Contacts of the helix formed by residues 203 - 220 (chain A) in PDB entry 2VLA
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 THR 203 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A ARG* 3.7 38.9 + - - +
201A LYS 4.0 0.4 + - - -
202A GLU* 1.3 76.2 + - - +
204A SER* 1.3 57.9 + - - +
206A SER* 3.0 7.6 + - - +
207A MET* 2.8 41.1 + - + +
202M C 6.1 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 204 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A ARG* 3.7 11.0 + - - -
202A GLU* 4.3 1.1 - - - +
203A THR* 1.3 79.0 - - - +
205A TYR* 1.3 65.7 + - - +
207A MET* 5.4 0.2 - - - -
208A GLN* 3.0 44.4 + - - +
209A HIS* 4.6 0.9 + - - -
108L G 4.6 1.6 + - - -
109L T 2.8 42.9 + - - +
110L G 5.1 0.2 - - - -
203M C 3.7 19.3 - - - +
204M A 4.3 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 205 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A ARG* 2.9 76.8 + - - +
15A ARG* 4.3 4.3 - - - +
198A HIS* 3.8 24.7 - + + -
201A LYS* 3.8 33.7 - - + -
202A GLU* 3.1 12.2 + - - +
204A SER* 1.3 82.3 + - - +
206A SER* 1.3 61.1 + - - +
209A HIS* 3.4 4.2 - - - -
107L C 4.1 19.4 + - - -
108L G 3.6 35.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 206 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A ASN* 5.0 0.3 - - - +
196A VAL* 3.4 28.2 - - - +
197A ARG* 3.5 4.7 - - - -
198A HIS* 2.7 46.0 + - - +
201A LYS* 4.9 1.2 + - - +
202A GLU 3.6 8.0 + - - -
203A THR* 3.0 10.6 + - - -
205A TYR* 1.3 79.5 - - - +
207A MET* 1.3 60.7 + - - +
209A HIS* 3.4 14.7 + - - -
210A ILE* 3.7 13.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 207 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A LYS* 3.8 43.7 - - + +
158A ASP* 4.1 11.4 - - - +
161A ALA* 3.5 29.6 - - + -
196A VAL* 4.1 9.6 - - - +
197A ARG* 3.8 23.1 - - - +
203A THR* 2.8 23.4 + - + +
206A SER* 1.3 85.4 - - - +
208A GLN* 1.3 66.2 + - - +
209A HIS 3.2 3.1 - - - -
210A ILE* 3.0 16.9 + - + +
211A ARG* 2.8 24.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 208 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A ARG* 3.3 28.5 + - + +
203A THR 4.1 0.4 + - - -
204A SER* 3.0 28.0 + - - +
207A MET* 1.3 78.2 - - - +
209A HIS* 1.3 58.7 + - - +
211A ARG* 3.5 6.6 + - + +
212A GLU* 2.9 64.1 + - + +
203M C 3.4 23.5 - - + +
204M A 2.9 49.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 209 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A ARG* 3.7 26.8 + - + +
11A CYS 3.4 27.9 + - - -
12A THR* 3.6 11.8 - - + +
13A ILE* 3.6 35.9 - - + +
15A ARG* 6.0 1.0 + - - +
165A LEU 5.7 1.3 + - - -
166A ASN* 4.5 3.0 + - - -
204A SER 4.7 0.8 + - - -
205A TYR 3.4 26.2 + - - -
206A SER 3.4 18.5 + - - -
208A GLN* 1.3 77.0 + - - +
210A ILE* 1.3 77.6 + - + +
212A GLU* 3.9 4.5 - - - +
213A GLN* 3.0 36.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 210 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A LYS 4.8 2.2 - - - +
161A ALA* 3.8 48.0 - - + +
165A LEU* 4.0 25.5 - - + +
166A ASN* 4.3 16.4 - - + +
196A VAL* 4.7 1.6 - - + -
206A SER 3.7 19.5 - - - +
207A MET* 3.0 16.7 + - + +
209A HIS* 1.3 96.8 - - + +
211A ARG* 1.3 67.4 + - - +
212A GLU 3.3 0.2 + - - -
213A GLN* 3.4 9.3 + - - +
214A LEU* 3.2 28.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 211 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A LYS* 3.9 35.1 - - + +
207A MET* 2.8 17.4 + - + +
208A GLN* 3.8 7.2 - - + +
210A ILE* 1.3 76.5 - - - +
212A GLU* 1.3 59.3 + - + +
214A LEU* 3.1 5.3 + - - +
215A ASN* 2.8 46.6 + - - +
218A GLU* 5.2 3.6 + - - -
225A ILE* 4.0 26.4 + - - +
202M C 2.8 47.5 + - + +
203M C 4.0 24.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 212 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A ILE* 4.4 4.7 - - + -
14A ILE 4.0 3.6 - - - +
15A ARG* 3.8 7.1 - - - -
16A GLY* 2.9 32.1 + - - -
19A LYS* 6.0 0.7 - - - +
208A GLN* 2.9 52.4 + - + +
209A HIS* 4.3 4.5 - - - +
211A ARG* 1.3 77.0 - - + +
213A GLN* 1.3 66.3 + - - +
215A ASN* 3.1 21.8 + - - +
216A TYR* 3.0 42.3 + - + +
203M C 3.5 18.9 - - - +
204M A 4.9 0.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 213 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A CYS 4.3 8.7 + - - -
13A ILE* 3.7 30.0 - - + +
113A PHE* 5.9 0.2 - - + -
115A PHE* 3.5 12.1 - - - -
137A GLN* 3.0 35.0 + - - +
138A PHE* 3.1 37.4 - - + -
165A LEU* 3.7 27.5 + - + +
209A HIS* 3.0 29.0 + - - +
210A ILE* 3.6 6.6 - - - +
212A GLU* 1.3 76.5 - - - +
214A LEU* 1.3 62.3 + - - +
216A TYR* 3.1 13.6 + - - +
217A LEU 3.3 2.6 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
141A ILE* 4.4 20.4 - - + -
157A LYS* 3.9 31.9 - - + -
160A ILE* 4.2 34.8 - - + -
165A LEU* 5.0 2.5 - - + -
210A ILE* 3.2 15.6 + - + +
211A ARG* 3.1 8.9 + - - +
213A GLN* 1.3 76.2 - - - +
215A ASN* 1.3 63.6 + - - +
217A LEU* 3.1 5.6 + - + -
218A GLU* 2.9 18.9 + - - +
223A ILE* 3.5 23.5 - - + +
225A ILE* 3.7 15.9 - - + -
230A VAL* 4.2 15.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 215 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A LYS* 3.9 31.8 - - + +
211A ARG* 2.8 44.2 + - - +
212A GLU* 3.1 28.0 + - + +
214A LEU* 1.3 73.2 - - - +
216A TYR* 1.3 62.9 + - + +
218A GLU* 3.2 11.2 + - - +
219A LEU* 2.8 32.2 + - - +
225A ILE* 3.7 5.1 - - - +
203M C 3.0 25.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 216 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A ILE* 3.8 22.9 - - + -
14A ILE 5.2 0.2 + - - -
16A GLY* 4.2 13.7 - - - -
19A LYS* 5.5 5.4 - - + +
76A LEU* 3.4 30.7 - - + +
77A PHE* 4.1 12.8 - + - -
106A PHE* 3.7 36.3 - + + +
109A ILE* 4.9 8.1 - - + -
110A CYS* 3.7 15.4 - - - -
113A PHE* 5.4 5.4 - + - -
138A PHE* 4.7 5.2 - + + -
212A GLU* 3.0 31.9 + - + +
213A GLN* 3.1 12.0 + - - +
215A ASN* 1.3 80.8 - - + +
217A LEU* 1.3 57.2 + - - +
219A LEU* 3.4 16.6 + - + +
220A ALA* 3.0 27.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 217 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A CYS* 3.8 22.6 - - + -
138A PHE* 3.9 17.7 - - + -
141A ILE* 3.9 24.0 - - + -
142A LEU* 3.7 31.2 - - + -
213A GLN 3.3 10.0 + - - +
214A LEU* 3.1 12.0 + - + +
216A TYR* 1.3 77.9 - - - +
218A GLU* 1.3 57.3 + - - +
220A ALA* 3.5 6.0 + - - +
222A LEU* 3.1 48.5 + - + -
223A ILE* 3.5 28.3 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 218 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A LYS* 4.7 11.4 + - - -
211A ARG* 5.2 3.6 + - - -
214A LEU 2.9 12.2 + - - +
215A ASN* 3.5 15.1 - - - +
217A LEU* 1.3 75.9 - - - +
219A LEU* 1.3 60.3 + - + +
220A ALA 3.2 0.2 - - - -
221A ASN* 2.9 25.6 + - - +
223A ILE* 3.5 26.6 - - + +
224A ARG* 3.3 31.2 + - - +
225A ILE* 2.9 42.5 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
19A LYS* 3.8 33.4 - - + +
22A LEU* 3.6 34.8 - - + -
102A GLN* 3.8 15.6 + - - +
103A PRO* 3.3 22.3 - - - +
106A PHE* 3.8 19.4 - - + +
215A ASN 2.8 19.2 + - - +
216A TYR* 3.4 25.5 + - + +
218A GLU* 1.3 77.0 - - + +
220A ALA* 1.3 57.3 + - - +
221A ASN* 3.1 5.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 220 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A PRO* 3.5 10.8 - - - -
106A PHE* 3.8 2.4 - - - +
107A LYS* 2.8 64.4 + - + +
110A CYS* 4.6 1.6 - - - -
216A TYR 3.0 16.9 + - - +
217A LEU* 3.6 9.9 - - - +
218A GLU 3.2 0.4 - - - -
219A LEU* 1.3 74.7 - - - +
221A ASN* 1.3 62.6 + - - +
222A LEU* 3.4 12.0 + - + +
----------------------------------------------------------
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