Contacts of the helix formed by residues 1290 - 1302 (chain A) in PDB entry 2H7C
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 THR1290 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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285A SO4 3.3 18.4 - - - +
1064A ARG* 4.2 1.6 - - - -
1288A GLN 4.9 3.6 - - - +
1289A LYS* 1.3 76.9 - - - +
1291A GLU* 1.3 67.1 + - - +
1292A GLU* 3.6 9.0 + - - +
1293A GLU* 2.8 49.6 + - - +
1294A LEU* 3.1 12.8 + - - +
2288B GLN* 5.6 2.9 - - - +
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Residues in contact with GLU1291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285A SO4 2.7 19.9 + - - +
1064A ARG* 4.4 0.4 - - - +
1088A THR* 2.6 42.0 + - + +
1112A LEU* 4.3 6.0 - - - +
1113A SER* 3.4 22.0 + - - -
1114A GLU* 3.4 29.6 + - + +
1175A TRP* 3.8 6.0 - - + -
1290A THR* 1.3 71.7 - - - +
1292A GLU* 1.3 64.8 + - - +
1294A LEU* 3.2 2.8 + - - -
1295A LEU* 3.0 22.6 + - + +
2275B LYS* 4.9 13.6 + - - +
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Residues in contact with GLU1292 (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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1290A THR* 3.2 8.8 + - - +
1291A GLU* 1.3 80.4 - - - +
1293A GLU* 1.3 57.0 + - - +
1295A LEU* 3.1 23.5 + - - +
1296A GLU* 2.9 47.5 + - - +
2275B LYS* 5.0 10.3 + - - +
6300F LYS* 3.1 29.9 + - - +
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Residues in contact with GLU1293 (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 ALA 6.1 0.7 - - - +
1288A GLN 4.6 0.7 - - - +
1289A LYS* 3.4 33.6 + - + +
1290A THR* 2.8 46.0 + - - +
1292A GLU* 1.3 78.0 - - + +
1294A LEU* 1.3 58.3 + - - +
1296A GLU* 3.3 17.0 + - - +
1297A THR* 3.0 30.6 + - - -
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Residues in contact with LEU1294 (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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1064A ARG* 3.4 41.1 - - - +
1065A PHE* 4.4 7.9 - - + -
1174A ILE* 3.8 18.9 - - + +
1175A TRP* 3.4 31.4 - - + +
1272A ALA* 4.9 1.1 - - + -
1286A LEU* 4.0 24.9 - - + +
1289A LYS* 3.9 19.3 - - + -
1290A THR 3.1 13.4 + - - +
1291A GLU 3.8 1.6 - - - +
1293A GLU* 1.3 73.9 - - - +
1295A LEU* 1.3 61.2 + - - +
1297A THR* 3.4 11.5 + - + +
1298A THR* 2.9 29.5 + - - -
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Residues in contact with LEU1295 (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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1088A THR* 4.4 13.5 - - + -
1089A GLN* 3.7 33.9 - - - +
1090A ASP* 4.1 6.5 - - - +
1091A PRO* 4.5 8.3 - - + -
1112A LEU* 4.4 14.1 - - + -
1175A TRP* 3.8 8.2 - - + -
1291A GLU* 3.0 15.0 + - + +
1292A GLU* 3.4 27.8 - - - +
1294A LEU* 1.3 73.6 - - - +
1296A GLU* 1.3 61.7 + - - +
1298A THR* 3.1 11.3 + - - -
1299A LEU* 2.9 46.3 + - + +
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Residues in contact with GLU1296 (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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1292A GLU* 2.9 38.1 + - - +
1293A GLU* 3.5 15.4 - - - +
1295A LEU* 1.3 74.3 - - - +
1297A THR* 1.3 59.3 + - - +
1299A LEU* 3.2 10.7 + - - +
1300A LYS* 2.8 38.1 + - - +
6296F GLU* 2.7 41.3 - - + +
6300F LYS* 2.9 33.0 + - - -
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Residues in contact with THR1297 (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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1174A ILE* 3.9 17.0 - - + -
1268A ILE* 4.0 27.6 - - + +
1271A THR* 4.2 14.9 + - - -
1272A ALA* 3.4 25.6 - - + +
1293A GLU 3.0 15.7 + - - -
1294A LEU* 3.4 13.7 - - + -
1296A GLU* 1.3 76.1 - - - +
1298A THR* 1.3 61.4 + - - +
1300A LYS* 3.3 9.9 + - - +
1301A MET* 3.0 32.1 + - + +
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Residues in contact with THR1298 (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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1A COA 5.6 2.9 - - - +
1089A GLN* 5.9 1.3 - - - -
1090A ASP* 5.3 9.2 - - + +
1145A MET* 4.2 13.9 - - + -
1174A ILE* 3.6 15.1 + - - +
1175A TRP* 3.9 15.1 - - + -
1294A LEU 2.9 18.8 + - - -
1295A LEU* 3.1 19.5 + - + -
1297A THR* 1.3 77.6 - - - +
1299A LEU* 1.3 67.8 + - + +
1301A MET* 3.1 13.3 + - - +
1302A LYS 3.4 8.1 + - - -
1303A PHE* 3.8 29.3 + - + +
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Residues in contact with LEU1299 (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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1A COA 4.1 25.6 + - - +
1090A ASP* 3.7 39.9 - - + +
1091A PRO* 5.2 3.6 - - + -
1295A LEU* 2.9 33.6 + - + +
1296A GLU* 3.6 11.4 - - - +
1298A THR* 1.3 77.7 - - + +
1300A LYS* 1.3 64.7 + - + +
1302A LYS* 3.1 12.6 + - - +
6F COA 3.1 16.2 + - - -
6299F LEU* 5.2 9.4 - - + -
6300F LYS* 3.9 33.2 - - + +
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Residues in contact with LYS1300 (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 THR* 3.7 38.9 + - + +
1296A GLU* 2.8 24.9 + - - +
1297A THR* 3.6 6.0 + - - +
1298A THR 3.3 0.2 - - - -
1299A LEU* 1.3 76.9 - - + +
1301A MET* 1.3 57.6 + - - +
1302A LYS* 3.3 1.4 + - - +
6F COA 4.3 6.1 + - - -
6092F LYS* 2.9 26.2 + - - -
6292F GLU* 3.2 19.5 + - - +
6296F GLU* 2.7 42.0 + - + -
6299F LEU* 3.9 21.3 - - + -
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Residues in contact with MET1301 (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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1174A ILE* 5.6 0.2 - - + -
1264A LEU* 4.3 4.3 - - + -
1267A GLN* 3.9 30.3 - - + +
1268A ILE* 3.9 23.1 - - + -
1271A THR* 3.6 26.7 - - + -
1297A THR* 3.0 31.2 + - + +
1298A THR 3.1 3.5 + - - +
1300A LYS* 1.3 74.0 - - - +
1302A LYS* 1.3 79.8 + - - +
1303A PHE* 3.2 54.6 + - + -
1316A GLN* 4.9 6.4 - - + +
6092F LYS* 3.5 5.2 + - - +
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Residues in contact with LYS1302 (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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1A COA 3.1 10.3 + - - -
1298A THR 3.4 2.0 + - - -
1299A LEU* 3.1 14.2 + - - +
1300A LYS 4.2 1.6 - - - +
1301A MET* 1.3 89.1 - - - +
1303A PHE* 1.3 66.6 + - - +
1305A SER* 3.7 16.2 + - - +
1307A ASP* 2.9 50.0 + - + +
1309A GLN* 5.8 0.4 + - - -
1316A GLN 5.1 1.2 - - - +
1317A PRO* 5.1 0.9 - - - +
6F COA 2.7 34.8 - - + +
6092F LYS* 3.0 47.4 - - + +
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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