Contacts of the helix formed by residues 1266 - 1278 (chain A) in PDB entry 5G04
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 HIS1266 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1220A MET* 3.5 20.1 - - + +
1261A TYR* 4.2 20.4 + + + -
1264A THR* 3.3 14.4 + - - +
1265A ALA* 1.3 75.4 - - - +
1267A ARG* 1.3 68.4 + - + +
1268A HIS* 3.3 37.1 + - + +
1269A THR* 3.4 26.7 - - - -
1270A ALA* 3.5 21.5 + - - +
1305A VAL* 3.7 5.7 - - + +
1316A MET* 4.7 0.2 - - - -
542C THR* 3.9 27.9 - - + +
544C GLU* 3.4 22.5 + - + +
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Residues in contact with ARG1267 (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 ALA 3.4 3.6 + - - -
1266A HIS* 1.3 80.3 + - + +
1268A HIS* 1.3 65.5 + - + +
1269A THR 3.5 0.2 + - - -
1270A ALA* 3.7 4.7 + - - +
1271A GLU* 3.7 18.5 + - - +
1315A GLY* 3.6 19.2 + - - -
1316A MET* 3.7 32.6 - - + +
1318A ASP* 3.8 21.0 - - - +
1319A LEU* 4.1 29.6 - - - +
544C GLU* 4.2 3.7 + - + +
348K SER* 3.9 27.0 + - - -
350K HIS* 5.2 9.5 + - - -
351K ASP* 5.6 7.6 - - - +
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Residues in contact with HIS1268 (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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1234A ALA 5.3 4.0 - - - -
1237A PRO* 6.6 0.2 - - + -
1266A HIS* 3.3 17.8 - - + +
1267A ARG* 1.3 80.4 - - + +
1269A THR* 1.3 65.2 + - - +
1271A GLU* 3.3 18.4 + - + +
1272A VAL* 3.3 40.5 + - + +
347K GLU* 5.7 0.4 + - - -
349K GLU* 3.8 29.0 + - + -
352K GLN* 6.0 1.3 - - - -
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Residues in contact with THR1269 (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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1235A LEU* 5.6 3.1 - - - +
1257A ILE* 3.9 16.9 - - + +
1261A TYR* 3.5 25.8 - - + -
1266A HIS* 3.4 23.1 - - - -
1267A ARG 3.4 0.4 - - - -
1268A HIS* 1.3 75.4 - - - +
1270A ALA* 1.3 66.3 + - - +
1272A VAL* 3.2 11.1 + - + +
1273A LEU* 3.0 46.2 + - + +
1305A VAL* 3.9 18.2 - - + -
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Residues in contact with ALA1270 (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 ALA 6.2 0.2 - - - -
1266A HIS 3.5 10.3 + - - +
1267A ARG* 3.8 10.1 - - - +
1269A THR* 1.3 77.7 - - - +
1271A GLU* 1.3 57.3 + - - +
1273A LEU* 3.4 1.7 + - - +
1274A LEU* 2.9 34.7 + - - +
1302A LEU* 4.2 20.7 - - + +
1305A VAL* 5.2 4.7 - - + +
1306A CYS* 5.4 9.6 - - - -
1316A MET* 5.7 6.5 - - + -
1319A LEU* 4.2 13.9 - - + -
1321A VAL* 5.1 7.6 - - + -
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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 ARG* 3.7 8.1 + - - +
1268A HIS* 3.3 26.8 + - + +
1269A THR 3.2 0.6 - - - -
1270A ALA* 1.3 78.9 - - - +
1272A VAL* 1.3 74.4 + - + +
1274A LEU* 3.5 4.5 + - - +
1275A ALA* 3.2 24.5 + - - +
1319A LEU* 3.8 26.3 - - + +
347K GLU* 5.5 6.8 - - - +
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Residues in contact with VAL1272 (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 ILE* 4.8 9.0 - - + -
1234A ALA* 4.1 33.8 - - + +
1235A LEU* 5.6 5.4 - - + -
1257A ILE* 6.2 0.4 - - + -
1268A HIS* 3.3 33.0 + - + +
1269A THR* 3.2 15.9 + - + +
1271A GLU* 1.3 83.1 - - + +
1273A LEU* 1.3 74.0 + - + +
1275A ALA* 3.3 8.3 + - - +
1276A GLU* 2.9 32.3 + - - +
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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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1232A ILE* 5.3 4.5 - - + -
1254A VAL* 4.3 9.0 - - + -
1257A ILE* 4.1 19.5 - - + -
1269A THR* 3.0 36.0 + - + +
1270A ALA 3.9 3.1 - - - +
1272A VAL* 1.3 83.9 - - + +
1274A LEU* 1.3 55.8 + - - +
1276A GLU* 3.3 20.3 + - - +
1277A ILE* 2.8 34.3 + - - +
1298A ALA* 3.7 16.2 - - - +
1301A ALA* 3.9 12.8 - - + +
1302A LEU* 3.5 41.8 - - + +
1305A VAL* 4.6 0.7 - - + -
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Residues in contact with LEU1274 (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 ALA 2.9 13.6 + - - +
1271A GLU* 3.8 5.6 - - - +
1273A LEU* 1.3 73.6 - - - +
1275A ALA* 1.3 64.0 + - - +
1277A ILE* 3.0 27.9 - - + +
1302A LEU* 3.7 15.6 - - + +
1319A LEU* 3.7 33.7 - - + -
1321A VAL* 3.9 23.3 - - + -
1324A GLN* 3.8 35.5 + - + +
1325A LEU* 3.8 29.4 - - + -
1328A TYR* 3.5 14.7 + - + -
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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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1234A ALA* 6.4 1.6 - - + -
1271A GLU* 3.2 19.0 + - - +
1272A VAL* 3.4 12.6 - - - +
1274A LEU* 1.3 75.8 - - - +
1276A GLU* 1.3 58.8 + - + +
1278A GLY 2.9 26.7 - - - +
1279A ARG* 4.0 5.4 + - - +
1328A TYR* 5.2 1.1 - - - -
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Residues in contact with GLU1276 (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 ILE* 3.2 29.7 - - - +
1233A PRO* 4.5 0.5 - - - +
1234A ALA* 4.1 12.6 + - + +
1254A VAL* 3.6 20.8 - - - +
1272A VAL 2.9 19.3 + - - +
1273A LEU* 3.3 11.6 + - - +
1275A ALA* 1.3 77.8 - - + +
1277A ILE* 1.3 63.7 + - - +
1278A GLY 3.4 0.3 + - - -
1279A ARG* 3.9 29.8 + - - +
1294A TYR* 2.6 52.1 + - + +
1295A SER* 4.7 2.4 - - - -
1298A ALA* 4.0 6.5 - - + -
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Residues in contact with ILE1277 (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 LEU 2.8 18.5 + - - +
1274A LEU* 3.0 33.9 - - + +
1276A GLU* 1.3 73.3 - - - +
1278A GLY* 1.3 56.9 + - - +
1279A ARG 4.1 0.9 + - - -
1295A SER* 3.0 42.8 + - - +
1298A ALA* 4.0 6.7 - - - +
1299A GLY* 3.7 19.5 - - - +
1302A LEU* 5.2 2.7 - - + -
1325A LEU* 4.5 11.9 - - + -
1328A TYR* 3.6 23.1 - - + -
1362A VAL* 4.9 0.9 - - - +
1363A THR* 3.3 15.0 - - - +
1367A ALA* 3.5 39.3 - - + +
1370A ALA* 5.3 0.2 - - + -
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Residues in contact with GLY1278 (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* 2.9 15.8 + - - +
1277A ILE* 1.3 81.9 - - - +
1279A ARG* 1.3 60.8 + - - -
1280A PRO* 4.3 3.3 - - - +
1328A TYR* 3.4 32.0 + - - -
1363A THR* 3.7 9.6 - - - -
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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