Contacts of the helix formed by residues 1274 - 1283 (chain B) in PDB entry 1KI1
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 THR1274 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1268B MET* 4.7 0.4 - - - -
1273B LEU* 1.3 76.9 - - - +
1275B GLU* 1.3 66.1 + - - +
1276B LYS* 3.5 10.1 + - - +
1277B GLU* 2.9 46.0 + - - +
1278B VAL* 3.0 12.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1275 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1268B MET* 4.2 29.1 - - + +
1273B LEU 4.1 0.2 + - - -
1274B THR* 1.3 73.8 - - - +
1276B LYS* 1.3 63.6 + - - +
1278B VAL* 3.3 1.7 + - - +
1279B ALA* 3.0 25.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1276 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1274B THR* 3.1 11.2 + - - +
1275B GLU* 1.3 79.5 - - - +
1277B GLU* 1.3 58.5 + - + +
1279B ALA* 3.5 6.6 + - - +
1280B MET* 3.1 51.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1277 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1272B LEU 4.4 0.3 - - - +
1273B LEU* 3.3 22.1 - - + +
1274B THR* 2.9 43.1 + - - +
1276B LYS* 1.3 77.3 - - + +
1278B VAL* 1.3 66.6 + - - +
1280B MET* 3.1 22.5 + - - +
1281B ILE* 3.3 18.3 + - - +
1342B LEU* 4.2 15.3 - - + +
1346B LYS* 3.1 31.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1278 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1264B GLN* 4.8 9.6 - - + +
1267B LEU* 4.3 4.9 - - + +
1268B MET* 3.7 55.0 - - + +
1273B LEU* 3.8 18.4 - - + -
1274B THR 3.0 14.2 + - - +
1275B GLU 3.8 6.3 - - - +
1277B GLU* 1.3 74.3 - - - +
1279B ALA* 1.3 59.9 + - - +
1281B ILE* 3.0 26.2 + - + +
1282B PHE* 3.1 30.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1279 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1275B GLU 3.0 16.9 + - - +
1276B LYS* 3.8 6.7 - - - +
1278B VAL* 1.3 80.4 - - - +
1280B MET* 1.3 56.1 + - - +
1282B PHE* 5.1 1.1 - - - -
1283B VAL* 2.7 39.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET1280 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1276B LYS* 3.1 48.0 + - + +
1277B GLU* 3.1 20.1 + - - +
1279B ALA* 1.3 77.4 - - - +
1281B ILE* 1.3 62.3 + - + +
1283B VAL* 3.9 9.7 - - - +
1335B ARG* 4.2 4.0 - - - +
1336B GLN* 5.3 0.2 - - - -
1338B ASN* 4.0 29.8 - - + +
1339B GLY* 3.1 22.0 + - - -
1342B LEU* 4.5 16.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1281 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1267B LEU* 5.1 7.0 - - + -
1273B LEU* 5.0 7.6 - - + -
1277B GLU 3.4 14.1 - - - +
1278B VAL* 3.0 10.6 + - + +
1280B MET* 1.3 82.0 - - - +
1282B PHE* 1.3 89.2 + - + +
1283B VAL* 3.5 5.1 - - - +
1332B PHE* 4.5 3.8 - - - -
1336B GLN* 5.4 2.3 - - - +
1339B GLY* 4.1 9.6 - - - +
1342B LEU* 3.6 29.8 - - + -
1343B ILE* 3.8 35.4 - - + -
1353B PHE* 4.9 10.5 - - + -
1371B LEU* 4.8 2.0 - - + -
1375B ILE* 3.9 20.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1282 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1259B VAL* 3.7 29.8 - - + -
1263B PHE* 4.0 7.6 - - + -
1264B GLN* 3.5 63.7 - - + +
1267B LEU* 4.0 20.9 - - + -
1278B VAL* 3.1 26.8 + - + +
1279B ALA* 5.3 1.1 - - - -
1281B ILE* 1.3 95.7 - - + +
1283B VAL* 1.3 74.2 + - - +
1284B ASN 3.0 0.2 + - - -
1285B TRP* 2.9 27.8 + + + +
1332B PHE* 3.8 7.4 - - - -
1371B LEU* 4.1 13.0 - - + -
1375B ILE* 4.4 7.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1283 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1264B GLN* 5.3 1.9 - - - +
1279B ALA* 2.7 34.9 + - - +
1280B MET* 3.9 15.3 - - - +
1281B ILE 4.1 4.9 - - - +
1282B PHE* 1.3 75.0 - - - +
1284B ASN* 1.3 72.9 + - - +
1285B TRP 3.5 1.2 + - - -
1331B ARG* 4.0 26.3 + - + +
1332B PHE* 4.0 15.7 - - + +
1335B ARG* 3.8 48.2 - - + +
1336B GLN* 4.7 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