Contacts of the helix formed by residues 1309 - 1320 (chain B) in PDB entry 3EFJ
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 PRO1309 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1178B VAL* 4.0 9.0 - - + -
1182B ILE* 4.3 4.7 - - + -
1277B MET* 3.8 15.0 - - + -
1304B GLN* 3.7 0.7 + - - -
1307B TYR 3.7 8.3 - - - +
1308B CYS* 1.3 92.4 - - + +
1310B ASP* 1.3 65.1 + - - +
1311B PRO* 4.0 14.8 - - + -
1312B LEU* 3.4 10.4 + - + -
1313B TYR 3.2 16.6 + - - -
1340B ILE* 5.2 0.7 - - + -
1344B PHE* 3.5 35.2 - - + -
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Residues in contact with ASP1310 (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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1304B GLN* 2.8 27.7 + - - +
1308B CYS 4.2 0.5 - - - +
1309B PRO* 1.3 69.6 - - - +
1311B PRO* 1.4 75.0 - - + +
1313B TYR* 3.1 4.3 + - - +
1314B GLU* 3.0 22.5 + - - +
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Residues in contact with PRO1311 (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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1309B PRO* 3.6 11.2 - - + -
1310B ASP* 1.4 94.3 - - + +
1312B LEU* 1.3 57.2 + - - +
1314B GLU* 3.3 11.6 - - + +
1315B VAL* 3.2 25.8 + - - +
1336B ARG* 4.5 2.9 + - - +
1340B ILE* 3.6 26.6 - - + +
1344B PHE* 6.1 0.9 - - + -
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Residues in contact with LEU1312 (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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1182B ILE* 4.0 18.8 - - + -
1273B LEU* 4.2 25.4 - - + -
1277B MET* 3.8 39.9 - - + -
1308B CYS* 4.1 2.9 - - - -
1309B PRO* 3.4 13.4 + - + +
1310B ASP 3.1 0.8 - - - -
1311B PRO* 1.3 78.5 - - - +
1313B TYR* 1.3 65.8 + - - +
1314B GLU 3.1 1.6 - - - -
1315B VAL* 3.1 16.4 + - + +
1316B MET* 3.1 21.7 + - + +
1337B ILE* 4.3 23.1 - - + -
1340B ILE* 3.8 25.3 - - + +
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Residues in contact with TYR1313 (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 TRP* 5.3 0.2 - + - -
1301B ARG* 4.7 2.1 - - - +
1302B LEU 2.6 29.9 + - - -
1303B LEU* 3.9 4.0 - - - +
1304B GLN* 3.4 64.9 + - + +
1305B PRO* 4.2 1.6 - - + -
1308B CYS* 3.7 7.7 - - - -
1309B PRO 3.2 5.3 + - - -
1310B ASP 3.1 7.8 + - - +
1312B LEU* 1.3 72.5 - - - +
1314B GLU* 1.3 65.5 + - - +
1316B MET* 3.3 18.7 + - - -
1317B LEU* 3.1 51.2 + - + +
1320B TRP* 4.4 13.0 - + - -
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Residues in contact with GLU1314 (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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1310B ASP 3.0 12.2 + - - +
1311B PRO* 3.3 14.4 - - + +
1313B TYR* 1.3 76.6 - - - +
1315B VAL* 1.3 62.1 + - - +
1317B LEU* 3.2 19.9 + - - +
1318B LYS* 2.5 56.6 + - - +
1336B ARG* 3.8 10.1 - - - +
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Residues in contact with VAL1315 (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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1273B LEU* 3.9 22.9 - - + -
1311B PRO 3.2 10.9 + - - +
1312B LEU* 3.1 13.6 + - + +
1314B GLU* 1.3 76.2 - - - +
1316B MET* 1.3 63.8 + - - +
1318B LYS* 3.0 7.1 + - - +
1319B CYS* 3.0 21.0 + - - -
1333B LEU* 3.6 26.5 - - + -
1336B ARG* 3.5 38.4 - - + +
1337B ILE* 4.6 9.2 - - + -
1340B ILE* 4.2 15.0 - - + -
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Residues in contact with MET1316 (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 GLY* 3.9 13.2 - - - +
1273B LEU* 3.7 38.4 - - + +
1274B TRP* 3.7 23.3 - - - +
1277B MET* 3.8 9.6 - - + -
1305B PRO* 4.6 1.6 - - + -
1308B CYS* 3.7 25.6 - - - -
1312B LEU* 3.1 13.1 + - + +
1313B TYR* 3.3 25.3 + - + +
1315B VAL* 1.3 76.6 - - - +
1317B LEU* 1.3 58.5 + - - +
1319B CYS* 2.9 27.4 + - - +
1320B TRP* 3.1 37.2 + - + -
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Residues in contact with LEU1317 (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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1301B ARG* 4.2 25.7 + - + -
1313B TYR* 3.1 52.5 + - + +
1314B GLU* 3.5 22.0 - - - +
1316B MET* 1.3 79.3 - - - +
1318B LYS* 1.3 60.8 + - - +
1320B TRP* 3.0 19.3 + - + +
1321B HIS* 3.4 9.9 + - - +
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Residues in contact with LYS1318 (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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1314B GLU* 2.5 41.1 + - - +
1315B VAL 3.0 9.5 + - - +
1317B LEU* 1.3 70.5 - - - +
1319B CYS* 1.3 62.8 + - - +
1320B TRP 3.0 5.9 + - - -
1321B HIS* 3.2 20.4 + - + +
1326B MET 5.7 3.6 - - - +
1327B ARG* 3.4 13.3 - - - +
1328B PRO* 3.6 25.4 - - + +
1336B ARG* 3.1 42.7 - - - +
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Residues in contact with CYS1319 (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 VAL* 3.4 37.2 - - - +
1267B TRP* 3.4 19.4 - - - +
1269B PHE* 4.3 3.6 - - - -
1270B GLY* 3.9 18.8 - - - -
1315B VAL* 3.0 23.8 + - - -
1316B MET 2.9 10.4 + - - +
1318B LYS* 1.3 74.9 - - - +
1320B TRP* 1.3 58.2 + - + +
1321B HIS 3.5 0.2 - - - -
1327B ARG* 3.6 14.7 + - - -
1328B PRO* 4.3 1.6 - - - -
1333B LEU* 3.8 29.2 - - - -
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Residues in contact with TRP1320 (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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1267B TRP* 3.1 55.5 + + + -
1270B GLY* 3.3 26.5 - - - -
1271B VAL* 3.4 12.0 - - + +
1274B TRP* 4.3 4.0 - + + -
1284B TYR* 5.5 1.6 - - - -
1301B ARG* 3.2 54.7 + - + +
1302B LEU* 3.6 52.3 - - + -
1313B TYR* 4.4 7.0 - + - -
1316B MET* 3.3 41.5 - - + -
1317B LEU* 3.0 15.2 + - + +
1318B LYS 3.0 1.2 - - - -
1319B CYS* 1.3 85.4 - - - +
1321B HIS* 1.3 62.6 + - - +
1322B PRO* 3.5 0.2 - - - +
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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