Contacts of the helix formed by residues 198 - 208 (chain A) in PDB entry 2VPI
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 198 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A LEU* 3.5 21.8 - - + +
144A GLN* 6.1 0.2 - - - +
147A GLU* 2.9 32.6 + - - +
148A VAL 4.8 0.6 + - - -
196A THR* 3.4 2.5 - - - +
197A GLU* 1.3 95.9 - - - +
199A GLY* 1.3 63.0 + - - +
200A LYS* 3.3 3.1 - - - +
201A VAL* 3.3 27.0 + - + +
202A ILE* 3.4 19.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 199 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191A PRO* 3.2 35.1 - - - +
196A THR* 3.0 20.2 + - - +
197A GLU 3.5 0.8 + - - -
198A ASN* 1.3 74.1 - - - +
200A LYS* 1.3 63.3 + - - +
202A ILE* 3.4 5.9 + - - +
203A LEU* 3.2 28.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 200 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A ARG* 2.6 56.6 + - - +
47A GLU* 3.3 27.2 + - - +
48A LEU* 3.5 28.4 - - + +
191A PRO 4.1 0.6 + - - +
197A GLU 5.2 0.8 + - - +
198A ASN* 3.3 1.1 - - - +
199A GLY* 1.3 73.6 - - - +
201A VAL* 1.3 63.1 + - + +
203A LEU* 3.4 6.9 + - + +
204A LYS* 2.9 30.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 201 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A ARG 3.6 23.8 - - - +
142A GLY* 4.9 5.6 - - - +
143A LEU* 3.8 16.4 - - + -
198A ASN* 3.3 28.8 + - + +
200A LYS* 1.3 76.5 - - + +
202A ILE* 1.3 57.4 + - - +
204A LYS* 3.3 13.5 + - + +
205A ASN* 2.9 37.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 202 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A LEU* 5.3 4.5 - - + -
139A LEU* 3.5 38.9 - - + +
140A PHE* 3.8 13.0 - - + -
143A LEU* 3.8 27.1 - - + -
147A GLU* 6.3 0.7 - - + -
149A VAL* 5.6 1.3 - - + -
189A PHE* 3.8 28.7 - - + -
191A PRO* 4.1 17.7 - - + -
196A THR* 4.8 2.7 - - + -
198A ASN* 3.4 18.0 + - + +
199A GLY* 3.6 12.6 - - - +
200A LYS 3.3 0.2 - - - -
201A VAL* 1.3 76.7 - - - +
203A LEU* 1.3 58.1 + - + +
205A ASN* 3.4 4.2 + - - +
206A PHE 3.1 22.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 203 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A ILE* 5.6 4.0 - - + -
44A ARG* 3.8 32.8 - - + -
45A VAL* 5.9 2.7 - - + -
48A LEU* 4.0 13.7 - - + -
73A ILE* 5.1 9.9 - - + -
101A LEU* 3.9 26.0 - - + -
103A ILE* 4.8 5.4 - - + -
191A PRO* 3.7 31.0 - - + +
192A GLU* 4.1 3.6 - - + +
199A GLY 3.2 21.2 + - - +
200A LYS* 3.8 9.6 - - + +
201A VAL 3.3 0.2 - - - -
202A ILE* 1.3 73.0 - - - +
204A LYS* 1.3 56.2 + - - +
206A PHE* 3.3 5.9 + - + +
207A LEU* 2.8 45.1 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
48A LEU* 3.7 25.7 - - + +
200A LYS 2.9 17.9 + - - +
201A VAL* 3.5 12.6 - - + +
203A LEU* 1.3 73.6 - - - +
205A ASN* 1.3 61.8 + - - +
207A LEU* 4.9 0.7 - - - -
208A TYR* 2.8 73.3 + - + +
209A ASP* 5.3 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 205 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A SER 3.5 15.9 - - - +
139A LEU* 2.8 30.6 + - - +
140A PHE* 3.9 1.2 - - - +
141A ARG* 2.9 37.3 + - - +
201A VAL* 2.9 27.2 + - - +
202A ILE* 3.4 4.0 - - - +
204A LYS* 1.3 72.9 - - - +
206A PHE* 1.3 58.4 + - - +
209A ASP* 3.1 27.5 + - - +
210A ILE* 2.9 29.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 206 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A ALA* 4.0 17.0 - - + -
72A ILE 3.5 12.6 - - - -
73A ILE* 4.0 11.9 - - + -
99A PRO* 3.8 20.0 - - + -
100A VAL 3.5 14.1 - - - -
101A LEU* 3.3 56.1 - - + -
139A LEU* 3.7 16.8 - - + -
185A TYR* 4.6 7.0 - + - -
202A ILE 3.1 9.2 + - - +
203A LEU* 3.3 6.9 + - + +
205A ASN* 1.3 76.6 - - - +
207A LEU* 1.3 73.7 + - + +
210A ILE* 3.4 22.5 - - + +
211A ALA* 2.8 30.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 207 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A VAL* 3.6 36.3 - - + -
45A VAL* 4.2 26.2 - - + -
48A LEU* 3.7 30.7 - - + -
50A VAL* 4.2 15.9 - - + -
71A ALA* 5.6 0.2 - - + -
73A ILE* 4.5 8.3 - - + -
203A LEU* 2.8 23.3 + - + +
204A LYS* 4.3 0.7 - - - +
206A PHE* 1.3 91.3 - - + +
208A TYR* 1.3 66.6 + - + +
211A ALA* 3.4 6.0 - - - +
212A GLY 3.2 7.1 + - - -
213A CYS* 2.9 28.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 208 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A LEU* 2.6 40.3 + - + +
49A PHE* 4.5 3.3 - - - -
50A VAL* 3.9 10.5 - - + -
204A LYS* 2.8 54.3 + - + +
207A LEU* 1.3 80.5 - - + +
209A ASP* 1.3 69.5 + - - +
212A GLY* 2.9 27.4 + - - -
213A CYS 3.4 16.5 - - - +
215A GLY* 3.4 29.5 + - - -
----------------------------------------------------------
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