Contacts of the helix formed by residues 1200 - 1208 (chain A) in PDB entry 4Z4Q
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 LYS1200 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1198A THR 3.7 2.0 + - - +
1199A ALA* 1.3 74.9 - - - +
1201A ILE* 1.3 68.9 + - - +
1202A ASP* 2.9 10.9 + - + +
1203A LYS* 3.1 11.8 + - + +
1204A LEU* 3.1 21.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1201 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1199A ALA 5.4 0.2 - - - +
1200A LYS* 1.3 72.6 - - - +
1202A ASP* 1.3 57.7 + - - +
1204A LEU* 3.2 8.8 + - - +
1205A MET* 2.8 56.3 + - + +
1226A LYS* 4.3 15.9 - - + +
1229A TYR* 3.9 31.6 - - + +
1230A GLU* 4.0 27.6 - - + +
1342A ILE* 4.6 7.4 - - + -
1343A VAL* 4.1 20.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1202 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1200A LYS* 2.9 8.4 + - + +
1201A ILE* 1.3 81.1 - - - +
1203A LYS* 1.3 63.1 + - - +
1205A MET* 3.4 14.3 + - - +
1206A GLU* 3.6 12.0 + - - +
1226A LYS* 4.3 18.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1203 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1192A TYR* 3.6 48.9 - - + +
1199A ALA* 5.2 0.4 - - + -
1200A LYS* 3.1 16.8 + - + +
1202A ASP* 1.3 76.5 - - - +
1204A LEU* 1.3 56.3 + - - +
1206A GLU* 2.7 68.0 + - - +
1207A PHE* 3.7 13.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1204 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1189A ALA* 4.0 31.7 - - + +
1192A TYR* 4.5 7.6 - - + -
1193A MET* 4.4 19.7 - - + -
1199A ALA* 4.2 22.9 - - + +
1200A LYS 3.1 18.5 + - - +
1201A ILE* 3.6 8.1 - - - +
1203A LYS* 1.3 75.0 - - - +
1205A MET* 1.3 58.8 + - + +
1207A PHE* 3.0 25.1 + - - +
1208A LEU* 3.0 16.7 + - + +
1342A ILE* 3.8 20.2 - - + -
1343A VAL* 3.6 30.7 - - + -
1346A LEU* 4.6 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET1205 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1201A ILE* 2.8 43.8 + - + +
1202A ASP* 3.8 11.0 - - - +
1203A LYS 3.1 0.6 - - - -
1204A LEU* 1.3 70.6 - - + +
1206A GLU* 1.3 62.8 + - - +
1207A PHE 3.2 0.7 - - - -
1208A LEU 3.4 15.7 - - - +
1209A PRO* 3.6 30.2 - - + +
1222A ARG* 4.6 10.3 - - + +
1225A ILE* 4.1 21.3 - - + -
1226A LYS* 3.8 22.2 - - + +
1229A TYR* 3.6 20.2 - - + -
1342A ILE* 6.3 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1206 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1202A ASP 3.6 9.7 + - - +
1203A LYS* 2.7 62.2 + - - +
1205A MET* 1.3 73.3 - - - +
1207A PHE* 1.3 70.4 + - + +
1209A PRO* 5.0 4.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1207 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1185A GLU* 3.2 30.9 - - - +
1188A ASP* 3.9 23.8 - - + +
1189A ALA* 3.7 21.1 - - - +
1192A TYR* 3.6 49.1 - + + -
1203A LYS* 3.7 27.1 - - - -
1204A LEU* 3.0 10.8 + - - +
1206A GLU* 1.3 91.3 - - + +
1208A LEU* 1.3 57.8 + - - +
1209A PRO* 3.4 4.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1208 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1163A LEU* 4.4 9.2 - - + -
1181A HIS* 3.6 31.9 - - + -
1185A GLU* 4.2 23.6 - - + +
1186A VAL* 4.5 6.1 - - + -
1189A ALA* 4.2 16.6 - - + -
1204A LEU* 3.0 12.8 + - + +
1205A MET* 3.4 14.5 - - - +
1207A PHE* 1.3 75.4 - - - +
1209A PRO* 1.3 66.9 - - - +
1210A GLY 3.3 12.5 + - - +
1229A TYR* 3.6 21.5 - - + +
1342A ILE* 3.6 36.8 - - + -
1346A LEU* 5.4 1.1 - - + -
----------------------------------------------------------
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