Contacts of the helix formed by residues 1246 - 1250 (chain A) in PDB entry 3ZC5
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 PRO1246 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1203A ARG 4.2 13.2 - - - +
1204A ASP* 3.4 20.9 - - - +
1208A ARG* 3.6 26.9 - - - +
1234A TYR 3.5 12.6 - - - +
1235A TYR* 3.7 15.0 - - + -
1244A LYS 4.6 0.2 - - - +
1245A LEU* 1.3 90.0 - - + +
1247A VAL* 1.3 64.7 + - - +
1248A LYS 3.2 3.6 - - - -
1249A TRP* 3.0 21.7 + - + -
1250A MET* 3.3 20.6 + - + +
1260A PHE* 6.0 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1247 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1234A TYR 4.5 1.9 + - - +
1236A SER* 4.2 12.1 - - - +
1238A HIS 4.3 6.5 - - - +
1239A ASN* 4.1 30.3 - - + +
1245A LEU* 2.9 23.2 + - + +
1246A PRO* 1.3 71.2 - - - +
1248A LYS* 1.3 69.4 + - + +
1249A TRP 3.2 0.4 - - - -
1250A MET* 3.4 22.8 + - - +
1255A LEU* 4.0 19.6 - - + +
1289A THR* 4.1 30.5 - - + +
1292A ILE* 4.0 23.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1248 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1234A TYR* 5.6 5.6 + - + -
1246A PRO 3.1 1.0 + - - -
1247A VAL* 1.3 87.8 - - + +
1249A TRP* 1.3 80.5 + - + +
1250A MET 3.5 0.7 - - - -
1267A TRP* 5.4 0.9 + - - -
1271A VAL* 4.1 9.9 - - - +
1283A PRO* 3.5 21.7 + - + +
1284A TYR* 2.7 62.9 + - + -
1285A PRO* 4.5 4.6 + - - +
1287A VAL* 2.7 23.3 + - - -
1288A ASN 4.8 0.7 - - - -
1289A THR* 4.4 19.7 - - + +
1292A ILE* 4.6 11.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP1249 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1166A ARG* 6.4 0.7 - - - -
1204A ASP* 5.6 1.8 - - - +
1205A LEU 3.5 14.6 - - - +
1206A ALA* 3.2 19.5 - - + +
1208A ARG* 3.2 34.3 - - - -
1234A TYR* 3.8 35.4 - + + -
1246A PRO* 3.0 19.5 + - + +
1248A LYS* 1.3 100.5 - - + +
1250A MET* 1.3 60.7 + - - +
1267A TRP* 3.6 6.9 - - - -
1268A SER* 2.8 36.7 + - - +
1271A VAL* 3.5 27.4 - - + +
1275A GLU* 2.9 37.3 + - - -
1283A PRO* 3.6 24.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET1250 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1203A ARG 5.5 0.7 - - - +
1239A ASN* 5.8 0.7 - - + -
1245A LEU* 3.9 31.9 - - + -
1246A PRO* 3.3 23.8 - - + +
1247A VAL* 3.4 27.1 + - - +
1248A LYS 3.5 0.7 - - - -
1249A TRP* 1.3 79.3 - - + +
1251A ALA* 1.3 66.0 + - - +
1252A LEU 3.7 0.9 + - - -
1254A SER* 3.9 22.7 - - - +
1255A LEU* 3.4 25.6 - - + +
1258A GLN* 5.9 0.2 - - - -
1260A PHE* 3.9 34.8 - - + -
1267A TRP* 3.5 12.4 + - - -
1268A SER* 4.7 2.0 - - - -
1296A LEU* 4.2 9.2 - - - +
----------------------------------------------------------
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