Contacts of the helix formed by residues 1309 - 1323 (chain B) in PDB entry 2O8C
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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733A ALA* 5.4 2.2 - - + +
736A LEU* 3.8 27.1 - - + -
737A ARG* 4.3 32.1 - - + +
769A TYR* 4.2 24.0 - - + +
1307B ASN 3.6 6.0 - - - +
1308B LEU* 1.3 94.1 - - + +
1310B GLU* 1.3 60.9 + - - +
1311B GLU* 4.4 4.0 - - + +
1312B VAL* 3.1 28.5 + - + +
1313B ILE* 3.2 10.2 + - - +
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Residues in contact with GLU1310 (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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737A ARG* 5.7 0.2 - - - +
1304B ARG* 3.4 43.8 + - - +
1308B LEU 4.2 5.9 - - - +
1309B PRO* 1.3 70.0 - - - +
1311B GLU* 1.3 62.3 + - - +
1312B VAL 3.2 0.2 - - - -
1313B ILE* 3.8 6.5 - - - +
1314B GLN* 3.2 37.0 + - + +
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Residues in contact with GLU1311 (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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769A TYR* 3.4 35.7 - - + -
772A THR* 6.0 2.9 - - - +
773A LYS* 3.9 15.9 - - - +
1309B PRO* 3.2 2.0 - - + -
1310B GLU* 1.3 78.5 - - - +
1312B VAL* 1.3 60.9 + - - +
1314B GLN* 5.1 1.6 - - - -
1315B LYS* 3.3 60.5 + - + +
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Residues in contact with VAL1312 (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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736A LEU* 4.2 10.5 - - + -
762A LEU* 4.5 5.2 - - + +
765A ALA* 3.3 24.8 - - + +
766A ILE* 3.8 17.9 - - + +
769A TYR* 3.9 31.4 - - + -
1308B LEU* 3.7 24.5 - - + -
1309B PRO* 3.1 27.7 + - + +
1311B GLU* 1.3 76.4 - - - +
1313B ILE* 1.3 64.6 + - - +
1316B GLY* 3.0 21.0 + - - -
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Residues in contact with ILE1313 (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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762A LEU* 4.8 6.1 - - + -
1300B PHE* 4.4 16.7 - - + +
1303B ALA* 3.8 7.0 - - + -
1304B ARG* 3.6 71.3 - - + +
1308B LEU* 3.7 30.5 - - + +
1309B PRO 3.2 13.9 + - - +
1310B GLU* 3.6 12.3 + - - +
1312B VAL* 1.3 76.2 - - - +
1314B GLN* 1.3 65.2 + - + +
1316B GLY* 4.0 0.5 - - - -
1317B HIS* 3.2 24.6 + - + +
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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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1304B ARG* 4.4 17.2 - - - +
1310B GLU* 3.2 23.7 + - + +
1311B GLU* 4.5 2.5 - - - +
1313B ILE* 1.3 81.0 - - + +
1315B LYS* 1.3 63.7 + - + +
1317B HIS* 3.2 15.1 + - - +
1318B ARG* 3.3 38.1 + - - +
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Residues in contact with LYS1315 (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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764A TRP* 5.2 4.3 - - + -
765A ALA* 4.4 5.6 - - + -
768A GLU* 3.3 29.3 + - + +
1311B GLU* 3.3 51.6 + - + +
1312B VAL 4.5 0.9 - - - +
1314B GLN* 1.3 80.6 - - + +
1316B GLY* 1.3 59.9 + - - +
1318B ARG* 3.5 36.8 + - - +
1319B LYS* 3.6 13.2 + - - +
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Residues in contact with GLY1316 (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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761A GLY* 3.4 41.9 - - - -
762A LEU* 4.5 1.1 - - - -
764A TRP* 6.0 0.4 - - - -
765A ALA* 3.7 4.6 - - - +
1300B PHE* 3.7 12.8 - - - -
1312B VAL 3.0 18.6 + - - -
1313B ILE 4.0 0.9 - - - -
1314B GLN 3.2 0.2 - - - -
1315B LYS* 1.3 74.0 - - - +
1317B HIS* 1.3 63.2 + - - +
1318B ARG 3.5 0.2 + - - -
1319B LYS* 3.5 7.4 + - - +
1320B ALA 3.6 3.6 + - - -
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Residues in contact with HIS1317 (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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1296B LYS 5.8 2.5 - - - -
1297B SER* 5.5 8.5 - - - -
1300B PHE* 3.6 41.3 - + + +
1313B ILE* 3.2 17.8 + - + +
1314B GLN* 3.2 6.7 + - - +
1316B GLY* 1.3 74.1 - - - +
1318B ARG* 1.3 65.6 + - + +
1320B ALA* 3.4 15.7 + - + +
1321B ARG* 3.6 40.0 + - + +
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Residues in contact with ARG1318 (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 GLN* 3.3 32.7 + - - +
1315B LYS* 3.7 32.7 - - - +
1316B GLY 3.3 0.4 - - - -
1317B HIS* 1.3 79.1 - - + +
1319B LYS* 1.3 57.3 + - - +
1321B ARG* 3.4 8.9 + - - +
1322B GLU* 3.0 30.7 + - - +
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Residues in contact with LYS1319 (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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760A PHE* 3.7 35.0 - - + -
761A GLY* 4.4 6.5 - - - -
764A TRP* 3.5 51.2 - - + +
793A GLN* 5.5 3.6 - - - +
1315B LYS 3.6 8.4 + - - +
1316B GLY* 3.5 9.8 + - - +
1317B HIS 3.3 0.4 - - - -
1318B ARG* 1.3 77.0 - - - +
1320B ALA* 1.3 63.5 + - - +
1322B GLU* 3.3 37.3 + - + +
1323B PHE* 3.3 25.5 + - + +
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Residues in contact with ALA1320 (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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757A TYR* 3.8 40.4 - - + +
758A ASP* 4.8 2.2 - - - +
760A PHE* 6.2 0.9 - - - -
761A GLY* 5.0 0.4 - - - -
1296B LYS* 5.4 5.2 - - - +
1300B PHE* 4.3 14.1 - - + -
1316B GLY 3.6 8.2 + - - +
1317B HIS* 3.4 13.9 + - + +
1318B ARG 3.2 0.4 - - - -
1319B LYS* 1.3 80.9 - - - +
1321B ARG* 1.3 61.7 + - + +
1323B PHE 3.8 5.4 + - - +
1324B GLU* 3.5 20.2 - - - +
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Residues in contact with ARG1321 (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 HIS* 3.6 36.6 + - + +
1318B ARG* 3.4 10.4 + - - +
1319B LYS 3.4 0.2 - - - -
1320B ALA* 1.3 78.2 - - + +
1322B GLU* 1.3 65.7 + - - +
1324B GLU* 3.3 32.5 + - - +
1325B LYS* 4.5 5.2 + - - +
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Residues in contact with GLU1322 (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 ARG* 3.0 20.0 + - - +
1319B LYS* 3.3 38.0 + - + +
1320B ALA 3.4 0.2 - - - -
1321B ARG* 1.3 77.0 - - - +
1323B PHE* 1.3 58.0 + - + +
1324B GLU 3.0 6.2 + - - -
1325B LYS* 3.5 41.9 + - + +
1326B MET* 5.0 1.9 + - - +
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Residues in contact with PHE1323 (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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757A TYR* 3.3 30.3 - + + -
760A PHE* 5.3 16.2 - + + -
785A HIS* 4.9 17.5 - + - -
786A GLU* 5.0 10.5 - - + -
854A PHE* 4.2 22.0 - - + -
855A GLN* 5.0 7.6 - - - -
1319B LYS* 3.3 18.1 + - + +
1320B ALA 4.1 2.0 - - - +
1321B ARG 3.3 0.6 - - - -
1322B GLU* 1.3 76.9 - - + +
1324B GLU* 1.3 60.0 + - - +
1325B LYS 3.8 0.4 - - - +
1326B MET* 4.6 16.8 - - + +
1327B ASN* 3.0 32.0 - - - +
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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