Contacts of the helix formed by residues 1266 - 1281 (chain A) in PDB entry 2XKK
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 SER1266 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1113A PRO 4.2 8.9 + - - -
1114A ASP* 2.9 36.4 + - - -
1116A PRO* 5.3 3.4 - - - -
1261A LEU* 4.3 0.7 - - - -
1264A GLN 3.8 3.8 + - - -
1265A VAL* 1.3 76.2 - - - +
1267A GLY* 1.3 66.1 + - - +
1268A SER* 3.1 8.1 + - - -
1269A LYS* 3.1 28.6 + - - +
1270A VAL* 3.3 7.3 + - - +
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Residues in contact with GLY1267 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1113A PRO 5.6 0.2 - - - -
1114A ASP* 3.4 10.6 + - - +
1261A LEU* 3.4 24.7 - - - +
1265A VAL 3.4 4.2 + - - -
1266A SER* 1.3 70.5 + - - +
1268A SER* 1.3 63.6 + - - +
1270A VAL* 3.1 14.2 + - - +
1271A ILE* 3.2 16.8 + - - +
1291A ASP* 5.3 2.0 - - - -
1299A THR* 5.8 0.2 - - - -
1301A LEU* 3.6 13.9 - - - +
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Residues in contact with SER1268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1114A ASP* 2.9 30.1 + - - -
1266A SER* 3.7 2.7 - - - -
1267A GLY* 1.3 70.2 - - - +
1269A LYS* 1.3 58.9 + - - +
1270A VAL 2.9 1.1 - - - -
1271A ILE* 2.5 42.0 + - - +
1272A THR* 2.6 14.5 + - - -
1291A ASP* 5.2 3.4 + - - -
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Residues in contact with LYS1269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1265A VAL* 5.7 1.8 - - + -
1266A SER* 3.1 23.3 + - - +
1268A SER* 1.3 75.7 - - - +
1270A VAL* 1.3 56.0 + - + +
1272A THR* 3.4 13.7 - - + -
1273A GLN* 2.8 52.8 + - + +
1324A ASP* 4.0 13.5 - - + +
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Residues in contact with VAL1270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1261A LEU* 5.1 3.1 - - + -
1265A VAL* 3.7 28.0 - - + -
1266A SER 3.3 2.9 + - - +
1267A GLY* 3.1 11.3 + - - +
1268A SER 2.6 4.6 + - - -
1269A LYS* 1.3 71.0 - - - +
1271A ILE* 1.3 59.8 + - - +
1272A THR 3.2 0.2 + - - -
1273A GLN* 3.3 7.6 + - - +
1274A ILE* 2.9 45.6 + - + +
1301A LEU* 4.0 18.6 - - + -
1323A THR* 4.6 2.2 - - - +
1324A ASP* 4.5 7.2 - - + +
1325A LEU* 4.0 41.1 - - + +
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Residues in contact with ILE1271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1267A GLY 3.5 13.7 - - - +
1268A SER* 2.5 23.3 + - - +
1270A VAL* 1.3 74.2 - - + +
1272A THR* 1.3 62.3 + - - +
1274A ILE* 3.8 5.6 - - - +
1275A ALA* 3.1 22.6 + - + +
1289A VAL* 4.1 33.2 - - + +
1291A ASP* 3.7 38.1 - - + +
1301A LEU* 4.1 14.4 - - + -
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Residues in contact with THR1272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1268A SER* 2.6 17.3 + - - -
1269A LYS* 3.4 17.9 - - + +
1271A ILE* 1.3 68.8 - - - +
1273A GLN* 1.3 74.1 + - + +
1275A ALA* 2.8 18.5 + - - +
1276A ASP* 2.9 27.3 + - - +
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Residues in contact with GLN1273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1269A LYS* 2.8 39.1 + - + +
1270A VAL* 3.6 5.3 - - - +
1272A THR* 1.3 78.7 - - + +
1274A ILE* 1.3 65.0 + - - +
1276A ASP* 3.3 19.7 + - - +
1277A GLN* 3.5 13.9 + - - +
1322A THR 5.1 2.7 - - - +
1323A THR* 3.1 20.0 - - + -
1324A ASP* 2.6 58.6 + - - +
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Residues in contact with ILE1274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1270A VAL* 2.9 32.4 + - + +
1271A ILE* 3.8 4.7 - - - +
1272A THR 2.8 3.2 + - - -
1273A GLN* 1.3 74.1 - - - +
1275A ALA* 1.3 65.2 + - - +
1276A ASP 3.0 2.0 + - - -
1277A GLN* 3.0 21.3 + - - +
1278A MET* 3.2 19.1 + - + +
1283A LEU* 5.1 8.4 - - + +
1286A VAL* 5.3 4.5 - - + -
1289A VAL* 3.6 29.2 - - + -
1303A ILE* 3.2 37.5 - - + -
1319A LEU* 4.1 13.2 - - + -
1323A THR* 4.0 15.5 - - + -
1325A LEU* 4.9 2.0 - - + -
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Residues in contact with ALA1275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1271A ILE* 3.1 18.8 + - + +
1272A THR* 2.8 9.1 + - - +
1274A ILE* 1.3 75.0 - - + +
1276A ASP* 1.3 57.7 + - - +
1277A GLN 3.4 0.2 - - - -
1278A MET* 3.6 17.1 - - + +
1279A GLN* 3.0 27.0 + - - +
1289A VAL* 6.3 0.9 - - + -
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Residues in contact with ASP1276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1272A THR* 2.9 27.9 + - - +
1273A GLN* 3.3 15.4 - - - +
1274A ILE 3.0 0.4 + - - -
1275A ALA* 1.3 74.7 - - - +
1277A GLN* 1.3 62.2 + - + +
1279A GLN* 3.3 7.6 + - - +
1280A ALA* 2.8 29.2 + - - +
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Residues in contact with GLN1277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1273A GLN 4.0 14.5 + - - +
1274A ILE* 3.0 10.6 + - - +
1276A ASP* 1.3 76.2 - - + +
1278A MET* 1.3 55.6 - - - +
1280A ALA* 4.1 6.1 - - - -
1281A LYS* 2.5 31.4 + - - -
1282A LYS* 2.8 31.6 + - + +
1283A LEU* 3.4 36.1 + - + +
1318A HIS* 4.6 3.3 + - - -
1319A LEU* 4.2 8.0 - - - +
1322A THR* 3.2 44.0 + - - +
1323A THR* 4.7 3.0 - - - +
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Residues in contact with MET1278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1274A ILE* 3.2 17.1 + - + +
1275A ALA* 3.6 23.6 - - + +
1276A ASP 3.2 0.2 - - - -
1277A GLN* 1.3 77.3 - - - +
1279A GLN* 1.3 57.2 + - - +
1281A LYS* 2.9 26.3 + - - +
1283A LEU* 4.2 20.9 - - + +
1286A VAL* 3.6 48.7 - - + +
1287A VAL 4.6 3.8 - - - +
1288A ASP* 4.6 9.4 - - - +
1289A VAL* 4.8 4.5 - - - -
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Residues in contact with GLN1279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1275A ALA 3.0 17.1 + - - +
1276A ASP* 3.7 7.2 - - - +
1278A MET* 1.3 73.9 - - - +
1280A ALA* 1.3 60.3 + - - +
1281A LYS* 3.3 3.1 + - - +
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Residues in contact with ALA1280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1276A ASP 2.8 17.9 + - - +
1277A GLN* 3.7 7.4 - - - +
1279A GLN* 1.3 73.8 - - - +
1281A LYS* 1.3 70.4 + - - +
1282A LYS* 3.3 29.6 + - + +
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Residues in contact with LYS1281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1277A GLN 2.5 13.3 + - - -
1278A MET 2.9 14.6 + - - +
1279A GLN 4.4 3.1 - - - +
1280A ALA* 1.3 78.6 - - - +
1282A LYS* 1.3 60.6 + - - +
1283A LEU 3.2 7.2 + - - +
1284A PRO* 3.4 45.7 + - + +
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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