Contacts of the helix formed by residues 1311 - 1318 (chain B) in PDB entry 1FO4
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 ASP1311 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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993B TRP* 3.9 14.4 - - + -
1166B CYS* 4.4 2.4 - - - +
1285B HIS* 4.0 29.8 + - + +
1306B ARG* 3.0 23.4 + - - -
1309B CYS* 3.3 11.9 - - - +
1310B VAL* 1.3 74.5 - - - +
1312B LYS* 1.3 58.4 + - + +
1313B PHE* 2.7 37.9 + - + +
1314B THR* 2.7 27.8 + - - +
1315B THR* 2.7 26.7 + - - -
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Residues in contact with LYS1312 (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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480B GLU* 4.2 17.0 + - - -
483B LEU* 4.4 3.6 - - - +
517B PHE* 4.3 14.8 - - - -
542B TYR* 4.7 9.9 + - - -
993B TRP* 4.3 12.6 - - + -
1285B HIS* 5.5 0.2 - - - +
1311B ASP* 1.3 78.8 - - + +
1313B PHE* 1.3 96.3 + - + +
1315B THR* 4.1 5.6 - - - -
1316B LEU* 2.7 38.4 + - + +
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Residues in contact with PHE1313 (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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483B LEU* 4.8 3.1 - - + -
487B CYS* 3.8 31.2 - - + -
510B THR* 4.8 2.7 - - + -
513B LEU* 4.0 25.7 - - + +
514B SER* 4.5 4.7 - - - +
517B PHE* 3.3 49.4 - + + -
993B TRP* 3.9 9.9 - + - -
1167B LEU* 4.1 3.8 - - + -
1306B ARG* 4.1 13.5 - - - +
1311B ASP* 2.7 26.5 + - - +
1312B LYS* 1.3 106.8 - - + +
1314B THR* 1.3 64.6 + - - +
1315B THR 3.1 1.3 - - - -
1316B LEU* 3.1 13.5 + - + +
1317B CYS* 3.3 19.2 + - - -
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Residues in contact with THR1314 (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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510B THR* 3.8 23.3 + - + +
1306B ARG* 3.4 36.3 - - - +
1307B ASN* 4.9 8.5 - - - +
1309B CYS 3.8 6.5 - - - +
1310B VAL* 3.2 14.6 - - - +
1311B ASP* 2.7 36.3 + - - +
1313B PHE* 1.3 70.8 - - - +
1315B THR* 1.3 61.0 + - - +
1317B CYS* 2.8 20.6 + - - +
1318B VAL* 3.0 24.6 + - - +
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Residues in contact with THR1315 (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 VAL* 4.3 10.1 - - - +
1311B ASP 2.7 21.2 + - - -
1312B LYS* 3.8 9.5 - - - -
1314B THR* 1.3 84.1 + - - +
1316B LEU* 1.3 67.7 + - + +
1318B VAL* 3.6 20.0 - - - +
1321B ALA* 3.6 6.6 - - - +
1322B PRO* 3.9 11.8 - - + +
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Residues in contact with LEU1316 (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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484B GLN 5.4 1.1 - - - +
487B CYS* 4.1 24.0 - - + +
488B ALA* 4.4 9.0 - - + +
491B ALA* 3.8 13.0 - - + +
509B ARG* 3.8 11.4 + - - -
513B LEU* 4.1 22.2 - - + -
1312B LYS* 2.7 27.8 - - + +
1313B PHE* 3.1 9.5 + - + +
1315B THR* 1.3 88.2 - - + +
1317B CYS* 1.3 59.3 + - - +
1318B VAL 3.8 0.2 - - - -
1321B ALA* 4.0 10.3 - - - +
1322B PRO* 4.9 11.3 - - + +
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Residues in contact with CYS1317 (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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491B ALA* 4.8 2.2 - - - -
505B ILE* 5.5 0.5 - - - +
506B GLU* 4.1 9.4 - - - +
509B ARG* 3.4 67.6 + - + +
510B THR* 3.5 22.7 - - - +
513B LEU* 3.7 19.1 - - - -
1313B PHE 3.5 12.6 - - - +
1314B THR 2.8 6.6 + - - +
1316B LEU* 1.3 81.4 - - - +
1318B VAL* 1.3 65.6 + - - +
1319B THR* 3.4 1.9 + - - -
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Residues in contact with VAL1318 (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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506B GLU* 3.2 22.0 - - + +
509B ARG* 5.3 0.9 + - - -
1314B THR* 3.0 21.1 + - - +
1315B THR* 3.6 14.4 - - - +
1317B CYS* 1.3 73.9 - - - +
1319B THR* 1.3 69.6 + - - +
1320B GLY 3.1 0.4 + - - -
1321B ALA* 2.9 41.1 + - + +
1322B PRO* 5.3 0.7 - - + -
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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