Contacts of the helix formed by residues 1283 - 1292 (chain C) in PDB entry 7KHE
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 ALA1283 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1278C LEU* 4.0 26.2 - - + +
1281C TYR* 3.0 10.9 + - + -
1282C GLY* 1.3 72.2 - - - +
1284C ALA* 1.3 62.3 + - - +
1286C THR* 3.8 19.8 + - + +
1287C LEU* 3.6 17.0 - - - +
479D GLU* 3.4 18.6 - - + +
483D LEU* 4.6 3.8 - - + -
484D MET* 4.1 16.2 - - + -
1357D ILE* 4.6 5.0 - - - +
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Residues in contact with ALA1284 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1282C GLY 3.0 1.2 + - - -
1283C ALA* 1.3 73.4 - - - +
1285C TYR* 1.3 59.2 + - + +
1287C LEU* 3.5 3.7 + - - +
1288C GLN* 2.9 28.4 + - - +
1356D LEU* 3.7 20.5 - - + +
1357D ILE* 3.8 26.9 + - + +
1359D ALA 4.0 2.2 - - - +
1361D THR* 2.8 22.9 + - - +
1362D GLY* 3.7 17.0 - - - +
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Residues in contact with TYR1285 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1284C ALA* 1.3 74.8 - - + +
1286C THR* 1.3 67.8 + - - +
1288C GLN* 3.2 9.3 + - - +
1289C GLU* 3.0 25.5 + - - +
1315C MET* 4.6 13.0 - - + +
473D THR* 5.1 2.6 + - - +
475D GLU* 3.2 39.3 - - + -
476D ALA* 4.5 6.1 - - - +
479D GLU* 3.0 23.3 + - + +
1356D LEU* 3.5 38.6 - - + +
1361D THR* 5.1 5.9 + - - -
1362D GLY* 5.7 0.2 - - - -
1365D TYR* 5.3 5.2 - - - +
20E VAL* 5.8 0.2 - - + -
21E LEU* 3.4 37.5 - - + +
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Residues in contact with THR1286 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1278C LEU* 3.4 27.9 - - - +
1283C ALA* 3.8 8.7 + - + +
1285C TYR* 1.3 76.4 - - - +
1287C LEU* 1.3 72.0 + - - +
1289C GLU* 3.0 18.2 - - - +
1290C MET* 2.9 30.0 + - - +
422D LEU* 5.7 4.3 - - + -
471D PRO* 5.2 4.0 - - + -
476D ALA* 3.7 30.7 - - + +
479D GLU* 3.2 19.7 + - + +
480D ALA* 4.7 3.4 - - + +
484D MET* 4.8 8.7 - - + -
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Residues in contact with LEU1287 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1275C VAL* 4.0 16.2 - - + +
1278C LEU* 4.0 27.1 - - + -
1279C GLU* 3.8 30.5 - - + +
1283C ALA 3.6 16.1 + - - +
1284C ALA* 3.5 5.6 + - - +
1285C TYR 3.3 0.4 - - - -
1286C THR* 1.3 82.9 + - - +
1288C GLN* 1.3 66.2 + - - +
1290C MET* 3.3 6.0 + - - +
1291C LEU* 2.9 55.8 + - + +
1351D VAL* 4.1 11.4 - - + -
1355D ARG 5.3 3.8 - - - +
1357D ILE* 4.2 15.3 - - + +
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Residues in contact with GLN1288 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1284C ALA 2.9 16.4 + - - +
1285C TYR* 3.2 11.3 + - - +
1287C LEU* 1.3 82.5 - - - +
1289C GLU* 1.3 66.2 + - - +
1291C LEU* 3.2 2.8 + - - +
1292C THR* 3.2 21.6 + - - +
1315C MET* 4.0 17.7 - - + +
1317C PRO* 3.3 38.3 - - + +
1354D GLY 4.4 11.8 + - - +
1355D ARG* 4.5 11.1 - - - +
1356D LEU* 2.8 41.9 - - + +
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Residues in contact with GLU1289 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1285C TYR 3.0 11.0 + - - +
1286C THR* 3.0 18.5 - - - +
1288C GLN* 1.3 76.1 - - - +
1290C MET* 1.3 80.3 - - + +
1291C LEU 3.0 1.2 + - - -
1293C VAL* 3.0 29.2 + - + +
1294C LYS* 3.2 23.1 + - + +
1304C MET* 5.1 1.3 - - + +
1315C MET* 3.6 24.9 - - - -
471D PRO* 3.7 8.5 - - - +
472D LEU* 3.5 18.3 + - - +
473D THR* 3.1 32.6 + - + +
476D ALA* 3.1 24.3 - - - +
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Residues in contact with MET1290 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1270C PHE* 3.0 57.7 - - + -
1278C LEU* 5.3 9.2 - - + -
1286C THR* 2.9 23.5 + - - +
1287C LEU* 3.6 7.4 - - + +
1289C GLU* 1.3 82.4 - - - +
1291C LEU* 1.3 64.6 - - + +
1294C LYS* 3.4 42.3 - - - +
1295C SER* 4.3 3.6 + - - -
345D LYS* 5.6 1.0 - - - +
347D VAL* 3.9 21.6 - - + +
422D LEU* 5.4 8.3 - - + -
469D HIS* 4.4 9.6 - - + -
470D VAL 5.3 2.2 - - - +
471D PRO* 6.1 1.3 - - + -
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Residues in contact with LEU1291 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1270C PHE* 5.9 5.2 - - + +
1275C VAL* 4.8 17.5 - - + -
1287C LEU* 2.9 42.1 + - + +
1288C GLN* 3.8 4.5 - - - +
1289C GLU 3.0 0.2 - - - -
1290C MET* 1.3 83.5 - - + +
1292C THR* 1.3 66.8 + - + +
1295C SER* 3.6 13.9 + - - -
1296C ASP* 3.8 10.2 - - - +
1320C PRO* 4.7 5.1 - - + +
340D GLN 5.8 3.4 - - - +
344D GLY 6.0 0.2 - - - +
345D LYS* 5.3 11.7 - - + -
1351D VAL* 3.6 42.2 - - + +
1354D GLY* 4.8 4.7 - - - -
1355D ARG 5.8 0.4 - - - +
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Residues in contact with THR1292 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1288C GLN 3.2 13.1 + - - +
1289C GLU 3.1 0.8 + - - -
1291C LEU* 1.3 85.2 - - + +
1293C VAL* 1.3 88.2 + - - +
1294C LYS 3.2 2.0 + - - -
1295C SER 4.1 0.2 - - - -
1296C ASP 3.3 6.3 + - - +
1297C ASP* 2.9 32.9 + - - +
1317C PRO* 3.5 24.0 + - + +
1318C GLY 4.9 0.2 - - - +
1320C PRO* 3.8 24.0 - - + -
1354D GLY* 3.4 31.0 - - - +
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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