Contacts of the helix formed by residues 36 - 42 (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 ASN 36 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3B LEU* 5.8 1.3 - - - +
12B SER* 3.6 5.6 + - - +
13B ALA* 4.3 5.2 - - + +
34B VAL 3.8 3.4 + - - +
35B PHE* 1.3 73.6 - - - +
37B HIS* 1.3 60.4 + - - +
38B LEU* 3.3 14.9 + - - +
39B ILE* 3.1 37.1 + - + +
40B HIS* 2.8 31.7 + - - +
163B VAL* 4.3 29.4 - - + +
166B GLN* 5.5 1.8 + - - -
1295B HEC 3.6 24.5 + - - +
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Residues in contact with HIS 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B THR* 4.8 0.2 - - + -
8B SER* 3.9 0.2 - - - -
10B ALA* 3.4 17.2 - - + +
11B PRO 3.2 20.0 - - - +
12B SER 2.9 5.2 + - - -
14B ILE* 3.9 4.9 - - + -
35B PHE* 3.2 23.1 + + + -
36B ASN* 1.3 69.3 - - - +
38B LEU* 1.3 67.5 + - - +
40B HIS 3.1 0.9 + - - -
41B GLU* 2.7 52.9 + - + +
1293B HEC 2.0 92.7 + + + -
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Residues in contact with LEU 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B LEU* 5.7 1.3 - - + -
4B GLU* 3.6 52.0 - - + +
5B PRO 4.0 8.5 - - - +
6B THR* 4.2 15.9 - - + +
7B ASP 5.6 0.4 - - - +
12B SER* 2.9 23.5 + - - +
36B ASN* 3.2 11.4 - - - +
37B HIS* 1.3 79.2 - - - +
39B ILE* 1.3 72.7 + - + +
41B GLU* 3.4 3.5 + - + +
42B LYS* 3.2 56.2 + - + +
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Residues in contact with ILE 39 (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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36B ASN* 3.1 39.6 + - + +
38B LEU* 1.3 85.6 - - + +
40B HIS* 1.3 71.8 + - - +
42B LYS* 3.4 13.1 + - - +
43B LYS* 3.4 16.3 + - - +
212B LYS* 4.2 27.4 - - + -
1295B HEC 3.7 68.6 - - + +
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Residues in contact with HIS 40 (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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35B PHE* 3.4 27.8 - + + -
36B ASN 2.8 27.1 + - - +
37B HIS* 3.1 5.4 + - - +
39B ILE* 1.3 86.7 - - + +
41B GLU* 1.3 59.6 + - - +
43B LYS* 2.9 5.7 + - - +
44B ILE* 2.8 32.7 + - + +
1293B HEC 3.9 12.3 - - + -
1295B HEC 2.0 101.9 + + + -
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Residues in contact with GLU 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B THR* 3.5 15.8 - - - +
7B ASP* 3.4 13.0 + - - +
8B SER* 2.8 40.2 + - - -
37B HIS* 2.7 50.8 + - + +
38B LEU* 3.5 7.9 - - + +
40B HIS* 1.3 79.0 - - - +
42B LYS* 1.3 69.0 + - + +
43B LYS 3.1 1.1 + - - -
44B ILE 3.3 18.4 - - - +
45B ASP* 5.1 1.7 - - - +
1293B HEC 4.3 19.4 - - + +
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Residues in contact with LYS 42 (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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4B GLU* 3.1 28.4 + - - -
7B ASP* 6.2 0.4 - - - +
38B LEU* 3.2 44.4 + - + +
39B ILE* 4.0 7.0 - - - +
40B HIS 3.1 1.0 - - - -
41B GLU* 1.3 85.3 - - + +
43B LYS* 1.3 64.1 + - + +
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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
------------------------------------------------------------
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