Contacts of the helix formed by residues 1274 - 1283 (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 THR1274 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1268D MET* 4.7 0.4 - - - -
1273D LEU* 1.3 76.9 - - - +
1275D GLU* 1.3 66.8 + - - +
1276D LYS* 3.5 9.8 + - - +
1277D GLU* 2.9 45.8 + - - +
1278D VAL* 3.0 12.5 + - - +
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Residues in contact with GLU1275 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1268D MET* 4.2 29.1 - - + +
1273D LEU 4.1 0.2 + - - -
1274D THR* 1.3 73.6 - - - +
1276D LYS* 1.3 64.1 + - - +
1278D VAL* 3.3 1.7 + - - +
1279D ALA* 3.0 25.1 + - - +
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Residues in contact with LYS1276 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1274D THR* 3.1 11.2 + - - +
1275D GLU* 1.3 80.3 - - - +
1277D GLU* 1.3 58.3 + - + +
1279D ALA* 3.5 6.8 + - - +
1280D MET* 3.1 52.1 + - + +
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Residues in contact with GLU1277 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1272D LEU 4.4 0.3 - - - +
1273D LEU* 3.3 22.1 - - + +
1274D THR* 2.9 43.3 + - - +
1276D LYS* 1.3 77.3 - - + +
1278D VAL* 1.3 67.3 + - - +
1280D MET* 3.1 22.5 + - - +
1281D ILE* 3.3 18.3 + - - +
1342D LEU* 4.2 15.4 - - + +
1346D LYS* 3.1 31.4 + - - -
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Residues in contact with VAL1278 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1264D GLN* 4.8 9.9 - - + +
1267D LEU* 4.3 4.9 - - + +
1268D MET* 3.7 55.2 - - + +
1273D LEU* 3.8 18.4 - - + -
1274D THR 3.0 14.2 + - - +
1275D GLU 3.8 6.3 - - - +
1277D GLU* 1.3 74.1 - - - +
1279D ALA* 1.3 59.9 + - - +
1281D ILE* 3.0 26.2 + - + +
1282D PHE* 3.1 30.4 + - + +
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Residues in contact with ALA1279 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1275D GLU 3.0 16.9 + - - +
1276D LYS* 3.8 6.7 - - - +
1278D VAL* 1.3 80.2 - - - +
1280D MET* 1.3 55.7 + - - +
1282D PHE* 5.1 1.3 - - - -
1283D VAL* 2.7 40.0 + - - +
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Residues in contact with MET1280 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1276D LYS* 3.1 48.0 + - + +
1277D GLU* 3.1 20.1 + - - +
1279D ALA* 1.3 77.6 - - - +
1281D ILE* 1.3 62.5 + - + +
1283D VAL* 3.9 9.7 - - - +
1335D ARG* 4.2 4.0 - - - +
1336D GLN* 5.3 0.2 - - - -
1338D ASN* 4.0 29.8 - - + +
1339D GLY* 3.1 22.0 + - - -
1342D LEU* 4.5 16.4 - - + -
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Residues in contact with ILE1281 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1267D LEU* 5.1 7.0 - - + -
1273D LEU* 5.0 7.6 - - + -
1277D GLU 3.4 14.1 - - - +
1278D VAL* 3.0 10.6 + - + +
1280D MET* 1.3 82.0 - - - +
1282D PHE* 1.3 89.6 + - + +
1283D VAL* 3.5 5.1 - - - +
1332D PHE* 4.5 4.2 - - - -
1336D GLN* 5.4 2.3 - - - +
1339D GLY* 4.1 9.6 - - - +
1342D LEU* 3.5 29.4 - - + -
1343D ILE* 3.8 35.4 - - + -
1353D PHE* 4.9 10.5 - - + -
1371D LEU* 4.7 2.0 - - + -
1375D ILE* 3.9 20.0 - - + +
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Residues in contact with PHE1282 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1259D VAL* 3.7 30.3 - - + -
1263D PHE* 4.0 7.9 - - + -
1264D GLN* 3.5 63.9 - - + +
1267D LEU* 4.0 20.9 - - + -
1278D VAL* 3.1 26.6 + - + +
1279D ALA* 5.3 1.1 - - - -
1281D ILE* 1.3 95.5 - - + +
1283D VAL* 1.3 74.0 + - - +
1284D ASN 3.0 0.2 + - - -
1285D TRP* 2.9 28.0 + + + +
1332D PHE* 3.8 7.4 - - - -
1371D LEU* 4.1 13.0 - - + -
1375D ILE* 4.4 7.0 - - + -
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Residues in contact with VAL1283 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1264D GLN* 5.3 1.9 - - - +
1279D ALA* 2.7 34.7 + - - +
1280D MET* 3.9 15.0 - - - +
1281D ILE 4.1 4.9 - - - +
1282D PHE* 1.3 75.9 - - - +
1284D ASN* 1.3 73.3 + - - +
1285D TRP 3.5 1.2 + - - -
1331D ARG* 4.0 26.1 + - + +
1332D PHE* 4.0 15.7 - - + +
1335D ARG* 3.8 48.0 - - + +
1336D GLN* 4.7 0.9 - - - +
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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