Contacts of the helix formed by residues 205 - 214 (chain A) in PDB entry 3VAS
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 ASN 205 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A ILE* 3.9 24.6 - - + +
172A ASN* 3.7 19.2 + - - +
200A PHE* 4.2 4.0 - - - +
201A LEU* 2.8 30.9 + - + +
204A PHE* 1.3 91.6 + - - +
206A THR* 1.3 63.7 + - - +
207A LYS 3.3 3.1 - - - -
208A GLU* 3.2 29.4 + - - +
209A VAL* 3.0 19.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 206 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A LEU 3.5 1.3 + - - -
202A SER* 2.6 26.3 + - - +
203A GLN 3.3 13.2 + - - -
204A PHE 3.6 1.0 - - - -
205A ASN* 1.3 73.7 - - - +
207A LYS* 1.3 64.3 + - - +
209A VAL* 3.2 4.9 + - + +
210A ASP* 3.0 27.3 + - - +
229A TYR* 5.8 0.4 - - + -
232A VAL* 3.6 16.0 - - + +
233A HIS* 3.7 32.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 207 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A TYR* 5.2 4.0 - - - -
205A ASN 3.3 0.6 - - - -
206A THR* 1.3 78.3 - - - +
208A GLU* 1.3 83.1 + - + +
210A ASP* 3.9 4.2 - - - +
211A GLU* 3.0 47.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 208 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A ILE* 3.6 26.1 - - + +
175A TYR* 3.6 43.5 + - + +
205A ASN* 3.2 38.9 + - - +
207A LYS* 1.3 92.9 + - + +
209A VAL* 1.3 65.3 + - - +
211A GLU 3.4 0.2 + - - -
212A MET* 3.0 29.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 209 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A GLY* 6.1 0.2 - - - -
171A ILE* 3.9 18.8 - - + -
194A PHE* 4.1 9.6 - - + -
196A LEU* 3.8 30.1 - - + +
201A LEU* 3.6 28.0 - - + +
202A SER* 4.1 8.1 - - - +
205A ASN 3.0 18.5 + - - +
206A THR* 3.7 8.1 - - - +
208A GLU* 1.3 75.8 - - - +
210A ASP* 1.3 57.7 + - - +
212A MET* 3.3 3.6 + - - +
213A ILE* 2.9 37.4 + - + +
229A TYR* 4.1 12.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 210 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A THR* 3.0 22.2 + - - +
207A LYS* 4.0 4.0 - - - +
209A VAL* 1.3 74.5 - - - +
211A GLU* 1.3 65.8 + - - +
213A ILE* 3.5 8.3 + - - +
214A SER* 3.2 20.4 + - - -
229A TYR* 2.6 35.0 + - - -
233A HIS* 2.8 26.7 + - - -
246A TYR* 5.1 1.4 + - - -
250A LEU* 4.1 13.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 211 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A TYR* 2.4 40.2 + - - +
179A LEU* 3.9 20.1 - - + +
183A LYS* 5.3 1.7 + - - -
207A LYS* 3.0 30.5 + - + +
208A GLU 3.8 0.2 - - - +
210A ASP* 1.3 77.6 - - - +
212A MET* 1.3 58.7 + - - +
214A SER* 2.6 26.1 + - - +
215A TYR* 3.1 28.8 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 212 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A ILE* 4.7 1.6 - - + -
175A TYR* 3.8 26.0 - - + -
178A MET* 3.6 39.5 - - + +
179A LEU* 4.5 10.1 - - - -
182A ALA* 4.0 6.7 - - + -
192A PHE* 3.4 37.9 - - + -
194A PHE* 3.7 27.6 - - + -
208A GLU 3.0 21.7 + - - +
209A VAL 3.6 4.0 - - - +
211A GLU* 1.3 73.5 - - - +
213A ILE* 1.3 61.3 + - - +
215A TYR* 2.9 15.4 + - - +
216A SER* 2.7 21.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 213 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A PHE* 4.3 14.4 - - + -
196A LEU* 4.4 3.1 - - + -
209A VAL* 2.9 26.1 + - + +
210A ASP* 3.7 7.9 - - - +
211A GLU 3.3 0.2 - - - -
212A MET* 1.3 75.1 - - - +
214A SER* 1.3 58.8 + - - +
216A SER* 3.0 25.6 + - - +
219A VAL* 4.4 6.1 - - + -
229A TYR* 3.8 34.5 - - + +
247A ILE* 3.8 28.0 - - + -
250A LEU* 3.8 17.5 - - + -
260A ARG* 3.1 39.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 214 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A LEU* 4.3 0.5 - - - +
210A ASP 3.2 12.0 + - - -
211A GLU* 2.6 23.0 + - - +
212A MET 3.1 1.6 - - - -
213A ILE* 1.3 76.6 - - - +
215A TYR* 1.3 68.1 + - - +
250A LEU* 5.7 2.0 - - - -
251A PRO 3.5 22.7 - - - -
252A PHE* 3.2 13.7 - - - -
253A ALA* 2.9 35.6 + - - +
260A ARG* 4.3 1.3 - - - +
----------------------------------------------------------
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