Contacts of the helix formed by residues 195 - 204 (chain A) in PDB entry 1VE3
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 GLY 195 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A PHE* 4.6 1.3 - - - -
144A ASP* 3.4 14.8 - - - -
146A ARG* 3.9 20.2 - - - +
174A ARG* 4.9 1.0 - - - +
193A VAL 4.5 0.2 + - - -
194A TRP* 1.3 77.4 - - - +
196A LYS* 1.3 67.0 + - - -
197A THR* 3.1 4.3 - - - -
198A GLY 2.9 14.9 + - - +
199A VAL* 3.1 14.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 196 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A PHE* 3.8 20.6 - - + -
144A ASP* 2.8 21.8 + - - +
195A GLY* 1.3 71.4 - - - -
197A THR* 1.3 62.2 + - - +
199A VAL* 3.5 1.4 + - - +
200A GLU* 2.7 67.0 + - - +
209A LYS* 3.9 0.8 - - - +
212A GLU* 2.8 30.1 + - - -
220A TYR* 3.4 45.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 197 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A GLY 3.0 1.8 + - - -
196A LYS* 1.3 78.7 - - - +
198A GLY* 1.3 62.3 + - - +
200A GLU* 4.3 4.3 - - - +
201A LEU* 3.3 26.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 198 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A ARG* 6.0 1.7 - - - +
174A ARG* 4.6 9.6 - - - -
194A TRP* 3.9 15.5 - - - -
195A GLY* 2.9 9.5 + - - -
197A THR* 1.3 76.7 - - - +
199A VAL* 1.3 67.0 + - - +
201A LEU* 3.6 9.2 - - - +
202A LEU* 3.4 23.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 199 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A ILE* 4.2 4.9 - - + -
121A LEU* 4.9 5.6 - - + -
125A PHE* 3.7 12.9 - - + -
140A MSE 4.1 26.5 - - + -
142A PHE* 3.7 36.6 - - + -
194A TRP* 3.8 32.1 - - + -
195A GLY 3.1 12.4 + - - +
196A LYS 3.9 5.6 - - - +
198A GLY* 1.3 76.3 - - - +
200A GLU* 1.3 58.6 + - + +
202A LEU* 3.2 3.7 + - - +
203A ALA* 3.0 24.6 + - + +
224A TYR* 5.3 5.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 200 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A PHE* 4.8 4.5 - - - -
196A LYS* 2.7 48.3 + - - +
197A THR* 4.3 4.6 - - - +
199A VAL* 1.3 81.5 - - + +
201A LEU* 1.3 55.7 + - - +
203A ALA* 3.1 6.8 + - - +
204A LYS* 2.8 46.6 + - + +
209A LYS* 3.5 17.0 + - - +
212A GLU* 2.7 24.4 - - - +
222A THR* 4.4 1.4 + - - -
224A TYR* 3.1 20.7 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
197A THR* 3.3 21.7 + - + +
198A GLY* 3.6 9.6 - - - +
200A GLU* 1.3 72.1 - - - +
202A LEU* 1.3 71.7 + - + +
204A LYS* 3.4 26.9 + - + +
205A LEU* 3.7 14.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 202 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A PRO* 3.8 20.9 - - + +
121A LEU* 4.4 6.1 - - + -
122A ASN* 4.4 21.5 - - + +
125A PHE* 3.8 12.8 - - + -
194A TRP* 3.6 33.0 - - + -
198A GLY 3.4 7.4 + - - +
199A VAL 3.2 8.2 + - - +
201A LEU* 1.3 85.9 - - + +
203A ALA* 1.3 65.2 + - - +
205A LEU* 3.2 35.2 + - + +
206A TYR* 3.6 11.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 203 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A PHE* 3.7 17.6 - - + -
199A VAL* 3.0 14.3 + - + +
200A GLU 3.3 8.1 - - - +
202A LEU* 1.3 78.3 - - - +
204A LYS* 1.3 53.0 + - + +
205A LEU 3.0 0.2 - - - -
206A TYR 2.9 5.4 + - - -
207A PHE* 2.8 41.4 + - + +
224A TYR* 3.5 40.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 204 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200A GLU* 2.8 33.5 + - + +
201A LEU* 3.7 21.3 - - + +
202A LEU 3.2 0.4 - - - -
203A ALA* 1.3 74.2 - - + +
205A LEU* 1.3 63.8 - - + +
206A TYR 3.3 0.4 - - - -
207A PHE 3.8 9.4 - - - +
209A LYS* 6.0 4.6 - - - +
224A TYR* 5.6 1.3 - - + -
227A LYS* 3.4 21.3 + - - -
----------------------------------------------------------
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