Contacts of the helix formed by residues 1370 - 1375 (chain D) 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 PRO1370 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3C THR* 5.5 13.5 - - + +
56C PHE* 6.1 0.4 - - + -
1263D PHE* 4.5 0.2 - - - -
1357D VAL* 6.4 0.7 - - + -
1361D GLU* 4.6 9.6 - - + -
1368D GLY 4.1 4.5 - - - +
1369D MET* 1.3 95.7 - - + +
1371D LEU* 1.3 64.8 + - - +
1372D SER* 4.0 18.4 - - - +
1373D SER* 2.6 34.4 + - - +
1374D PHE* 3.2 8.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1371 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1259D VAL* 4.5 5.2 - - + -
1263D PHE* 3.8 54.1 - - + -
1267D LEU* 4.0 26.7 - - + -
1281D ILE* 4.7 1.8 - - + -
1282D PHE* 4.1 18.2 - - + -
1343D ILE* 4.2 25.6 - - + -
1353D PHE* 6.2 0.7 - - + -
1357D VAL* 4.5 18.6 - - + +
1361D GLU* 5.1 0.6 - - - +
1370D PRO* 1.3 72.7 - - - +
1372D SER* 1.3 63.5 + - - +
1374D PHE* 2.9 16.9 + - + +
1375D ILE* 3.2 20.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER1372 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74C GLN* 5.7 6.3 - - - +
1340D ALA* 5.9 6.7 - - - -
1343D ILE* 4.9 18.3 - - - +
1344D GLN* 6.1 0.7 - - - -
1370D PRO* 4.0 14.8 - - - +
1371D LEU* 1.3 80.4 - - - +
1373D SER* 1.3 62.6 + - - +
1375D ILE* 3.7 19.9 - - - +
1376D LEU* 4.0 11.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER1373 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C ASN* 3.1 22.7 + - - -
56C PHE* 3.7 21.1 - - - -
1369D MET* 3.3 41.4 - - - +
1370D PRO* 2.6 26.8 + - - -
1372D SER* 1.3 78.7 + - - +
1374D PHE* 1.3 67.5 + - - +
1376D LEU* 3.3 13.9 + - - +
1377D LYS* 4.0 0.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1374 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1255D ASP* 4.2 19.5 - - + -
1258D LEU* 5.3 6.1 - - + -
1259D VAL* 3.5 31.0 - - + -
1263D PHE* 4.2 13.2 - + - -
1285D TRP* 3.5 10.4 - - - -
1365D ARG 4.8 2.9 - - - -
1366D CYS* 3.6 35.0 - - + -
1369D MET* 3.5 31.4 - - + -
1370D PRO 3.2 22.0 - - - -
1371D LEU* 2.9 8.3 + - + +
1373D SER* 1.3 78.2 + - - +
1375D ILE* 1.3 61.5 + - - +
1376D LEU 3.0 5.4 - - - -
1377D LYS* 3.0 51.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1375 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1281D ILE* 3.9 23.8 - - + +
1282D PHE* 4.4 12.6 - - + -
1285D TRP* 3.9 21.3 - - + -
1332D PHE* 3.5 20.8 - - + -
1336D GLN* 3.8 27.4 + - + +
1339D GLY 6.3 0.4 - - - -
1340D ALA* 5.6 8.3 - - + +
1343D ILE* 4.7 8.7 - - + -
1371D LEU* 3.2 34.0 + - + +
1372D SER* 3.7 13.7 - - - +
1374D PHE* 1.3 76.8 - - - +
1376D LEU* 1.3 61.1 + - + +
1378D PRO* 3.4 12.1 - - - +
----------------------------------------------------------
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