Contacts of the helix formed by residues 108 - 113 (chain B) in PDB entry 1OFY
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 ARG 108 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43B LYS* 6.2 3.7 - - - +
104B GLN* 3.1 44.6 + - - +
107B GLU* 1.3 82.3 - - + +
109B ARG* 1.3 56.3 + - - +
110B GLU* 2.9 32.2 + - - +
111B CYS* 2.7 32.8 + - - +
112B ALA* 2.8 13.9 + - - -
211B ASP* 2.5 33.7 + - - +
213B LEU* 5.3 1.8 - - - +
1295B HEC 5.2 7.5 + - - +
1296B HEC 3.6 22.6 - - - +
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Residues in contact with ARG 109 (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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107B GLU 3.8 3.8 + - - -
108B ARG* 1.3 70.6 - - - +
110B GLU* 1.3 65.8 + - - +
111B CYS 3.1 1.4 + - - -
112B ALA* 3.5 10.1 + - - +
207B ARG* 6.2 2.2 - - - +
273B GLY 5.2 0.2 - - - -
274B MET* 3.2 49.6 + - + +
275B ASP* 3.2 49.2 + - - +
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Residues in contact with GLU 110 (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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108B ARG* 2.9 47.1 + - - +
109B ARG* 1.3 79.4 + - - +
111B CYS* 1.3 65.8 + - - +
113B GLY 5.1 0.2 + - - -
114B CYS 5.7 0.2 + - - -
204B LEU* 5.8 0.3 - - - +
207B ARG* 3.8 39.5 - - + +
208B ILE* 3.8 4.2 - - + +
274B MET* 4.4 13.9 - - - +
1296B HEC 3.6 29.0 - - + +
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Residues in contact with CYS 111 (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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104B GLN 4.1 2.2 - - - -
105B THR* 3.6 18.2 - - - -
108B ARG* 2.7 36.0 + - - +
110B GLU* 1.3 73.7 - - - +
112B ALA* 1.3 56.0 + - - +
113B GLY 3.1 6.8 + - - -
114B CYS* 3.6 4.0 + - - +
115B HIS* 3.0 30.0 + - - -
1296B HEC 1.8 83.0 - - + -
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Residues in contact with ALA 112 (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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105B THR 3.2 17.3 - - - +
106B LYS* 3.7 18.2 - - - +
108B ARG 2.8 14.9 + - - +
109B ARG* 3.5 4.4 + - - +
111B CYS* 1.3 74.5 - - - +
113B GLY* 1.3 58.3 + - - +
115B HIS* 4.4 2.7 - - - +
116B ALA* 3.1 27.6 + - - +
273B GLY* 3.5 22.8 - - - +
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Residues in contact with GLY 113 (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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109B ARG 4.0 0.4 + - - -
111B CYS 3.1 1.8 + - - -
112B ALA* 1.3 75.7 - - - +
114B CYS* 1.3 65.6 + - - +
116B ALA* 3.1 17.2 + - - +
117B ILE* 3.8 2.6 + - - +
270B CYS* 3.4 40.7 - - - +
274B MET* 3.7 25.5 - - - +
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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