Contacts of the helix formed by residues 1221 - 1232 (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 GLY1221 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1219A ILE 4.1 0.8 + - - -
1220A GLN* 1.3 73.8 - - - +
1222A ARG* 1.3 65.7 + - - -
1223A ASP 3.2 3.6 + - - -
1224A GLU* 3.2 8.4 + - - -
1225A ILE* 3.0 29.0 + - - +
1236A VAL* 3.6 5.7 - - - +
1483A GLU 3.0 11.9 + - - -
1484A ASP* 4.1 8.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1222 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1205A MET* 4.6 9.2 - - + +
1221A GLY* 1.3 72.7 - - - +
1223A ASP* 1.3 57.3 + - - +
1225A ILE* 3.3 12.6 + - + +
1226A LYS* 2.9 28.1 + - - +
1483A GLU 3.9 3.8 + - - +
1484A ASP* 3.5 24.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1223 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1221A GLY 3.2 1.2 - - - -
1222A ARG* 1.3 78.4 - - - +
1224A GLU* 1.3 59.9 + - + +
1226A LYS* 3.3 8.0 + - - +
1227A LYS* 2.8 28.6 + - - +
1484A ASP* 5.2 1.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1224 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1221A GLY* 3.2 10.1 + - - +
1223A ASP* 1.3 78.2 - - + +
1225A ILE* 1.3 59.5 + - - +
1227A LYS* 3.6 24.6 - - - +
1228A ALA* 2.9 30.3 + - - +
1234A GLY* 3.6 10.3 - - - -
1235A ARG* 2.6 57.4 + - - +
1236A VAL* 4.5 3.6 - - + +
1327A PHE* 5.2 0.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1225 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1205A MET* 4.1 4.5 - - + -
1209A PRO 3.9 21.5 - - - +
1210A GLY* 4.1 2.2 - - - -
1211A PRO* 4.1 19.7 - - + -
1219A ILE* 4.3 9.6 - - + +
1221A GLY 3.0 24.7 + - - +
1222A ARG* 3.6 11.0 - - + +
1223A ASP 3.3 0.2 - - - -
1224A GLU* 1.3 72.2 - - - +
1226A LYS* 1.3 67.3 + - - +
1228A ALA* 3.2 6.8 + - - +
1229A TYR* 2.9 54.9 + - + -
1236A VAL* 3.6 20.4 - - + -
1327A PHE* 4.9 6.5 - - + -
1482A LEU* 4.4 8.5 - - + -
1483A GLU 5.8 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1226 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1201A ILE* 4.3 16.6 - - + +
1202A ASP* 4.3 14.4 - - - +
1205A MET* 3.8 18.1 - - + +
1222A ARG 2.9 14.0 + - - +
1223A ASP* 3.5 11.0 - - - +
1225A ILE* 1.3 73.6 - - - +
1227A LYS* 1.3 65.3 + - - +
1229A TYR* 3.1 4.2 + - - +
1230A GLU* 3.0 40.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1227 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1223A ASP 2.8 21.1 + - - +
1224A GLU* 3.6 30.7 - - - +
1225A ILE 3.2 0.4 - - - -
1226A LYS* 1.3 73.3 - - - +
1228A ALA* 1.3 57.4 + - - +
1230A GLU* 3.0 14.3 + - - +
1231A THR* 2.9 39.7 + - + +
1233A LYS 3.5 12.8 - - - +
1234A GLY* 4.9 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1228 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1224A GLU 2.9 16.6 + - - +
1225A ILE 3.6 3.4 - - - +
1227A LYS* 1.3 76.1 - - - +
1229A TYR* 1.3 60.2 + - - +
1232A GLY* 2.6 30.7 + - - -
1233A LYS 3.1 15.1 + - - +
1234A GLY* 3.8 1.1 - - - -
1327A PHE* 3.4 48.9 - - + -
1329A MET* 3.8 4.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR1229 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1181A HIS* 3.0 34.2 + + - -
1201A ILE* 3.9 20.5 - - + +
1205A MET* 3.6 24.7 - - + -
1208A LEU* 3.6 28.9 - - + +
1210A GLY* 3.0 21.2 + - - -
1211A PRO* 3.4 2.1 - - + +
1225A ILE* 2.9 36.7 + - + +
1226A LYS 3.1 4.7 + - - +
1228A ALA* 1.3 74.5 - - - +
1230A GLU* 1.3 58.7 + - - +
1327A PHE* 4.1 16.6 - + - -
1329A MET* 4.4 5.6 - - + -
1341A GLY* 3.4 1.6 - - - -
1342A ILE* 2.9 55.9 + - + +
1343A VAL* 4.4 1.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1230 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1201A ILE* 4.0 28.3 - - + +
1226A LYS* 3.0 28.4 + - - +
1227A LYS* 3.0 14.3 + - - +
1229A TYR* 1.3 81.0 - - - +
1231A THR* 1.3 68.8 + - + +
1232A GLY 3.7 0.4 - - - -
1341A GLY* 4.6 5.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR1231 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1227A LYS* 2.9 19.0 + - + +
1230A GLU* 1.3 89.1 - - + +
1232A GLY* 1.3 58.4 + - - +
1233A LYS* 3.1 26.2 + - - +
1339A GLN* 3.1 30.8 + - - +
1340A VAL* 4.6 0.8 + - - -
1341A GLY 4.5 5.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY1232 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1228A ALA* 2.6 24.1 + - - -
1230A GLU 3.7 0.4 - - - -
1231A THR* 1.3 70.6 - - - +
1233A LYS* 1.3 58.9 + - - +
1327A PHE* 3.6 2.4 - - - -
1328A ASN* 3.3 6.6 + - - -
1329A MET* 2.8 35.3 + - - +
1339A GLN* 4.6 3.6 - - - -
1340A VAL 3.4 23.1 - - - -
1341A GLY* 4.0 3.0 - - - -
----------------------------------------------------------
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