Contacts of the helix formed by residues 1264 - 1278 (chain B) 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 ASN1264 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1108B MET 3.7 4.5 + - - -
1109B ASP 3.2 18.2 + - - +
1110B GLY* 3.3 18.8 + - - +
1262B GLU 4.0 2.0 + - - -
1263B ILE* 1.3 74.7 - - - +
1265B LYS* 1.3 64.8 + - - +
1266B ALA* 3.0 23.6 + - - +
1267B ASN* 3.2 34.2 + - + +
1268B LEU* 3.1 21.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1265 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447A ARG* 5.3 0.7 - - - +
1108B MET* 3.0 24.1 + - + +
1109B ASP* 2.8 31.4 - - - +
1259B ILE* 4.0 18.4 - - + -
1263B ILE 3.5 4.0 + - - -
1264B ASN* 1.3 71.2 - - - +
1266B ALA* 1.3 60.2 + - - +
1268B LEU* 3.4 4.3 - - - +
1269B VAL* 3.0 23.8 + - + +
1289B ASP* 3.2 25.1 - - - +
1291B SER* 3.6 27.6 - - - +
1296B LEU* 3.9 20.9 - - + -
1298B ILE* 4.1 18.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1266 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1109B ASP* 3.5 30.6 + - + +
1264B ASN* 3.0 11.7 + - - +
1265B LYS* 1.3 80.2 - - - +
1267B ASN* 1.3 61.4 + - - +
1269B VAL* 3.5 6.5 + - - +
1270B LYS* 3.0 24.8 + - - +
1289B ASP* 5.5 2.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN1267 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1264B ASN* 3.2 33.5 + - + +
1266B ALA* 1.3 77.1 - - - +
1268B LEU* 1.3 57.2 + - - +
1270B LYS* 2.8 10.6 + - - +
1271B LYS* 2.6 37.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1268 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1259B ILE* 3.8 38.4 - - + -
1263B ILE* 4.1 15.9 - - + +
1264B ASN 3.1 10.6 + - - +
1265B LYS* 3.4 9.2 - - - +
1267B ASN* 1.3 77.5 - - - +
1269B VAL* 1.3 58.0 + - - +
1271B LYS* 3.1 6.0 + - + -
1272B ILE* 2.9 45.5 + - + +
1298B ILE* 4.4 11.4 - - + -
1319B THR* 4.1 6.3 - - - +
1320B ASP* 4.3 8.1 - - + +
1321B LEU* 3.9 36.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1269 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1265B LYS 3.0 14.4 + - - +
1266B ALA* 3.7 8.3 - - - +
1268B LEU* 1.3 80.7 - - - +
1270B LYS* 1.3 64.0 + - - +
1272B ILE* 3.2 8.3 + - - +
1273B ASP* 3.0 22.9 + - + +
1287B VAL* 3.7 21.5 - - + +
1289B ASP* 4.3 27.4 - - + +
1298B ILE* 3.8 37.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1270 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1266B ALA 3.0 13.1 + - - +
1267B ASN* 2.8 17.7 + - - +
1269B VAL* 1.3 72.7 - - - +
1271B LYS* 1.3 56.1 + - - +
1273B ASP* 3.2 7.6 + - + +
1274B ASP* 2.8 42.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1271 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1267B ASN* 2.6 19.7 + - + +
1268B LEU* 3.7 6.5 - - + +
1270B LYS* 1.3 72.9 - - - +
1272B ILE* 1.3 62.1 + - - +
1274B ASP* 3.4 12.9 - - - +
1275B VAL* 3.3 22.7 + - - +
1319B THR* 4.2 14.3 - - + +
1320B ASP 6.1 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1272 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1256B ILE* 4.3 7.4 - - + -
1268B LEU* 2.9 43.4 + - + +
1269B VAL* 3.7 8.1 - - - +
1271B LYS* 1.3 73.7 - - - +
1273B ASP* 1.3 66.6 + - - +
1275B VAL* 2.9 17.3 + - - +
1276B ARG* 3.2 9.9 + - - +
1284B ILE* 4.9 4.5 - - + +
1287B VAL* 3.8 18.6 - - + -
1298B ILE* 5.0 7.0 - - + -
1300B ILE* 4.0 27.1 - - + -
1315B LEU* 3.9 19.7 - - + -
1319B THR* 4.3 12.8 - - + +
1321B LEU* 4.3 15.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1273 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1269B VAL* 3.0 18.0 + - + +
1270B LYS* 3.7 7.2 - - + +
1272B ILE* 1.3 76.2 - - - +
1274B ASP* 1.3 57.9 + - - +
1276B ARG* 3.0 37.7 + - - +
1277B VAL* 2.7 33.8 + - - +
1287B VAL* 3.8 31.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1274 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1270B LYS* 2.8 31.4 + - - +
1271B LYS* 3.4 16.0 + - - +
1272B ILE 3.1 0.2 - - - -
1273B ASP* 1.3 76.7 + - - +
1275B VAL* 1.3 57.3 + - - +
1277B VAL* 4.4 8.1 - - - +
1278B ASN* 2.8 50.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1275 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1271B LYS 3.3 12.8 + - - +
1272B ILE 2.9 10.9 + - - +
1274B ASP* 1.3 77.0 - - + +
1276B ARG* 1.3 60.1 + - - +
1278B ASN 3.7 0.2 - - - -
1279B ASN* 2.9 22.7 + - - -
1280B LYS* 3.0 31.1 + - + -
1281B VAL* 3.7 30.8 + - + +
1284B ILE* 4.5 4.9 - - + -
1314B TYR* 3.9 17.5 - - + -
1315B LEU* 4.3 10.8 - - + -
1318B TYR* 5.5 1.3 - - + +
1319B THR* 4.0 20.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1276 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1272B ILE 3.2 7.0 + - - +
1273B ASP* 3.0 35.9 + - - +
1275B VAL* 1.3 76.6 - - - +
1277B VAL* 1.3 98.2 + - - +
1279B ASN* 2.9 16.6 + - - +
1281B VAL 5.7 1.6 - - - -
1284B ILE* 3.2 57.3 + - + +
1285B ALA 3.7 18.0 + - - -
1286B GLU* 4.1 5.5 - - - +
1287B VAL* 4.7 0.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1277 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1273B ASP* 2.7 27.9 + - - +
1274B ASP* 3.9 10.8 - - - +
1276B ARG* 1.3 107.5 - - - +
1278B ASN* 1.3 68.5 + - - +
1279B ASN* 3.5 3.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN1278 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1274B ASP* 2.8 42.2 + - - +
1275B VAL* 5.0 0.2 - - - +
1277B VAL* 1.3 81.4 - - - +
1279B ASN* 1.3 73.0 + - - +
1280B LYS* 3.1 19.8 + - + +
----------------------------------------------------------
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