Contacts of the helix formed by residues 1143 - 1150 (chain B) 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 ALA1143 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
500A GLU* 3.0 39.1 - - + +
501A LEU* 6.1 0.9 - - + -
504A LEU* 4.7 2.2 - - + +
505A CYS* 4.7 7.2 - - - -
1436A ILE* 5.1 1.5 - - - +
1138B MET* 3.0 26.7 + - + +
1139B ILE* 5.5 0.2 - - - -
1141B HIS* 3.1 11.2 + - + -
1142B GLY* 1.3 75.9 - - - +
1144B ALA* 1.3 59.2 + - - +
1146B PHE* 4.4 6.7 - - + -
1147B LEU* 3.5 21.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1144 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
500A GLU* 3.0 3.8 + - - -
1433A MET* 3.7 17.9 - - + +
1434A ALA* 4.2 5.8 - - + +
1436A ILE* 3.3 34.3 - - + +
1438A THR* 3.6 12.0 - - + -
1439A GLY* 3.6 5.4 - - - +
1142B GLY 3.0 5.3 + - - -
1143B ALA* 1.3 71.8 - - - +
1145B SER* 1.3 66.9 + - - +
1146B PHE 3.4 0.2 + - - -
1147B LEU* 3.6 9.5 + - - +
1148B LYS* 3.2 22.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER1145 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496A GLU* 4.0 32.1 - - - +
497A THR* 4.7 3.6 + - - -
500A GLU* 2.8 26.3 + - - -
1433A MET* 3.2 31.1 - - - +
1438A THR* 3.6 5.7 - - - +
1144B ALA* 1.3 72.9 - - - +
1146B PHE* 1.3 60.2 + - - +
1148B LYS* 3.4 6.2 - - - +
1149B GLU* 3.3 19.4 + - - +
92F ARG* 4.7 5.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1146 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443A LEU* 3.4 35.0 - - + -
490A HIS* 4.6 4.0 - - + -
492A PRO* 4.7 7.9 - - + -
497A THR* 3.1 35.6 - - + +
500A GLU* 2.7 21.3 + - + +
501A LEU* 3.8 20.2 - - + -
1130B PHE* 4.3 4.5 - + - -
1138B MET* 3.5 24.2 - - + -
1143B ALA* 4.2 6.3 - - + +
1145B SER* 1.3 69.3 - - - +
1147B LEU* 1.3 63.8 + - - +
1148B LYS 2.8 10.0 + - - -
1149B GLU* 3.0 6.4 + - - +
1150B ARG* 2.8 76.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1147 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1424A VAL* 5.9 0.4 - - + -
1428A VAL* 4.5 17.5 - - + -
1432A GLN 5.3 4.0 - - - +
1434A ALA* 5.2 17.3 - - + +
1436A ILE* 6.5 0.7 - - + -
1130B PHE* 5.2 7.0 - - + -
1135B ARG* 3.3 40.2 - - + +
1138B MET* 3.9 14.4 - - + -
1139B ILE* 3.7 22.2 - - + +
1143B ALA 3.5 15.8 + - - +
1144B ALA* 3.6 8.2 + - - +
1146B PHE* 1.3 85.8 - - - +
1148B LYS* 1.3 63.0 + - + +
1150B ARG* 4.1 6.5 - - - +
1151B LEU* 3.2 29.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1148 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1431A GLY* 4.1 11.0 - - - +
1432A GLN* 3.8 10.3 - - - +
1433A MET* 3.8 40.8 - - + +
1144B ALA 3.2 12.6 + - - +
1145B SER* 3.4 10.5 - - - +
1146B PHE 2.8 1.6 + - - -
1147B LEU* 1.3 77.2 - - + +
1149B GLU* 1.3 85.8 + - - +
1151B LEU* 2.9 19.2 + - - +
1152B MET* 3.0 29.2 + - - +
1153B GLU* 3.2 27.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1149 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
492A PRO* 3.6 4.9 - - - +
493A GLN* 3.2 29.0 + - + +
494A SER* 3.4 18.2 + - - -
497A THR* 3.0 37.8 + - - +
1145B SER 3.3 8.1 + - - +
1146B PHE* 3.0 8.0 + - - +
1148B LYS* 1.3 86.2 - - - +
1150B ARG* 1.3 65.3 + - - +
1151B LEU 2.6 18.3 + - - -
1152B MET 2.8 10.0 + - - -
1153B GLU* 2.9 29.2 + - + +
1154B ALA* 3.1 9.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1150 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345A VAL* 3.6 20.5 - - - +
346A ASP 3.4 8.2 + - - -
347A PHE* 3.4 18.8 + - - +
490A HIS* 2.7 53.0 + - - +
491A VAL 2.9 30.3 + - - -
492A PRO* 4.1 0.6 - - - +
493A GLN* 4.7 3.0 - - - +
1130B PHE* 3.5 27.3 - - + -
1146B PHE* 2.8 42.3 + - + +
1147B LEU* 4.1 3.1 - - - -
1149B GLU* 1.3 83.4 + - + +
1151B LEU* 1.3 66.3 - - - +
1154B ALA* 3.8 21.6 - - - +
----------------------------------------------------------
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