Contacts of the helix formed by residues 1259 - 1274 (chain A) in PDB entry 6A5T
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 GLU1259 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1191A SER* 2.3 36.0 + - - -
1192A PRO* 3.7 7.3 - - - +
1193A TRP* 2.8 39.0 - - + +
1244A VAL* 5.4 4.2 - - + +
1258A GLU* 1.3 79.1 - - - +
1260A ASP* 1.3 68.7 + - - +
1261A GLN 3.7 0.2 - - - -
1262A MET* 3.9 20.9 - - + +
1263A LEU* 3.2 25.3 + - + +
18I GLU* 5.6 0.9 - - - -
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Residues in contact with ASP1260 (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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1154A ILE* 4.3 11.3 - - - +
1193A TRP* 5.2 5.6 - - + +
1258A GLU* 2.9 6.7 + - - +
1259A GLU* 1.3 77.9 - - - +
1261A GLN* 1.3 66.5 + - + +
1263A LEU* 3.1 5.5 + - - +
1264A LYS* 2.8 70.5 + - - +
16I PRO* 5.2 15.0 - - + +
43I VAL* 5.5 4.9 - - - +
44I TYR* 4.9 2.3 - - - +
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Residues in contact with GLN1261 (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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1258A GLU* 2.1 33.6 + - + +
1260A ASP* 1.3 73.5 - - + +
1262A MET* 1.3 63.8 + - - +
1264A LYS* 3.1 36.4 + - - +
1265A ARG* 2.8 51.2 + - - +
257B THR* 4.7 14.1 + - - +
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Residues in contact with MET1262 (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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1244A VAL* 4.3 22.2 - - + -
1258A GLU* 2.8 42.3 + - + +
1259A GLU* 3.9 19.3 - - + +
1260A ASP 3.2 0.2 - - - -
1261A GLN* 1.3 75.8 - - - +
1263A LEU* 1.3 65.2 + - - +
1265A ARG* 3.4 16.0 + - - +
1266A ILE* 3.0 34.7 + - + +
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Residues in contact with LEU1263 (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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1154A ILE* 4.4 16.4 - - + -
1193A TRP* 3.4 37.7 - - + +
1195A LEU* 3.6 46.7 - - + +
1226A LEU* 5.3 3.4 - - + -
1242A CYS 5.5 0.7 - - - +
1244A VAL* 3.9 25.6 - - + -
1259A GLU* 3.2 15.4 + - + +
1260A ASP* 3.1 4.4 + - - +
1262A MET* 1.3 78.9 - - - +
1264A LYS* 1.3 57.8 + - - +
1266A ILE* 3.2 15.8 - - + +
1267A GLU* 2.8 25.7 + - - +
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Residues in contact with LYS1264 (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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1154A ILE* 3.6 14.6 - - + -
1260A ASP* 2.8 47.5 + - - +
1261A GLN* 3.1 30.1 + - - +
1262A MET 3.1 0.2 - - - -
1263A LEU* 1.3 75.3 - - - +
1265A ARG* 1.3 61.0 + - - +
1266A ILE 3.1 0.9 - - - -
1267A GLU* 3.0 8.4 + - + +
1268A ALA* 2.9 31.2 + - - +
304B GLU* 5.3 0.2 + - - -
4I PHE* 5.6 7.9 - - - -
44I TYR* 3.4 50.5 - - + +
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Residues in contact with ARG1265 (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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1258A GLU* 4.7 4.4 + - - -
1261A GLN* 2.8 38.0 + - - +
1262A MET* 3.8 21.7 - - - +
1264A LYS* 1.3 74.7 - - - +
1266A ILE* 1.3 63.9 + - + +
1268A ALA* 4.2 4.2 - - - +
1269A HIS* 2.9 28.3 + - - +
257B THR* 5.2 14.6 - - + -
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Residues in contact with ILE1266 (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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1195A LEU* 4.3 1.3 - - + -
1222A PHE* 5.0 5.8 - - + -
1225A ASP* 5.5 4.0 - - + +
1226A LEU* 4.7 16.2 - - + -
1244A VAL* 3.9 31.9 - - + -
1262A MET* 3.0 27.2 + - + +
1263A LEU* 3.2 22.9 - - + +
1265A ARG* 1.3 76.9 - - - +
1267A GLU* 1.3 56.0 + - - +
1269A HIS* 3.7 4.5 - - - +
1270A MET* 2.8 54.2 + - + +
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Residues in contact with GLU1267 (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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1152A THR* 3.0 38.7 - - - +
1153A GLU 5.7 0.4 - - - +
1154A ILE* 5.8 1.3 - - + -
1195A LEU* 4.1 26.5 - - + -
1196A ARG 6.0 0.2 - - - +
1197A LEU* 5.9 4.9 - - + +
1263A LEU 2.8 18.3 + - - +
1264A LYS* 3.0 11.6 + - + +
1266A ILE* 1.3 74.7 - - - +
1268A ALA* 1.3 62.5 + - - +
1270A MET* 3.2 14.0 - - + +
1271A LEU* 3.0 44.2 + - + +
44I TYR* 4.4 18.9 + - + -
46I HIS* 5.7 0.5 + - - +
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Residues in contact with ALA1268 (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 LYS 2.9 15.0 + - - +
1265A ARG* 4.2 4.3 - - - +
1267A GLU* 1.3 79.5 + - - +
1269A HIS* 1.3 60.9 + - - +
1271A LEU* 3.3 6.1 + - - +
1272A ASP* 2.9 30.8 + - - +
257B THR* 5.2 13.7 - - + -
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Residues in contact with HIS1269 (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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1221A VAL* 6.0 0.2 - - + -
1222A PHE* 4.1 23.9 - + - -
1265A ARG 2.9 20.6 + - - +
1266A ILE* 3.7 5.2 - - - +
1268A ALA* 1.3 75.9 - - - +
1270A MET* 1.3 57.1 + - - +
1272A ASP* 3.3 8.4 + - - +
1273A LEU* 2.9 63.1 + - + +
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Residues in contact with MET1270 (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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1145A LEU* 5.2 2.7 - - + -
1195A LEU* 3.6 29.6 - - + -
1197A LEU* 3.6 30.5 - - + -
1218A ILE* 5.1 11.7 - - + -
1222A PHE* 3.5 26.0 - - + -
1226A LEU* 4.7 12.3 - - + -
1242A CYS* 4.9 9.2 - - - -
1266A ILE* 2.8 32.4 + - + +
1267A GLU* 3.2 9.6 - - - +
1269A HIS* 1.3 72.1 + - - +
1271A LEU* 1.3 62.2 - - + +
1272A ASP 2.8 10.3 + - - -
1273A LEU 2.8 0.3 + - - -
1274A ILE* 2.8 46.9 + - + +
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Residues in contact with LEU1271 (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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1144A THR* 4.4 3.5 - - - -
1145A LEU* 3.9 19.7 - - + -
1146A LYS* 3.4 40.3 + - + +
1149A THR* 3.7 28.0 - - + +
1152A THR* 3.7 16.8 - - + -
1197A LEU* 4.9 6.7 - - + -
1267A GLU* 3.0 38.2 + - + +
1268A ALA* 4.0 6.1 - - - +
1270A MET* 1.3 80.0 - - + +
1272A ASP* 1.3 59.6 + - - +
1274A ILE* 4.9 0.7 - - - -
48I LEU* 3.9 18.6 - - + -
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Residues in contact with ASP1272 (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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1142A TYR* 4.7 3.5 + - - -
1144A THR* 4.0 17.4 - - - +
1146A LYS* 5.7 1.1 - - - +
1268A ALA 2.9 17.1 + - - +
1269A HIS* 3.6 10.3 - - + +
1270A MET 2.8 1.2 + - - -
1271A LEU* 1.3 79.7 - - - +
1273A LEU* 1.3 70.5 + - - +
1274A ILE 3.7 0.4 - - - -
254B ASP* 5.6 6.5 - - + +
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Residues in contact with LEU1273 (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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1142A TYR* 5.5 1.7 + - - +
1144A THR* 5.8 0.4 - - - -
1221A VAL* 5.2 15.7 - - + -
1222A PHE* 6.5 0.2 - - + -
1269A HIS* 2.9 45.1 + - + +
1270A MET 2.8 5.7 + - - -
1272A ASP* 1.3 83.5 - - - +
1274A ILE* 1.3 57.1 + - + +
1275A ALA* 2.6 25.6 + - + +
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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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1144A THR* 3.2 5.5 - - - -
1145A LEU* 2.7 60.4 + - + -
1214A VAL* 5.0 0.7 - - + -
1217A LYS* 5.1 4.5 - - + +
1218A ILE* 4.5 34.8 - - + +
1221A VAL* 5.1 9.4 - - + -
1222A PHE* 4.1 27.1 - - + -
1270A MET* 2.8 35.7 + - + +
1271A LEU 4.9 0.4 - - - -
1272A ASP 3.7 0.6 - - - -
1273A LEU* 1.3 75.6 - - + +
1275A ALA* 1.3 57.2 + - - +
1276A LEU* 3.8 16.2 - - + -
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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