Contacts of the helix formed by residues 1388 - 1392 (chain A) in PDB entry 2NVT
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 GLY1388 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1378A GLN* 5.4 0.2 + - - -
1382A THR* 4.3 14.2 - - - +
1383A SER* 3.0 28.2 + - - -
1385A THR 2.8 6.0 + - - -
1387A HIS* 1.3 79.6 - - - +
1389A PHE* 1.3 68.3 + - - +
1390A ASN 3.0 2.7 + - - -
1391A ARG* 3.0 22.0 + - - +
1392A SER* 3.8 1.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1389 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
840A ARG 3.9 3.8 - - - -
843A LYS 3.5 21.1 - - - -
844A ALA* 3.6 34.3 - - + +
1374A VAL* 5.6 8.3 - - + -
1378A GLN* 5.1 5.4 - - - -
1382A THR* 4.7 3.5 - - - -
1383A SER 3.2 4.5 + - - +
1384A VAL* 3.3 41.7 - - + -
1385A THR* 3.4 10.8 - - - -
1388A GLY* 1.3 70.1 - - - -
1390A ASN* 1.3 80.5 + - + +
1392A SER* 3.0 27.8 + - - +
1394A THR* 4.8 4.2 + - - -
1398A MET* 5.8 4.5 - - + -
1399A ARG* 5.1 0.7 - - - +
1402A PHE* 3.7 37.9 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN1390 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1385A THR 3.9 0.4 + - - -
1386A ARG* 3.8 26.9 + - - +
1388A GLY 3.0 2.4 + - - -
1389A PHE* 1.3 90.1 - - + +
1391A ARG* 1.3 59.4 + - - +
1392A SER 4.2 0.2 - - - -
1398A MET* 5.8 1.0 - - - +
1399A ARG* 3.0 61.0 + - - +
1402A PHE* 3.7 25.7 - - + +
1403A GLU 3.6 17.0 + - - -
1404A GLU* 5.4 1.6 + - - +
1408A ILE* 4.3 16.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1391 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A LYS* 4.4 6.6 + - - -
133A LYS* 3.3 52.6 + - - +
1378A GLN* 4.4 19.2 - - - +
1382A THR* 5.5 2.7 - - - -
1386A ARG 3.8 10.5 + - - +
1387A HIS* 3.8 22.9 - - - +
1388A GLY* 3.0 24.2 + - - +
1390A ASN* 1.3 74.0 - - - +
1392A SER* 1.3 69.2 + - - +
1399A ARG* 5.2 1.9 + - - +
1408A ILE* 6.1 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER1392 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A LYS* 5.3 0.4 - - - +
860A LEU* 4.9 4.2 - - - +
1378A GLN* 4.4 22.4 - - - +
1388A GLY 3.8 3.0 + - - -
1389A PHE* 3.0 17.8 + - - -
1391A ARG* 1.3 89.5 - - - +
1393A ASN* 1.3 63.9 + - - +
1394A THR* 3.3 16.0 + - - -
1399A ARG* 2.9 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