Contacts of the helix formed by residues 1311 - 1323 (chain B) in PDB entry 1G50
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 THR1311 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1309B SER 4.2 2.5 - - - +
1310B LEU* 1.3 72.8 - - - +
1312B ALA* 1.3 55.9 + - - +
1313B ASP* 2.6 24.7 + - - +
1314B GLN* 2.7 66.4 + - - +
1315B MET* 3.0 9.9 + - - +
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Residues in contact with ALA1312 (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 LEU 3.5 3.5 + - - -
1311B THR* 1.3 70.8 - - - +
1313B ASP* 1.3 59.0 + - - +
1315B MET* 3.4 7.7 - - - +
1316B VAL* 3.4 5.9 - - - +
1481B LYS* 4.8 5.8 - - - +
1484B ASP* 4.9 4.3 - - + +
1485B THR* 3.2 36.7 - - - +
1488B HIS* 3.6 37.3 - - + -
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Residues in contact with ASP1313 (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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1311B THR* 2.6 15.3 + - - +
1312B ALA* 1.3 76.3 + - - +
1314B GLN* 1.3 64.2 + - + +
1315B MET 3.1 1.3 - - - -
1316B VAL* 3.3 9.1 + - - +
1317B SER* 3.1 22.3 + - - -
1488B HIS* 3.2 32.9 + - - -
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Residues in contact with GLN1314 (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 SER 5.2 0.4 + - - -
1310B LEU* 3.6 27.1 - - + +
1311B THR* 2.7 58.3 + - + +
1313B ASP* 1.3 71.2 - - + +
1315B MET* 1.3 57.1 + - - +
1317B SER* 3.3 6.6 + - - +
1318B ALA* 2.7 39.7 + - - +
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Residues in contact with MET1315 (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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1307B ALA* 6.3 0.2 - - + -
1310B LEU* 4.6 12.0 - - + +
1311B THR 3.0 10.0 + - - +
1312B ALA* 3.4 15.5 - - - +
1314B GLN* 1.3 76.3 - - - +
1316B VAL* 1.3 61.8 + - - +
1318B ALA* 3.0 19.1 - - - +
1319B LEU* 3.1 29.7 + - + +
1365B PRO* 4.1 28.0 - - + -
1478B VAL* 4.7 4.5 - - + +
1481B LYS* 3.3 42.4 - - + -
1482B ILE* 3.7 25.4 - - + -
1485B THR* 3.0 26.0 - - + +
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Residues in contact with VAL1316 (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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1312B ALA 3.4 17.9 - - - +
1313B ASP* 3.5 10.3 - - - +
1314B GLN 3.2 0.2 - - - -
1315B MET* 1.3 71.6 - - - +
1317B SER* 1.3 55.6 + - - +
1318B ALA 2.7 14.3 + - - -
1319B LEU* 3.0 9.5 + - - +
1320B LEU* 2.9 46.7 + - + +
1443B GLU* 4.0 23.6 - - + -
1446B VAL* 5.0 3.1 - - + -
1447B CYS* 5.5 2.2 - - - -
1485B THR* 3.5 16.6 - - + -
1489B LEU* 4.0 16.8 - - + -
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Residues in contact with SER1317 (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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1313B ASP 3.1 13.3 + - - -
1314B GLN* 3.5 6.1 - - - -
1316B VAL* 1.3 79.5 - - - +
1318B ALA* 1.3 55.5 + - - +
1320B LEU* 4.0 13.0 - - - +
1321B ASP* 3.3 24.3 + - - +
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Residues in contact with ALA1318 (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 LEU* 5.3 6.1 - - + -
1314B GLN* 2.7 19.2 + - + +
1315B MET* 3.0 12.8 - - - +
1316B VAL 2.7 1.6 + - - -
1317B SER* 1.3 77.4 - - - +
1319B LEU* 1.3 62.9 + - - +
1320B LEU 3.1 1.1 - - - -
1321B ASP* 3.2 5.2 + - - +
1322B ALA* 3.1 22.4 + - - +
1363B ARG 5.5 2.6 - - - +
1365B PRO* 4.5 17.9 - - + -
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Residues in contact with LEU1319 (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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1315B MET* 3.3 29.4 - - + +
1316B VAL* 3.0 5.0 + - - +
1318B ALA* 1.3 75.5 - - - +
1320B LEU* 1.3 57.3 + - - +
1322B ALA* 3.4 8.0 - - - +
1323B GLU* 3.2 28.6 + - - +
1360B TRP* 4.5 4.5 + - - +
1364B VAL* 4.4 7.2 - - + -
1365B PRO* 3.5 30.5 - - + -
1446B VAL* 3.5 44.8 - - + +
1447B CYS* 4.0 14.6 - - - +
1450B SER* 3.2 25.1 - - - +
1482B ILE* 5.4 3.4 - - + -
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Residues in contact with LEU1320 (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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1316B VAL* 2.9 41.2 + - + +
1317B SER* 4.1 8.3 - - - -
1319B LEU* 1.3 77.3 - - - +
1321B ASP* 1.3 64.2 + - - +
1323B GLU* 3.7 18.7 + - + +
1442B GLY* 4.5 12.3 - - - +
1443B GLU* 4.5 10.8 - - + -
1446B VAL* 3.7 25.8 - - + -
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Residues in contact with ASP1321 (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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1317B SER 3.3 17.8 + - - +
1318B ALA* 3.2 8.3 + - - +
1320B LEU* 1.3 79.9 - - - +
1322B ALA* 1.3 63.9 + - - +
1323B GLU 3.3 5.9 + - - +
1363B ARG* 5.6 3.1 - - - -
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Residues in contact with ALA1322 (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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1318B ALA 3.1 10.4 + - - +
1319B LEU* 3.4 13.9 - - - +
1320B LEU 3.2 0.2 - - - -
1321B ASP* 1.3 79.8 - - - +
1323B GLU* 1.3 66.9 + - - +
1324B PRO* 3.3 2.8 - - - +
1360B TRP* 3.6 29.9 - - + +
1363B ARG* 3.8 41.6 + - + +
1364B VAL* 5.2 1.3 - - + +
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Residues in contact with GLU1323 (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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1319B LEU 3.2 16.5 + - - +
1320B LEU* 3.7 17.3 - - + +
1321B ASP 3.3 6.0 - - - +
1322B ALA* 1.3 78.5 - - - +
1324B PRO* 1.3 77.3 - - - +
1325B PRO* 4.2 0.7 - - - +
1360B TRP* 4.0 6.4 + - - -
1445B PHE* 4.3 13.3 - - + -
1446B VAL* 3.9 21.4 - - + +
1449B LYS* 2.9 40.3 + - - +
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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