Contacts of the helix formed by residues 157 - 160 (chain A) in PDB entry 2CVP
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 ILE 157 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A GLY* 1.3 75.2 - - - +
158A GLY* 1.3 76.7 + - - +
159A GLY 3.2 0.9 + - - -
160A SER* 3.1 15.3 + - - -
161A ASP* 3.8 4.7 - - - -
185A SER 3.3 24.7 - - - +
215A THR* 3.8 22.0 - - + -
217A GLU* 4.1 8.1 - - + -
218A THR* 3.6 15.7 + - - +
801A ACT 4.2 12.0 - - + +
385B THR* 3.7 18.4 - - - +
386B ASN* 3.9 24.5 - - - +
389B HIS* 3.5 37.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 158 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A ILE* 1.3 78.6 - - - +
159A GLY* 1.3 58.5 + - - -
161A ASP* 2.9 7.9 + - - +
162A LEU* 2.9 33.9 + - - +
354A GLN* 3.1 10.9 - - - +
801A ACT 5.9 0.4 - - - -
386B ASN* 5.2 2.4 + - - +
389B HIS* 3.5 29.8 - - - -
390B ALA* 5.7 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 159 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A ILE 3.2 2.2 + - - -
158A GLY* 1.3 70.3 - - - -
160A SER* 1.3 59.9 + - - +
161A ASP 3.2 1.6 + - - -
162A LEU* 4.6 1.8 - - - -
163A GLY* 4.6 3.7 + - - -
164A PRO* 4.4 5.9 - - - +
272A GLY* 3.3 31.1 - - - +
273A ARG* 4.2 1.6 - - - -
275A SER* 3.2 17.0 + - - -
276A LEU 5.2 1.0 + - - -
280A ILE* 3.8 5.5 - - - +
354A GLN* 3.2 18.4 + - - +
801A ACT 5.5 4.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 160 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A ASN* 3.1 21.3 + - - -
156A GLY* 4.2 0.3 - - - -
157A ILE 3.1 16.9 + - - -
158A GLY 3.1 1.2 - - - -
159A GLY* 1.3 76.0 - - - +
161A ASP* 1.3 57.6 + - - +
164A PRO* 4.1 10.2 - - - +
209A ALA* 3.3 34.6 + - - +
210A SER* 3.8 0.5 - - - -
211A LYS* 4.1 1.2 + - - +
266A PHE* 5.4 0.2 - - - -
272A GLY* 6.0 0.5 - - - -
275A SER* 5.3 0.3 + - - -
280A ILE* 3.6 23.0 - - - +
801A ACT 3.0 22.9 + - - -
----------------------------------------------------------
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