Contacts of the helix formed by residues 1461 - 1468 (chain N) in PDB entry 4G7H
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 GLY1461 (chain N).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1103N HIS* 4.1 0.4 - - - -
1104N GLU* 3.7 25.7 + - - -
1108N ARG* 5.0 0.9 - - - -
1460N ILE* 1.3 79.5 - - - +
1462N LEU* 1.3 56.7 + - - -
1464N GLU* 3.0 24.5 + - - +
1465N ASN* 2.5 34.3 + - - -
1473N PRO* 3.7 5.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1462 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1041M GLU* 3.8 28.9 - - + +
1103N HIS* 3.2 35.8 + - + +
1104N GLU* 5.6 0.2 - - - -
1106N VAL* 4.4 7.2 - - + -
1220N ALA* 4.2 11.7 - - + -
1223N ILE* 3.7 26.5 - - + -
1461N GLY* 1.3 70.0 - - - +
1463N LYS* 1.3 68.4 + - + +
1464N GLU 3.2 1.8 - - - -
1465N ASN* 2.9 15.6 + - - +
1466N VAL* 2.9 16.7 + - - +
1472N ILE* 4.0 13.9 - - + +
1473N PRO* 3.8 26.9 - - + -
1474N ALA* 4.1 15.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1463 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1034M GLU* 5.7 0.4 + - - -
1038M TRP* 6.2 2.0 - - - +
1041M GLU* 5.2 2.2 - - - +
619N LEU* 3.8 23.6 - - + +
1096N ARG* 4.8 2.4 - - - +
1099N VAL* 5.5 4.9 - - + +
1100N ASP* 2.5 37.5 + - - +
1103N HIS* 3.3 37.5 + - + +
1436N SER* 3.3 18.5 + - - +
1439N SER* 3.1 40.7 + - - +
1440N PHE* 4.0 0.4 - - - +
1462N LEU* 1.3 74.8 - - + +
1464N GLU* 1.3 64.3 + - - +
1466N VAL* 3.2 8.4 + - - +
1467N ILE* 2.9 31.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1464 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1103N HIS* 3.1 22.6 - - - -
1104N GLU* 4.9 2.8 - - - +
1433N SER* 3.0 37.4 + - - +
1435N LEU* 4.4 12.6 - - + -
1436N SER* 4.0 7.2 - - - -
1457N ASP* 3.6 14.3 - - - +
1459N LEU* 3.8 24.9 - - + -
1460N ILE* 3.9 5.0 + - - +
1461N GLY* 3.0 31.3 + - - +
1463N LYS* 1.3 73.3 - - - +
1465N ASN* 1.3 62.4 + - - +
1467N ILE* 3.3 5.2 + - - +
1468N LEU* 3.2 28.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN1465 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1459N LEU* 3.2 24.4 + - - +
1461N GLY 2.5 27.9 + - - -
1462N LEU 2.9 7.1 + - - +
1464N GLU* 1.3 77.9 - - - +
1466N VAL* 1.3 61.3 + - - +
1468N LEU 3.3 0.9 + - - +
1469N GLY 2.8 7.6 + - - -
1470N ARG* 2.7 80.0 + - + +
1471N LEU 4.4 2.4 - - - +
1472N ILE* 4.4 9.2 - - - -
1473N PRO* 3.4 21.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1466 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1037M VAL* 4.3 14.8 - - + -
1041M GLU* 3.3 27.1 - - - +
1049M LEU* 4.3 4.7 - - + -
1053M LEU* 3.6 29.1 - - + +
618N LEU 3.7 18.8 - - - +
619N LEU* 4.1 16.6 - - + -
621N LYS* 4.7 1.6 + - - -
1462N LEU 2.9 16.7 + - - +
1463N LYS* 3.5 10.1 - - - +
1465N ASN* 1.3 76.6 - - - +
1467N ILE* 1.3 59.1 + - - +
1469N GLY* 2.8 19.4 + - - -
1470N ARG 5.1 0.7 - - - -
1472N ILE* 4.0 13.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1467 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1082M PRO* 4.8 2.9 - - - +
1085M PHE* 3.8 25.7 - - + +
614N PHE* 4.2 7.2 - - + -
618N LEU* 3.9 42.3 - - + +
619N LEU* 3.6 18.8 - - + -
621N LYS* 5.2 0.9 + - - -
1435N LEU* 3.7 37.0 - - + +
1439N SER* 3.6 31.2 - - - +
1463N LYS 2.9 25.9 + - - +
1464N GLU 3.6 5.2 - - - +
1465N ASN 3.2 0.2 - - - -
1466N VAL* 1.3 75.6 - - - +
1468N LEU* 1.3 60.1 + - + +
1469N GLY 3.6 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1468 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1081M VAL* 5.0 2.4 - - - +
1082M PRO* 3.3 20.7 - - - +
1085M PHE* 3.7 40.8 - - + -
1101M THR* 5.1 1.3 - - + -
5N VAL* 4.1 26.0 - - + -
8N VAL* 4.0 11.9 - - + -
1435N LEU* 4.0 19.5 - - + -
1459N LEU* 4.2 6.7 - - + -
1464N GLU 3.2 18.9 + - - +
1466N VAL 3.2 0.6 - - - -
1467N ILE* 1.3 76.6 - - + +
1469N GLY* 1.3 63.3 + - - +
1470N ARG* 3.4 32.7 + - + +
----------------------------------------------------------
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