Contacts of the helix formed by residues 1404 - 1415 (chain A) in PDB entry 2NVX
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 GLU1404 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1386A ARG* 3.3 48.9 + - + +
1390A ASN* 5.6 4.1 - - - +
1399A ARG 5.3 2.1 + - - -
1400A CYS 5.0 0.4 - - - -
1402A PHE* 5.0 1.0 - - - -
1403A GLU* 1.3 77.8 - - - +
1405A THR* 1.3 60.4 + - - +
1407A GLU* 3.1 31.6 - - + +
1408A ILE* 3.2 32.3 + - + +
15T A 3.9 15.5 + - - +
16T C 4.5 7.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR1405 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329A LEU* 4.2 10.8 - - + +
330A LYS* 4.9 0.9 - - - -
331A GLY* 4.2 14.5 + - - -
336A ILE* 4.0 31.2 - - + -
1400A CYS* 3.2 43.0 + - + +
1402A PHE 3.8 13.3 + - - -
1403A GLU 3.2 6.1 + - - -
1404A GLU* 1.3 73.8 - - - +
1406A VAL* 1.3 68.0 + - - +
1407A GLU* 3.4 1.2 + - - -
1408A ILE* 3.7 0.5 - - - +
1409A LEU* 3.3 22.5 + - + +
16T C 5.3 0.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1406 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326A ARG* 3.4 56.8 - - + +
329A LEU* 4.6 12.1 - - + -
330A LYS* 4.6 9.2 - - + +
1405A THR* 1.3 74.9 - - - +
1407A GLU* 1.3 76.6 + - - +
1409A LEU* 2.9 24.8 + - + +
1410A PHE* 3.0 35.0 + - + -
1210B MET* 4.1 14.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1407 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326A ARG* 3.6 21.4 + - - -
1404A GLU* 3.1 38.2 - - + +
1405A THR 3.4 0.7 + - - -
1406A VAL* 1.3 94.1 + - - +
1408A ILE* 1.3 57.6 + - + +
1410A PHE* 2.8 34.6 + - + +
1411A GLU* 2.9 26.0 + - - +
15T A 5.6 6.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1408 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1390A ASN* 4.3 11.9 - - + +
1396A ALA* 3.7 32.1 - - + +
1399A ARG* 3.7 40.8 - - + +
1400A CYS* 3.9 14.8 - - - +
1404A GLU* 3.2 31.1 + - + +
1405A THR 3.7 4.0 - - - +
1406A VAL 3.2 0.4 - - - -
1407A GLU* 1.3 76.8 - - + +
1409A LEU* 1.3 63.4 + - - +
1411A GLU* 3.4 20.6 - - - +
1412A ALA* 3.2 23.2 + - - +
1417A GLU* 4.3 1.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1409 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A PHE* 4.4 19.6 - - + -
329A LEU* 4.0 17.3 - - + -
336A ILE* 5.4 0.7 - - + -
1397A LEU* 5.0 4.5 - - + -
1400A CYS* 3.2 24.0 - - - -
1405A THR* 3.3 20.4 - - + +
1406A VAL* 2.9 19.3 + - + +
1408A ILE* 1.3 78.4 - - - +
1410A PHE* 1.3 63.8 - - + +
1412A ALA* 3.3 7.7 - - - +
1413A GLY* 3.1 14.0 + - - -
1203B LEU* 5.3 5.6 - - + -
1207B LEU* 3.7 45.8 - - + -
1210B MET* 5.8 0.7 - - + -
1212B ILE* 4.0 15.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1410 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A HIS* 3.8 21.3 - + - -
93A VAL* 6.3 0.2 - - + -
94A GLY* 3.9 27.8 - - - +
95A PHE* 3.5 29.4 - + + -
304A MET* 5.2 6.1 - - + -
305A ASP* 5.5 7.2 - - + -
326A ARG* 5.5 1.1 - - + -
1406A VAL* 3.0 22.9 + - + -
1407A GLU* 2.8 32.6 + - + +
1409A LEU* 1.3 70.7 - - + +
1411A GLU* 1.3 55.5 + - - +
1413A GLY* 2.6 27.7 + - - -
1414A ALA 3.1 7.1 + - - -
1210B MET* 3.6 39.0 - - + -
1212B ILE* 3.5 17.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1411 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A PHE* 4.5 2.0 - - - -
98A LYS* 4.1 23.1 + - - +
132A LYS* 4.7 13.3 + - + -
1407A GLU* 2.9 20.1 + - - +
1408A ILE* 3.4 34.9 + - + +
1410A PHE* 1.3 76.7 - - - +
1412A ALA* 1.3 56.6 + - - +
1413A GLY 3.2 0.2 - - - -
1414A ALA* 3.5 9.6 - - - -
1415A SER* 2.7 38.1 + - - +
1417A GLU* 4.0 9.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1412 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A PHE* 3.1 41.3 - - + +
1396A ALA* 3.9 4.3 - - + -
1408A ILE 3.2 21.4 + - - +
1409A LEU 3.3 4.9 - - - +
1410A PHE 3.0 0.4 + - - -
1411A GLU* 1.3 78.3 - - - +
1413A GLY* 1.3 59.7 + - - +
1416A ALA 3.4 0.9 + - - -
1417A GLU* 3.1 47.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY1413 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A PHE* 3.8 2.2 - - - +
20A GLY* 3.1 45.4 - - - +
21A LEU* 3.4 8.1 - - - +
229A SER* 3.2 15.2 + - - -
1409A LEU 3.1 8.0 + - - -
1410A PHE 2.6 17.7 + - - -
1412A ALA* 1.3 73.2 - - - +
1414A ALA* 1.3 54.5 + - - -
1416A ALA 4.1 0.2 - - - -
1212B ILE* 4.6 4.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1414 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A LEU* 4.5 7.2 - - + -
95A PHE* 3.6 29.4 - - + -
98A LYS* 4.5 15.9 - - + +
223A GLY 3.0 14.8 - - - +
224A PHE* 3.5 19.3 - - + -
229A SER* 3.1 17.1 + - - -
234A MET* 5.8 1.6 - - + -
1410A PHE 3.1 3.2 + - - -
1411A GLU* 3.1 11.4 + - - +
1413A GLY* 1.3 76.0 - - - +
1415A SER* 1.3 57.5 + - - +
1416A ALA 3.2 4.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER1415 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A LYS* 3.6 19.8 + - - -
131A SER* 4.2 27.7 + - - -
132A LYS* 4.6 15.8 - - - +
223A GLY* 3.5 18.6 + - - -
224A PHE 4.9 1.7 + - - +
1411A GLU* 2.7 21.8 + - - +
1414A ALA* 1.3 70.0 - - - +
1416A ALA* 1.3 69.8 + - - +
1417A GLU* 3.3 13.5 + - - +
----------------------------------------------------------
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