Contacts of the helix formed by residues 1264 - 1279 (chain A) in PDB entry 4Z4Q
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 ASN1264 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1108A MET 3.8 3.8 - - - -
1109A ASP 3.2 19.2 + - - +
1110A GLY* 3.3 17.2 - - - -
1262A GLU 4.0 2.0 + - - -
1263A ILE* 1.3 73.3 - - - +
1265A LYS* 1.3 64.6 + - - +
1266A ALA* 2.9 12.6 + - - +
1267A ASN* 2.9 47.0 + - + +
1268A LEU* 3.1 22.0 + - - +
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Residues in contact with LYS1265 (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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1108A MET* 2.9 26.0 + - + +
1109A ASP* 2.9 36.1 - - - +
1259A ILE* 4.0 18.8 - - + -
1263A ILE 3.5 3.8 + - - -
1264A ASN* 1.3 71.8 - - - +
1266A ALA* 1.3 58.4 + - - +
1268A LEU* 3.1 4.2 + - - +
1269A VAL* 2.9 30.8 + - + +
1289A ASP* 3.2 22.0 - - - +
1291A SER* 3.6 29.6 - - - +
1296A LEU* 3.9 21.8 - - + -
1298A ILE* 4.2 16.4 - - + -
447B ARG* 5.8 0.7 - - - +
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Residues in contact with ALA1266 (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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1109A ASP* 3.3 33.4 + - + +
1264A ASN* 2.9 8.7 + - - +
1265A LYS* 1.3 79.3 - - - +
1267A ASN* 1.3 64.5 + - - +
1269A VAL* 3.3 8.1 + - - +
1270A LYS* 3.0 23.0 + - - +
1289A ASP* 5.5 1.3 - - - -
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Residues in contact with ASN1267 (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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1264A ASN* 2.9 43.6 + - + +
1266A ALA* 1.3 71.5 - - - +
1268A LEU* 1.3 56.5 + - - +
1270A LYS* 3.3 7.9 + - - +
1271A LYS* 2.7 37.5 + - - +
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Residues in contact with LEU1268 (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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1259A ILE* 4.1 32.8 - - + -
1263A ILE* 4.3 12.6 - - + -
1264A ASN 3.1 12.6 + - - +
1265A LYS* 3.1 9.4 - - - +
1267A ASN* 1.3 75.8 - - - +
1269A VAL* 1.3 57.1 + - - +
1271A LYS* 3.0 9.3 + - - +
1272A ILE* 2.9 42.1 + - + +
1298A ILE* 4.4 14.6 - - + -
1319A THR* 3.9 13.2 - - - +
1320A ASP* 4.2 8.1 - - + +
1321A LEU* 3.8 37.0 - - + +
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Residues in contact with VAL1269 (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 LYS* 2.9 18.1 + - + +
1266A ALA* 3.3 8.9 + - - +
1268A LEU* 1.3 75.7 - - - +
1270A LYS* 1.3 62.0 + - - +
1272A ILE* 3.6 9.3 + - - +
1273A ASP* 3.2 22.4 + - + +
1287A VAL* 3.9 21.9 - - + +
1289A ASP* 4.1 35.4 - - + +
1298A ILE* 3.7 31.0 - - + -
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Residues in contact with LYS1270 (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 ALA 3.0 13.2 + - - +
1267A ASN* 3.5 11.4 - - - +
1269A VAL* 1.3 76.5 - - - +
1271A LYS* 1.3 64.2 + - - +
1273A ASP* 3.0 12.1 + - + +
1274A ASP* 3.0 40.9 + - - +
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Residues in contact with LYS1271 (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 ASN 2.7 21.7 + - - +
1268A LEU* 3.6 9.2 - - - +
1270A LYS* 1.3 73.9 - - - +
1272A ILE* 1.3 61.9 + - - +
1274A ASP* 3.4 13.8 + - + +
1275A VAL* 3.4 21.0 + - + +
1318A TYR 4.2 5.3 + - - +
1319A THR* 3.4 32.6 - - + +
1320A ASP* 3.0 44.9 + - - +
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Residues in contact with ILE1272 (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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1256A ILE* 4.5 15.3 - - + -
1268A LEU* 2.9 46.0 + - + +
1269A VAL* 3.8 8.5 - - - +
1271A LYS* 1.3 71.9 - - - +
1273A ASP* 1.3 64.0 + - - +
1275A VAL* 2.9 26.9 + - - +
1276A ARG* 3.2 4.3 + - - +
1284A ILE* 4.7 5.3 - - + +
1287A VAL* 3.6 22.7 - - + -
1298A ILE* 5.0 7.4 - - + -
1300A ILE* 4.1 28.9 - - + -
1315A LEU* 4.3 17.0 - - + -
1319A THR* 4.3 9.9 - - - +
1321A LEU* 4.6 6.1 - - + -
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Residues in contact with ASP1273 (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 VAL* 3.2 12.0 + - + +
1270A LYS* 3.0 14.8 + - + +
1272A ILE* 1.3 77.0 - - - +
1274A ASP* 1.3 54.6 + - - +
1276A ARG* 2.9 36.4 + - - +
1277A VAL* 2.7 51.5 + - - +
1287A VAL* 4.0 23.4 + - + +
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Residues in contact with ASP1274 (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 LYS* 3.0 36.0 + - - +
1271A LYS* 3.5 16.1 - - + +
1272A ILE 3.2 0.2 - - - -
1273A ASP* 1.3 76.9 - - - +
1275A VAL* 1.3 54.8 + - + +
1277A VAL* 3.0 7.5 + - - +
1278A ASN* 2.7 54.3 + - - +
1280A LYS* 5.4 0.2 - - - -
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Residues in contact with VAL1275 (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 LYS* 3.4 15.0 + - + +
1272A ILE 2.9 12.5 + - - +
1274A ASP* 1.3 77.9 - - + +
1276A ARG* 1.3 60.1 + - - +
1279A ASN* 3.0 19.6 + - - -
1280A LYS* 3.4 18.7 + - + -
1281A VAL* 4.0 13.8 - - + +
1284A ILE* 3.7 19.5 - - + -
1314A TYR* 3.9 33.7 - - + +
1315A LEU* 4.1 15.3 - - + -
1318A TYR 5.8 0.2 - - - +
1319A THR* 4.2 10.1 - - + -
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Residues in contact with ARG1276 (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 ILE 3.2 2.7 + - - +
1273A ASP* 2.9 36.0 + - - +
1275A VAL* 1.3 80.7 - - - +
1277A VAL* 1.3 82.4 + - - +
1279A ASN* 3.3 23.7 + - - +
1281A VAL 5.8 0.9 - - - -
1284A ILE* 3.3 45.3 - - + +
1285A ALA 3.7 26.3 + - - -
1286A GLU* 4.1 19.0 - - - +
1287A VAL* 4.4 1.1 - - + +
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Residues in contact with VAL1277 (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 ASP* 2.7 39.3 + - - +
1274A ASP* 3.8 7.9 - - - +
1276A ARG* 1.3 96.1 - - - +
1278A ASN* 1.3 68.8 + - - +
1279A ASN* 3.7 1.0 + - - +
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Residues in contact with ASN1278 (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 ASP* 2.7 39.1 + - - +
1277A VAL* 1.3 82.1 - - - +
1279A ASN* 1.3 70.8 + - - +
1280A LYS* 3.2 24.5 + - + +
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Residues in contact with ASN1279 (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 VAL 3.0 9.7 + - - -
1276A ARG* 3.3 20.1 + - - +
1277A VAL 3.4 1.4 - - - +
1278A ASN* 1.3 79.2 - - - +
1280A LYS* 1.3 63.5 + - - +
1281A VAL 3.4 8.3 - - - +
1282A ALA* 4.2 24.0 - - - +
1283A GLY 5.0 1.0 + - - +
1284A ILE 5.6 1.6 - - - +
1303A LYS* 4.7 15.6 + - - +
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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