Contacts of the helix formed by residues 1311 - 1317 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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993A TRP* 3.9 19.7 - - + -
1166A CYS* 4.6 1.6 - - - +
1285A HIS* 4.0 24.9 - - + +
1306A ARG* 3.1 26.4 + - - -
1309A CYS 3.5 7.8 - - - +
1310A VAL* 1.3 76.0 - - - +
1312A LYS* 1.3 63.7 + - - +
1313A PHE* 2.8 19.3 + - + +
1314A THR* 2.8 36.6 + - - +
1315A THR* 2.7 22.3 + - - -
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Residues in contact with LYS1312 (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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480A GLU* 4.0 19.0 + - - -
483A LEU* 4.4 12.3 - - - +
517A PHE* 4.5 5.8 - - - -
542A TYR* 5.3 6.0 + - - -
993A TRP* 4.5 14.1 - - + -
1285A HIS* 5.5 0.2 - - - +
1311A ASP* 1.3 77.9 - - + +
1313A PHE* 1.3 96.8 + - + +
1315A THR* 3.8 6.4 - - - -
1316A LEU* 3.0 36.7 + - + +
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Residues in contact with PHE1313 (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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483A LEU* 5.0 2.2 - - + -
487A CYS* 3.9 31.0 - - + -
510A THR* 4.6 3.1 - - + -
513A LEU* 4.2 22.9 - - + -
514A SER* 4.4 7.4 - - - +
517A PHE* 3.4 44.4 - + + -
993A TRP* 3.8 26.5 - + - -
1167A LEU* 4.1 3.6 - - + -
1306A ARG* 4.0 15.0 - - - +
1311A ASP* 2.8 22.1 + - - +
1312A LYS* 1.3 100.0 - - + +
1314A THR* 1.3 65.5 + - - +
1315A THR 3.0 1.8 - - - -
1316A LEU* 3.1 12.2 + - - +
1317A CYS* 3.2 19.4 + - - -
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Residues in contact with THR1314 (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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510A THR* 3.8 22.7 - - + +
1306A ARG* 3.6 29.2 - - - +
1307A ASN* 4.6 9.2 - - - +
1309A CYS 3.8 7.2 - - - +
1310A VAL* 3.3 15.7 - - - +
1311A ASP* 2.8 45.0 + - - +
1313A PHE* 1.3 71.8 - - - +
1315A THR* 1.3 61.3 + - - +
1317A CYS* 3.2 3.1 + - - +
1318A VAL* 3.1 22.5 + - - +
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Residues in contact with THR1315 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1310A VAL* 4.5 8.5 - - - +
1311A ASP 2.7 22.0 + - - -
1312A LYS* 3.8 8.8 - - - -
1313A PHE 3.0 0.6 - - - -
1314A THR* 1.3 82.3 + - - +
1316A LEU* 1.3 65.0 + - + +
1317A CYS 3.1 0.2 - - - -
1318A VAL* 3.0 34.5 - - + +
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Residues in contact with LEU1316 (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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487A CYS* 5.3 5.8 - - + -
488A ALA* 4.4 26.5 - - + +
491A ALA* 3.6 19.5 - - + +
509A ARG* 4.2 3.3 + - - -
513A LEU* 4.0 17.3 - - + -
1312A LYS* 3.0 24.0 - - + +
1313A PHE* 3.1 8.9 + - - +
1315A THR* 1.3 84.8 - - + +
1317A CYS* 1.3 59.3 + - - +
1318A VAL* 3.5 3.5 - - - +
1322A PRO* 6.2 0.2 - - - +
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Residues in contact with CYS1317 (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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491A ALA* 5.0 2.0 - - - -
506A GLU* 4.4 9.8 - - + +
509A ARG* 2.5 70.0 + - + +
510A THR* 3.5 21.1 - - - +
513A LEU* 3.7 18.8 - - - -
1313A PHE 3.2 16.1 + - - +
1314A THR 3.2 3.3 + - - +
1315A THR 3.1 0.6 - - - -
1316A LEU* 1.3 80.6 - - - +
1318A VAL* 1.3 63.8 + - - +
1319A THR* 2.9 5.0 + - - -
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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