Contacts of the helix formed by residues 1070 - 1076 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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459B MET* 4.5 7.2 - - + +
460B VAL* 4.1 25.8 - - + -
471B PRO* 3.1 32.9 + - + +
473B PHE* 4.0 27.6 - - + +
786B VAL* 4.2 35.4 - - + -
1068B SER 3.4 2.6 + - - -
1069B PRO* 1.3 70.9 - - - +
1071B SER* 1.3 63.8 + - - +
1073B ILE* 3.4 11.8 + - + +
1074B LYS* 3.1 42.0 + - + +
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Residues in contact with SER1071 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470B GLU* 2.6 29.8 + - - -
471B PRO* 4.8 1.0 + - - +
497B GLN* 5.4 4.7 - - - -
649B SER* 6.5 1.3 - - - -
650B THR* 4.3 18.5 - - - +
651B HIS 5.3 1.8 - - - -
713B LYS* 4.9 2.9 - - - +
714B ILE* 5.9 0.7 - - - +
717B LYS* 5.0 3.1 + - - -
1069B PRO* 3.7 6.1 - - - +
1070B LEU* 1.3 78.4 - - - +
1072B SER* 1.3 61.2 + - - +
1074B LYS* 3.2 1.6 + - - -
1075B HIS* 2.8 56.1 + - - +
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Residues in contact with SER1072 (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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713B LYS* 4.4 1.0 - - - +
717B LYS* 3.2 18.9 + - - +
970B GLY 4.8 0.2 - - - +
971B ALA 3.0 20.4 - - - +
972B LYS* 3.9 10.3 - - - -
975B GLU* 2.4 29.9 + - - -
1069B PRO* 3.1 18.9 + - - +
1071B SER* 1.3 76.7 + - - +
1073B ILE* 1.3 66.5 + - - +
1075B HIS* 5.3 0.2 - - - -
1076B ALA* 3.2 27.7 + - - +
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Residues in contact with ILE1073 (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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473B PHE* 4.0 11.2 - - + -
474B CYS 3.9 23.8 - - - +
475B MET 3.5 22.2 - - - +
476B GLY* 4.0 2.7 - - - +
477B ASP* 3.3 42.2 - - + +
496B LYS* 5.3 0.5 + - - -
971B ALA* 3.5 16.2 - - + +
1061B HIS* 4.3 10.0 - - - +
1065B THR* 4.2 0.9 - - + -
1068B SER* 3.8 26.2 - - - +
1069B PRO 3.0 18.8 + - - +
1070B LEU* 3.6 11.0 - - + +
1071B SER 3.3 0.2 - - - -
1072B SER* 1.3 76.7 - - - +
1074B LYS* 1.3 70.4 + - + +
1076B ALA 5.2 0.9 + - - +
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Residues in contact with LYS1074 (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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477B ASP* 2.8 37.4 + - - +
478B ASP 5.0 0.2 - - - +
479B THR* 3.7 10.9 + - - +
489B ARG* 5.8 6.1 + - - +
493B ASP 5.7 0.2 - - - +
496B LYS* 2.8 24.2 + - - -
785B PHE* 2.8 36.5 + - - +
786B VAL* 4.8 6.7 + - + +
795B HIS* 4.8 1.2 - - - -
1070B LEU* 3.1 36.0 + - + +
1072B SER 3.2 0.2 - - - -
1073B ILE* 1.3 86.0 - - + +
1075B HIS* 1.3 83.2 + - + +
1076B ALA 4.0 0.4 - - - -
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Residues in contact with HIS1075 (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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489B ARG* 6.3 0.2 - - - -
493B ASP* 3.5 29.8 + - + -
495B PHE 4.6 2.2 + - - -
496B LYS* 3.4 14.2 + - - -
497B GLN* 2.8 31.4 + - - +
649B SER* 4.9 6.2 + - - -
651B HIS* 3.5 57.3 + + + +
652B HIS* 5.5 3.8 - + - -
1071B SER* 2.8 35.3 + - - +
1074B LYS* 1.3 96.0 + - + +
1076B ALA* 1.3 61.0 + - - +
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Residues in contact with ALA1076 (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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496B LYS* 4.6 0.4 - - - +
497B GLN* 3.9 14.4 - - + +
499B PHE* 5.3 1.1 - - + -
717B LYS* 3.8 28.9 - - + +
970B GLY 3.5 9.2 - - - +
973B PRO* 3.5 30.1 - - + +
1061B HIS* 4.4 4.2 - - - +
1072B SER* 3.2 16.2 + - - +
1073B ILE 5.2 1.4 + - - +
1074B LYS 4.0 0.2 - - - -
1075B HIS* 1.3 81.1 - - - +
1077B 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