PHE* 3.5 35.0 - + - -
206A LEU* 4.6 3.4 - - + -
208A THR* 3.8 2.7 - - + -
211A GLY* 3.4 26.9 + - - +
214A PHE 3.1 0.8 + - - -
215A ALA* 1.3 78.8 - - - +
217A ALA* 1.3 57.4 + - - +
219A LEU* 3.9 5.6 - - - +
220A LYS* 3.0 27.0 + - - +
230A PHE* 4.3 8.7 - + - -
232A LEU* 3.6 25.8 - - + -
239A PRO* 3.5 30.7 - - + +
241A ILE* 4.7 4.0 - - + +
250A VAL* 3.6 21.5 - - + -
252A VAL* 3.8 20.2 - - + -
257A HIS* 3.7 29.8 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 217 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A PHE* 3.8 26.1 - - + -
211A GLY 4.7 0.8 + - - -
212A ASP 5.7 2.7 + - - +
213A ASN 4.2 11.9 - - - +
214A PHE 2.9 11.6 + - - +
216A PHE* 1.3 72.9 - - - +
218A TYR* 1.3 69.3 + - - +
220A LYS* 3.3 3.6 + - - +
221A LYS* 3.1 17.0 + - - +
241A ILE* 4.2 20.6 - - + +
250A VAL* 5.4 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 218 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A ILE* 3.8 12.6 - - + -
144A THR* 3.3 35.5 + - + -
145A LEU 3.9 2.9 + - - -
152A PHE* 3.6 24.5 - + - -
153A ALA* 3.4 25.8 - - + +
155A GLY* 2.7 38.3 + - - -
157A ILE* 3.4 29.4 - - + -
214A PHE* 3.0 26.2 + + + +
215A ALA* 3.2 8.0 + - - +
217A ALA* 1.3 74.6 - - - +
219A LEU* 1.3 65.0 + - - +
221A LYS* 2.9 15.2 + - - +
222A ARG* 3.0 22.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 219 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A PHE* 4.0 24.7 - - + -
142A ILE* 4.2 14.6 - - + -
157A ILE* 3.7 27.1 - - + -
160A ILE* 4.1 21.3 - - + -
191A ILE* 4.8 6.7 - - + -
194A PHE* 4.8 5.8 - - + -
215A ALA 2.9 26.7 + - - +
216A PHE* 4.0 3.8 - - - +
218A TYR* 1.3 75.4 - - - +
220A LYS* 1.3 55.4 + - - +
222A ARG* 4.0 1.0 - - - +
223A SER* 2.7 37.5 + - - -
230A PHE* 3.5 39.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 220 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216A PHE 3.0 20.4 + - - +
217A ALA* 3.5 8.7 - - - +
218A TYR 3.0 0.4 + - - -
219A LEU* 1.3 77.5 - - - +
221A LYS* 1.3 66.2 + - + +
223A SER* 3.3 5.2 + - - -
224A GLU* 3.1 45.7 + - - +
230A PHE* 4.6 10.7 - - + -
238A GLU* 4.4 23.4 + - - -
239A PRO* 5.1 10.2 + - + +
241A ILE* 4.2 22.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 221 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A PHE* 4.6 13.5 - - + +
153A ALA* 3.9 22.4 - - + +
217A ALA 3.1 8.6 + - - +
218A TYR 2.9 6.9 + - - +
220A LYS* 1.3 80.5 - - - +
222A ARG* 1.3 57.6 + - - +
224A GLU* 3.2 14.8 + - + +
225A LYS* 3.0 36.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 222 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A ALA* 3.6 15.9 + - + +
154A GLU* 3.9 8.7 + - - +
155A GLY 3.4 18.1 + - - -
156A PRO* 2.9 26.3 - - - +
157A ILE* 3.6 32.5 - - + +
187A GLU* 2.9 26.5 + - - +
191A ILE* 4.2 9.4 - - + -
218A TYR* 3.0 27.6 + - + +
219A LEU 4.0 3.4 - - - +
221A LYS* 1.3 73.9 - - - +
223A SER* 1.3 60.5 + - - +
225A LYS* 3.1 33.3 + - - +
226A LEU* 3.0 37.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 223 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191A ILE* 4.0 15.1 - - - +
219A LEU 2.7 23.2 + - - -
220A LYS 3.3 4.7 + - - -
222A ARG* 1.3 75.1 - - - +
224A GLU* 1.3 57.3 + - - +
226A LEU 4.0 0.4 - - - -
227A GLY* 3.2 5.4 + - - -
228A VAL* 2.9 54.5 + - - +
230A PHE* 3.6 30.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 224 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220A LYS* 3.1 45.5 + - - +
221A LYS* 3.5 15.2 - - + +
222A ARG 3.1 0.2 - - - -
223A SER* 1.3 76.2 - - - +
225A LYS* 1.3 65.3 + - - +
226A LEU 3.2 0.6 + - - -
227A GLY* 3.5 9.1 + - - -
238A GLU* 5.1 2.9 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
153A ALA 5.5 1.3 - - - +
221A LYS* 3.0 25.0 + - + +
222A ARG* 3.1 35.4 + - - +
224A GLU* 1.3 77.3 - - + +
226A LEU* 1.3 69.3 + - + +
227A GLY 3.9 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 226 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A GLU* 3.3 44.4 - - + +
188A LYS* 3.4 48.2 + - + +
191A ILE* 4.6 6.3 - - + -
222A ARG* 3.0 19.3 + - - +
225A LYS* 1.3 92.1 - - + +
227A GLY* 1.3 65.3 + - - +
228A VAL* 3.3 6.6 + - + -
----------------------------------------------------------
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