Contacts of the helix formed by residues 1070 - 1076 (chain A) in PDB entry 1OFD
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 LEU1070 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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459A MET* 4.7 6.5 - - + +
460A VAL* 4.2 23.6 - - + -
471A PRO* 3.0 31.6 + - + +
473A PHE* 4.0 34.5 - - + -
786A VAL* 4.1 28.9 - - + -
1068A SER 3.4 2.2 + - - -
1069A PRO* 1.3 68.3 - - - +
1071A SER* 1.3 64.4 + - - +
1073A ILE* 3.3 13.7 + - + +
1074A LYS* 3.1 46.8 + - + +
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Residues in contact with SER1071 (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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470A GLU* 2.5 29.9 + - - -
471A PRO* 4.8 1.2 + - - +
497A GLN* 5.5 3.1 - - - -
649A SER* 6.3 2.0 - - - -
650A THR* 4.1 19.8 - - - +
651A HIS* 5.3 2.2 - - - -
713A LYS* 4.9 2.6 - - - +
714A ILE* 5.8 0.7 - - - +
717A LYS* 5.0 3.5 + - - -
1069A PRO* 3.9 4.3 - - - +
1070A LEU* 1.3 79.3 - - - +
1072A SER* 1.3 62.0 + - - +
1074A LYS* 3.3 0.7 + - - -
1075A HIS* 2.8 51.0 + - - +
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Residues in contact with SER1072 (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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713A LYS* 4.3 1.2 - - - +
717A LYS* 3.1 20.0 + - - +
970A GLY 4.9 0.2 - - - +
971A ALA 3.1 19.2 - - - +
972A LYS* 4.0 9.0 - - - -
975A GLU* 2.5 29.2 + - - -
1069A PRO* 3.1 21.4 + - - +
1071A SER* 1.3 76.1 + - - +
1073A ILE* 1.3 66.8 + - - +
1076A ALA* 3.2 27.4 + - - +
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Residues in contact with ILE1073 (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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473A PHE* 4.0 11.7 - - + -
474A CYS 3.8 22.9 - - - +
475A MET 3.6 18.4 - - - +
476A GLY* 3.9 7.0 - - - +
477A ASP* 3.3 41.3 - - + +
971A ALA* 3.6 12.6 - - + +
1061A HIS* 4.3 10.4 - - - +
1065A THR* 4.2 4.5 - - + -
1068A SER* 3.9 25.8 - - - +
1069A PRO 3.1 18.7 + - - +
1070A LEU* 3.3 11.2 + - + +
1072A SER* 1.3 78.4 - - - +
1074A LYS* 1.3 69.6 + - + +
1076A ALA 5.2 1.4 + - - +
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Residues in contact with LYS1074 (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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477A ASP* 3.0 39.6 + - - +
478A ASP 5.1 0.4 - - - +
479A THR* 3.7 9.5 + - - +
489A ARG* 6.0 3.7 + - - +
493A ASP 5.6 0.3 - - - +
496A LYS* 2.9 23.1 + - - -
785A PHE* 2.9 35.8 + - - +
786A VAL* 4.8 5.8 + - - +
795A HIS* 4.9 1.2 - - - -
1070A LEU* 3.1 39.1 + - + +
1073A ILE* 1.3 83.3 - - - +
1075A HIS* 1.3 85.3 + - + +
1076A ALA 4.0 0.4 - - - -
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Residues in contact with HIS1075 (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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492A TYR* 5.7 0.2 - - + -
493A ASP* 3.3 31.6 + - - -
495A PHE 4.1 2.0 + - - +
496A LYS* 3.3 16.1 + - - -
497A GLN* 2.8 29.7 + - - +
649A SER* 5.0 5.8 + - - -
651A HIS* 3.4 56.4 + + + +
652A HIS* 5.5 3.1 - + - -
1071A SER* 2.8 34.8 + - - +
1074A LYS* 1.3 95.5 + - + +
1076A ALA* 1.3 60.4 + - - +
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Residues in contact with ALA1076 (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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496A LYS* 4.6 0.4 - - - +
497A GLN* 3.9 27.8 - - + +
499A PHE* 5.3 1.3 - - + -
717A LYS* 3.9 16.2 - - + +
970A GLY 3.5 9.2 - - - +
973A PRO* 3.4 32.1 - - + +
1061A HIS* 4.5 3.9 - - - +
1072A SER* 3.2 15.5 + - - +
1073A ILE 5.1 1.1 - - - +
1074A LYS 4.0 0.4 - - - -
1075A HIS* 1.3 79.5 - - - +
1077A GLY* 1.3 60.6 + - - +
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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