Contacts of the helix formed by residues 1317 - 1331 (chain A) in PDB entry 3F2B
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 GLY1317 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1313A ALA 3.0 7.7 + - - -
1314A MET 3.5 14.4 - - - -
1315A ILE 3.0 2.1 - - - -
1316A LYS* 1.3 81.1 - - - +
1318A SER* 1.3 67.6 + - - -
1319A ALA 3.4 2.0 - - - -
1320A ALA 3.0 13.1 + - - -
1321A ILE* 3.0 20.0 + - - +
1353A CYS* 4.3 6.7 - - - -
1358A SER* 6.4 1.1 - - - -
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Residues in contact with SER1318 (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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1316A LYS 4.4 0.2 + - - -
1317A GLY* 1.3 71.6 - - - +
1319A ALA* 1.3 63.0 + - - +
1321A ILE* 3.4 6.2 + - - +
1322A ARG* 3.1 22.1 + - - +
1350A LEU* 3.3 27.4 - - - +
1353A CYS* 4.1 16.1 - - - +
1354A GLU* 2.4 32.9 + - - +
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Residues in contact with ALA1319 (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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1317A GLY 3.4 0.6 - - - -
1318A SER* 1.3 78.7 - - - +
1320A ALA* 1.3 63.4 + - - +
1322A ARG* 3.4 12.4 + - - +
1323A LYS* 3.0 22.3 + - - +
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Residues in contact with ALA1320 (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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1313A ALA* 3.7 15.8 - - + +
1316A LYS* 3.6 40.4 - - + +
1317A GLY 3.0 4.9 + - - +
1319A ALA* 1.3 79.5 - - - +
1321A ILE* 1.3 62.5 + - - +
1323A LYS* 3.1 17.0 + - - +
1324A ARG* 3.2 15.8 + - - +
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Residues in contact with ILE1321 (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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1313A ALA* 3.7 20.2 - - + +
1314A MET* 3.8 18.2 - - + +
1317A GLY* 3.0 26.1 + - - +
1318A SER 3.7 5.2 - - - +
1320A ALA* 1.3 74.1 - - - +
1322A ARG* 1.3 63.2 + - - +
1324A ARG* 3.0 14.8 + - - +
1325A ILE* 3.0 14.4 + - + +
1346A LEU* 3.5 42.1 - - + +
1349A ALA* 3.9 14.4 - - + +
1350A LEU* 3.7 15.3 - - + -
1353A CYS* 3.6 23.1 - - - -
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Residues in contact with ARG1322 (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 GLU* 3.6 25.7 + - - -
1145A GLN* 3.6 15.7 + - - +
1147A MET* 3.9 30.4 - - - +
1318A SER* 3.1 21.2 + - - +
1319A ALA* 3.6 9.7 - - - +
1321A ILE* 1.3 81.2 - - - +
1323A LYS* 1.3 62.3 + - - +
1325A ILE* 3.2 10.3 + - - +
1326A GLU* 2.9 46.4 + - - +
1350A LEU* 4.0 9.0 - - + +
1354A GLU* 3.5 23.8 + - - -
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Residues in contact with LYS1323 (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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1319A ALA 3.0 14.4 + - - +
1320A ALA* 3.1 13.0 + - - +
1322A ARG* 1.3 77.4 - - - +
1324A ARG* 1.3 61.5 + - + +
1326A GLU* 3.5 11.9 + - - +
1327A GLU* 3.2 40.5 + - + +
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Residues in contact with ARG1324 (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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1310A ASP* 2.6 50.8 + - - +
1313A ALA* 4.2 12.6 - - + -
1320A ALA 3.2 6.5 + - - +
1321A ILE* 3.0 10.9 + - - +
1323A LYS* 1.3 74.1 - - + +
1325A ILE* 1.3 65.9 + - - +
1327A GLU* 3.1 41.9 + - - +
1328A ILE* 3.1 28.4 + - - +
1339A GLU* 5.5 4.6 - - - +
1342A LEU* 3.4 28.9 - - - +
1346A LEU* 3.8 16.6 - - + -
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Residues in contact with ILE1325 (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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1147A MET* 3.2 39.9 - - + -
1161A ARG* 4.7 0.4 - - - +
1321A ILE* 3.0 22.2 + - + +
1322A ARG* 3.2 7.2 + - - +
1324A ARG* 1.3 75.6 - - - +
1326A GLU* 1.3 58.5 + - - +
1328A ILE* 3.2 3.3 + - - +
1329A ASN* 2.7 41.2 + - - +
1343A LEU* 3.7 23.5 - - + +
1346A LEU* 3.8 42.8 - - + +
1347A GLU* 4.0 9.0 - - + +
1350A LEU* 4.4 8.5 - - + -
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Residues in contact with GLU1326 (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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1147A MET* 4.8 11.4 - - - +
1322A ARG* 2.9 45.4 + - + +
1323A LYS* 3.9 9.9 - - - +
1325A ILE* 1.3 73.8 - - + +
1327A GLU* 1.3 66.9 + - - +
1329A ASN* 3.8 9.2 - - + +
1330A ALA* 2.9 24.9 + - - +
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Residues in contact with GLU1327 (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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1323A LYS* 3.2 42.3 + - + +
1324A ARG* 3.1 39.3 + - - +
1326A GLU* 1.3 79.8 - - - +
1328A ILE* 1.3 63.7 + - + +
1330A ALA* 3.4 15.1 + - - +
1331A LYS* 3.6 13.1 + - - +
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Residues in contact with ILE1328 (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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1324A ARG* 3.1 24.5 + - - +
1325A ILE 3.2 5.1 + - - +
1327A GLU* 1.3 75.4 - - + +
1329A ASN* 1.3 67.0 + - - +
1331A LYS* 3.0 22.4 + - + +
1332A GLY 3.8 5.4 + - - +
1335A ALA* 4.7 8.5 - - + +
1339A GLU* 3.7 50.5 - - + +
1340A LYS* 5.1 0.7 - - - +
1342A LEU* 3.9 28.3 - - + -
1343A LEU* 4.0 30.3 - - + +
1346A LEU* 4.6 5.8 - - + -
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Residues in contact with ASN1329 (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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1147A MET* 4.8 4.5 - - - +
1161A ARG* 3.0 44.7 + - - +
1325A ILE* 2.7 31.5 + - - +
1326A GLU* 3.8 9.8 - - + +
1328A ILE* 1.3 72.8 - - - +
1330A ALA* 1.3 63.4 + - - +
1332A GLY* 2.9 17.6 + - - -
1343A LEU* 3.7 13.9 - - - +
1T A 4.2 11.7 - - + +
2T T 5.5 0.5 - - - +
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Residues in contact with ALA1330 (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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1326A GLU 2.9 17.4 + - - +
1327A GLU* 3.5 9.2 - - - +
1328A ILE 3.1 0.4 - - - -
1329A ASN* 1.3 78.2 - - - +
1331A LYS* 1.3 60.0 + - + +
1332A GLY 3.1 1.1 + - - -
1T A 3.4 15.7 + - - +
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Residues in contact with LYS1331 (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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1327A GLU 4.0 11.7 - - - +
1328A ILE* 3.0 12.7 + - - +
1330A ALA* 1.3 76.2 - - + +
1332A GLY* 1.3 58.0 + - - +
1333A ILE 3.4 0.2 + - - -
1334A GLN* 2.8 53.9 + - + +
1335A ALA* 4.3 4.9 - - + +
1336A THR* 6.0 0.4 - - - +
1339A GLU* 3.1 32.8 + - - +
1T A 4.3 1.6 - - - -
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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