Contacts of the helix formed by residues 1212 - 1220 (chain A) in PDB entry 2RFI
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 GLY1212 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1170A HIS* 4.6 0.6 - - - -
1210A ASP* 2.9 19.8 + - - -
1211A TYR* 1.3 80.9 - - - +
1213A GLU* 1.3 67.9 + - - -
1214A ARG 3.4 2.9 - - - -
1215A PHE 3.2 10.7 + - - -
1216A TRP* 3.4 18.9 + - - -
1234A HIS* 5.4 0.9 - - - -
8P SER* 4.4 8.1 - - - -
9P THR 6.4 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1213 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1212A GLY* 1.3 68.5 - - - -
1214A ARG* 1.3 81.3 + - - +
1215A PHE 3.1 4.9 - - - -
1216A TRP* 4.5 2.0 - - - +
1217A ASP* 2.8 47.2 + - - +
1233A ARG* 4.1 12.8 + - - -
1234A HIS* 3.5 26.8 - - - -
8P SER* 4.9 1.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1214 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1145A ASP* 5.2 4.9 - - - +
1148A ASN* 5.6 4.0 - - + +
1212A GLY 3.4 0.8 - - - -
1213A GLU* 1.3 97.1 - - - +
1215A PHE* 1.3 58.5 + - - +
1217A ASP* 2.7 36.7 + - - +
1218A ILE* 4.1 9.0 - - - +
2P LYS* 5.8 10.1 - - + -
4P THR 4.5 1.2 - - - +
5P ALA* 3.7 5.7 - - - -
6P ARG* 3.2 37.1 + - + +
8P SER* 4.6 16.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1215 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A SAH 3.5 21.5 - - - -
1140A ASP 5.1 0.7 - - - -
1141A SER* 4.1 21.1 - - - -
1211A TYR* 3.6 47.3 - + + +
1212A GLY 3.2 9.1 + - - +
1213A GLU 3.1 0.6 - - - -
1214A ARG* 1.3 79.5 - - - +
1216A TRP* 1.3 88.7 + + - +
1217A ASP 3.3 0.2 - - - -
1218A ILE* 3.2 6.1 + - - +
1219A LYS* 2.9 55.5 + - + +
1223A PHE* 4.5 1.8 - + - -
5P ALA* 3.9 14.1 - - + +
6P ARG 3.0 15.1 + - - +
7P MLY 4.2 13.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP1216 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A SAH 4.2 7.2 - + - -
1170A HIS* 3.3 52.1 + + + -
1211A TYR* 4.5 0.7 - - + -
1212A GLY 3.4 22.1 + - - +
1213A GLU* 3.4 3.9 + - - +
1215A PHE* 1.3 92.3 - + - +
1217A ASP* 1.3 63.2 + - - +
1218A ILE 3.1 1.6 - - - -
1219A LYS* 4.4 2.2 - - + -
1220A GLY* 2.9 43.6 + - - +
1223A PHE* 3.6 48.0 - + - -
1224A SER* 4.6 0.2 - - - -
1225A CYS* 3.7 31.2 - - + -
1234A HIS* 3.5 47.6 - + + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1217 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1213A GLU* 2.8 31.0 + - - +
1214A ARG* 2.7 37.7 + - - +
1215A PHE 3.3 0.2 - - - -
1216A TRP* 1.3 77.0 - - - +
1218A ILE* 1.3 67.1 + - + +
1221A LYS* 3.7 21.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1218 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1140A ASP* 4.1 9.0 - - - +
1214A ARG 4.1 6.5 - - - +
1215A PHE 3.2 6.5 + - - +
1216A TRP 3.1 0.2 - - - -
1217A ASP* 1.3 83.8 - - + +
1219A LYS* 1.3 67.7 + - + +
1220A GLY 3.4 0.6 + - - -
1221A LYS* 3.5 32.0 + - - +
1222A LEU* 4.3 12.3 + - + +
2P LYS 3.5 24.2 - - - +
3P GLN 4.5 10.8 - - - +
4P THR 4.0 3.8 - - - +
5P ALA* 3.8 33.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1219 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A SAH 4.5 1.6 - - - -
1140A ASP* 2.7 31.9 + - - -
1141A SER* 3.7 21.2 + - - +
1215A PHE* 2.9 51.4 + - + +
1216A TRP* 4.4 2.7 - - + -
1218A ILE* 1.3 74.7 - - + +
1220A GLY* 1.3 53.8 + - - +
1221A LYS 3.1 5.6 - - - -
1222A LEU* 2.8 43.7 + - + +
1223A PHE* 3.0 40.2 + - + +
5P ALA* 3.8 15.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY1220 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1216A TRP* 2.9 30.5 + - - -
1219A LYS* 1.3 76.5 - - - +
1221A LYS* 1.3 60.1 + - - +
1222A LEU 3.2 1.0 + - - -
1223A PHE 3.4 17.9 + - - +
1224A SER* 5.5 0.2 - - - -
1234A HIS 6.0 0.9 - - - -
----------------------------------------------------------
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