Contacts of the helix formed by residues 1275 - 1288 (chain B) in PDB entry 4E70
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 ASP1275 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1274B PRO* 1.3 74.8 - - - +
1276B GLU* 1.3 58.8 + - - +
1278B VAL* 4.5 0.7 - - - -
1279B LEU* 2.7 35.5 + - - +
1335B ARG* 3.0 31.5 + - - +
1342B LYS* 5.6 3.6 + - - -
1343B LEU* 3.8 22.9 - - + +
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Residues in contact with GLU1276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1274B PRO* 3.3 2.0 - - + +
1275B ASP* 1.3 78.4 - - - +
1277B PRO* 1.3 72.2 - - + +
1279B LEU* 3.9 5.8 - - - +
1280B LYS* 3.2 21.8 + - - +
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Residues in contact with PRO1277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1254B PHE* 3.7 29.3 - - + -
1273B TRP* 4.5 7.9 - - + -
1274B PRO* 3.3 39.0 - - + +
1276B GLU* 1.3 91.9 - - + +
1278B VAL* 1.3 62.5 + - - +
1280B LYS* 3.4 6.4 + - + +
1281B MET* 3.0 24.9 + - - +
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Residues in contact with VAL1278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1270B LEU* 3.9 35.0 - - + +
1273B TRP* 3.7 30.3 - - + +
1274B PRO 3.3 18.0 + - - +
1275B ASP* 3.8 2.7 - - - +
1277B PRO* 1.3 74.4 - - - +
1279B LEU* 1.3 60.1 + - - +
1281B MET* 3.2 10.3 + - + +
1282B LEU* 2.8 49.1 + - + +
1335B ARG* 4.0 6.3 - - - +
1340B TRP* 5.3 1.3 - - + -
1343B LEU* 4.4 15.9 - - + -
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Residues in contact with LEU1279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1275B ASP 2.7 21.7 + - - +
1276B GLU* 3.9 5.2 - - - +
1278B VAL* 1.3 72.8 - - - +
1280B LYS* 1.3 58.9 + - - +
1282B LEU* 3.2 3.6 + - - +
1283B LYS* 2.9 55.0 + - - +
1343B LEU* 3.9 20.6 - - + +
1346B GLU* 3.7 24.9 - - + +
1347B ALA* 3.7 33.2 - - + +
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Residues in contact with LYS1280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1276B GLU 3.2 14.9 + - - +
1277B PRO* 3.8 7.2 - - + +
1278B VAL 3.3 0.2 - - - -
1279B LEU* 1.3 80.6 - - - +
1281B MET* 1.3 62.2 + - - +
1283B LYS* 3.5 10.2 + - - +
1284B GLN* 3.3 31.0 + - - +
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Residues in contact with MET1281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1253B MET* 3.5 52.9 - - + +
1254B PHE* 3.8 24.2 - - + -
1258B ILE* 4.2 12.6 - - + -
1266B PHE* 3.9 18.2 - - + -
1270B LEU* 3.6 31.2 - - + -
1273B TRP* 5.7 0.4 - - + -
1277B PRO 3.0 13.5 + - - +
1278B VAL* 3.6 8.3 - - + +
1280B LYS* 1.3 75.0 - - - +
1282B LEU* 1.3 65.7 + - + +
1284B GLN* 3.2 15.8 + - - +
1285B CYS* 3.0 22.1 + - - -
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Residues in contact with LEU1282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1266B PHE* 4.8 6.7 - - + -
1270B LEU* 4.3 22.2 - - + -
1278B VAL* 2.8 40.0 + - + +
1279B LEU* 3.6 5.8 - - - +
1281B MET* 1.3 74.0 - - + +
1283B LYS* 1.3 56.1 + - - +
1285B CYS* 3.1 6.2 + - - +
1286B LYS 2.8 23.7 + - - -
1298B LEU* 3.6 31.2 - - + -
1300B ILE* 5.0 0.2 - - + -
1340B TRP* 5.7 0.7 - - + -
1343B LEU* 4.3 26.2 - - + +
1344B PHE* 4.3 19.1 - - + -
1347B ALA* 3.7 12.6 - - + -
1349B PHE* 3.4 11.4 - - + -
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Residues in contact with LYS1283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1279B LEU* 2.9 44.1 + - + +
1280B LYS* 3.8 8.3 - - - +
1281B MET 3.3 0.2 - - - -
1282B LEU* 1.3 75.9 - - - +
1284B GLN* 1.3 58.0 + - + +
1286B LYS* 3.2 12.0 + - + +
1287B LYS* 3.0 27.5 + - - +
1346B GLU 3.4 21.2 + - - -
1347B ALA* 3.8 16.8 - - - +
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Residues in contact with GLN1284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1253B MET 4.4 7.8 - - - +
1254B PHE 4.4 16.8 + - - +
1255B THR* 6.2 1.2 - - - +
1256B ASP 5.2 5.1 - - - +
1258B ILE* 6.0 3.2 - - + +
1280B LYS* 3.3 18.6 + - - +
1281B MET* 3.2 17.7 + - + +
1283B LYS* 1.3 78.2 - - + +
1285B CYS* 1.3 57.4 - - - +
1287B LYS* 3.4 7.3 + - - +
1288B ALA* 3.1 27.9 + - - +
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Residues in contact with CYS1285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1258B ILE* 4.0 26.5 - - - -
1264B VAL* 4.4 12.1 - - + -
1266B PHE* 4.1 24.0 - - - -
1281B MET 3.0 19.5 + - - -
1282B LEU* 3.1 11.9 + - - +
1284B GLN* 1.3 74.3 - - - +
1286B LYS* 1.3 55.2 + - - +
1288B ALA* 3.6 4.4 - - - -
1289B LEU* 2.7 51.5 + - + +
1298B LEU* 4.7 4.0 - - + -
1349B PHE* 4.3 8.5 - - + -
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Residues in contact with LYS1286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1282B LEU 2.8 11.4 + - - +
1283B LYS* 3.3 10.1 - - + +
1285B CYS* 1.3 78.4 - - - +
1287B LYS* 1.3 60.3 + - + +
1289B LEU* 3.6 2.0 + - - +
1290B THR* 2.8 35.8 + - - +
1347B ALA 3.5 20.2 - - - +
1348B GLY* 2.9 35.8 + - - +
1349B PHE* 3.7 14.7 - - + +
1350B LYS* 3.0 10.7 - - - +
1368B PRO* 2.9 33.0 + - + +
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Residues in contact with LYS1287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1283B LYS 3.0 12.7 + - - +
1284B GLN* 3.7 10.1 - - - +
1286B LYS* 1.3 77.6 - - + +
1288B ALA* 1.3 63.1 + - - +
1290B THR* 3.3 22.1 + - - +
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Residues in contact with ALA1288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1258B ILE* 5.3 9.6 - - + +
1260B HIS* 5.9 10.4 - - + +
1284B GLN 3.1 17.3 + - - +
1285B CYS* 3.7 6.7 - - - +
1287B LYS* 1.3 74.3 - - - +
1289B LEU* 1.3 62.3 + - + +
1290B THR 3.0 14.3 + - - -
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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