Contacts of the helix formed by residues 1264 - 1280 (chain A) in PDB entry 6O0Z
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 HIS1264 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1262A HIS* 3.6 20.9 - - + +
1263A LYS* 1.3 81.0 - - - +
1265A TYR* 1.3 79.2 + + - +
1266A LEU* 3.2 6.2 + - - -
1267A ASP* 3.7 16.8 + - + +
1268A GLU* 3.7 19.9 + - + +
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Residues in contact with TYR1265 (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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1231A LYS* 4.2 33.8 + - + +
1232A TYR* 3.9 26.1 - + + -
1235A PHE* 3.7 43.9 - + + -
1262A HIS* 3.5 37.2 + + - +
1263A LYS* 3.7 1.0 - - - +
1264A HIS* 1.3 94.8 - + - +
1266A LEU* 1.3 57.9 + - - +
1268A GLU* 2.9 14.6 + - + +
1269A ILE* 2.9 28.1 + - - +
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Residues in contact with LEU1266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1235A PHE* 4.3 11.8 - - + -
1263A LYS* 3.3 29.2 - - + +
1264A HIS* 3.2 3.0 - - - -
1265A TYR* 1.3 79.6 - - - +
1267A ASP* 1.3 74.1 + - - +
1269A ILE* 3.3 16.0 + - + +
1270A ILE* 2.9 31.7 + - - +
1294A TYR* 3.4 15.3 - - + +
1302A ILE* 5.6 8.5 - - + -
1305A GLN* 3.8 37.2 - - + +
1309A ILE* 5.2 16.4 - - + +
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Residues in contact with ASP1267 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1264A HIS* 3.7 15.4 + - - +
1265A TYR 3.2 0.4 - - - -
1266A LEU* 1.3 88.7 - - - +
1268A GLU* 1.3 58.4 + - + +
1270A ILE* 3.3 8.1 + - - +
1271A GLU* 2.9 27.3 + - - +
1294A TYR* 2.4 35.6 + - + -
1298A ARG* 3.0 27.5 + - - -
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Residues in contact with GLU1268 (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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1232A TYR* 3.7 22.7 - - + +
1264A HIS* 3.7 25.1 - - + +
1265A TYR* 2.9 13.8 + - + +
1267A ASP* 1.3 78.9 - - + +
1269A ILE* 1.3 56.1 + - - +
1271A GLU* 3.3 7.9 + - - +
1272A GLN* 2.9 33.8 + - + +
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Residues in contact with ILE1269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1228A LEU* 4.7 8.1 - - + -
1232A TYR* 3.9 31.4 - - + -
1235A PHE* 4.3 7.2 - - + -
1236A LEU* 3.7 27.8 - - + -
1265A TYR 2.9 18.1 + - - +
1266A LEU* 3.6 17.5 - - + +
1267A ASP 3.3 0.2 - - - -
1268A GLU* 1.3 73.8 - - - +
1270A ILE* 1.3 59.9 + - - +
1272A GLN* 3.2 8.3 + - - +
1273A ILE* 3.0 32.5 + - + +
1309A ILE* 4.6 17.5 - - + -
1313A PHE* 4.1 26.0 - - + -
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Residues in contact with ILE1270 (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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1266A LEU* 2.9 17.8 + - + +
1267A ASP* 3.5 11.0 - - - +
1269A ILE* 1.3 76.4 - - - +
1271A GLU* 1.3 57.1 + - - +
1273A ILE* 3.4 11.2 - - + +
1274A SER* 2.9 29.4 + - - -
1290A VAL* 5.3 2.7 - - + -
1291A LEU* 4.0 26.2 - - + -
1294A TYR* 3.9 38.8 - - + -
1309A ILE* 3.7 26.7 - - + -
1312A LEU* 3.9 16.2 - - + -
1326A TYR* 5.8 0.4 - - - +
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Residues in contact with GLU1271 (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 ASP 2.9 13.8 + - - +
1268A GLU* 3.6 11.0 - - - +
1269A ILE 3.3 0.2 - - - -
1270A ILE* 1.3 76.8 - - - +
1272A GLN* 1.3 57.9 + - + +
1274A SER* 3.4 7.4 + - - -
1275A GLU* 3.0 30.5 + - - +
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Residues in contact with GLN1272 (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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1226A LEU* 4.9 5.6 - - + +
1227A ALA 4.7 0.6 + - - -
1228A LEU* 3.6 30.5 - - + +
1229A PRO* 4.3 3.4 - - - +
1232A TYR* 4.6 14.7 - - + +
1268A GLU* 2.9 19.5 + - + +
1269A ILE* 3.2 13.2 + - - +
1271A GLU* 1.3 77.1 - - + +
1273A ILE* 1.3 59.0 + - + +
1275A GLU* 3.3 5.0 + - - +
1276A PHE* 3.0 28.2 + - - +
89B G 2.9 46.6 + - - +
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Residues in contact with ILE1273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1226A LEU* 4.2 11.7 - - + -
1228A LEU* 5.8 0.7 - - + -
1269A ILE* 3.0 15.9 + - + +
1270A ILE* 3.4 20.2 - - + +
1272A GLN* 1.3 75.8 - - + +
1274A SER* 1.3 62.9 + - - +
1276A PHE* 3.9 6.9 - - - +
1277A SER* 2.9 32.2 + - - -
1287A LEU* 5.1 4.6 - - + +
1290A VAL* 5.4 4.0 - - + -
1309A ILE* 5.3 2.2 - - + -
1312A LEU* 3.7 39.0 - - + +
1313A PHE* 3.7 32.1 - - + -
1315A LEU* 5.5 10.2 - - + +
1316A THR* 4.7 12.5 - - + +
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Residues in contact with SER1274 (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 ILE* 2.9 20.5 + - - -
1271A GLU* 3.6 9.0 - - - -
1273A ILE* 1.3 75.6 - - - +
1275A GLU* 1.3 60.2 + - - +
1277A SER* 4.1 0.5 - - - -
1278A LYS* 2.9 43.2 + - - +
1287A LEU* 4.5 21.2 - - - +
1291A LEU* 5.0 14.3 - - - +
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Residues in contact with GLU1275 (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 GLU 3.0 17.2 + - - +
1272A GLN* 3.8 4.3 - - - +
1274A SER* 1.3 76.7 + - - +
1276A PHE* 1.3 57.6 + - - +
1278A LYS* 3.4 7.6 + - - +
1279A ARG* 3.0 28.6 + - - +
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Residues in contact with PHE1276 (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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1224A ASN* 4.1 3.1 - - + -
1225A GLU* 3.5 41.3 - - - -
1226A LEU* 3.7 24.5 - - + -
1272A GLN 3.0 17.5 + - - +
1273A ILE* 3.9 6.5 - - - +
1275A GLU* 1.3 77.9 - - - +
1277A SER* 1.3 56.8 + - - +
1279A ARG* 3.0 29.3 + - - +
1280A VAL* 3.0 53.8 + - + +
1281A ILE* 4.4 5.4 - - + -
1316A THR* 3.6 41.7 - - + -
89B G 5.0 4.7 - - - +
90B U 4.7 4.3 - - - -
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Residues in contact with SER1277 (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 ILE 2.9 18.3 + - - -
1274A SER 4.1 2.0 - - - -
1276A PHE* 1.3 74.4 - - - +
1278A LYS* 1.3 63.5 + - - +
1281A ILE* 3.4 30.1 + - - +
1282A LEU* 3.1 25.8 + - - -
1283A ALA* 4.6 6.6 + - - +
1287A LEU* 4.3 24.5 - - - +
1315A LEU* 4.4 9.7 - - - +
1316A THR* 4.6 8.3 - - - -
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Residues in contact with LYS1278 (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 SER* 2.9 29.5 + - - +
1275A GLU* 3.8 6.3 - - - +
1277A SER* 1.3 77.9 - - - +
1279A ARG* 1.3 62.6 + - - +
1282A LEU* 3.6 14.6 - - - +
1287A LEU* 4.1 18.8 - - + -
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Residues in contact with ARG1279 (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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1208A ASN* 4.2 32.7 + - + +
1209A GLY* 5.3 2.2 + - - -
1210A ARG* 4.6 7.1 + - - +
1224A ASN* 4.7 9.3 - - - +
1225A GLU 5.5 0.2 + - - -
1275A GLU 3.0 17.7 + - - +
1276A PHE* 3.0 27.6 + - - +
1278A LYS* 1.3 81.4 - - - +
1280A VAL* 1.3 80.7 + - + +
1282A LEU* 4.1 8.1 - - - +
89B G 4.7 16.4 + - - +
90B U 4.7 27.9 + - - +
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Residues in contact with VAL1280 (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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1208A ASN 4.8 1.1 - - - +
1209A GLY 4.5 1.6 - - - +
1210A ARG* 3.4 22.8 - - + +
1212A ARG* 3.0 28.3 + - - +
1224A ASN* 3.4 33.2 - - + +
1276A PHE* 3.0 43.1 + - + +
1279A ARG* 1.3 109.5 - - + +
1281A ILE* 1.3 70.5 + - + +
1282A LEU* 3.7 1.3 - - - -
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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