Contacts of the helix formed by residues 39 - 47 (chain B) in PDB entry 1R37
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 HIS 39 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38B CYS* 1.3 70.9 - - - +
40B SER* 1.3 60.2 + - - +
41B ASP 3.1 0.2 - - - -
42B VAL* 3.0 31.2 + - + +
43B HIS* 3.6 23.4 - - - -
273B PHE* 4.0 11.4 - + - -
334B LEU* 3.1 41.3 + - + +
335B GLU* 4.4 1.9 - - - -
337B PHE* 3.7 22.0 - + - -
403B NAD 2.7 68.3 + - - +
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Residues in contact with SER 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B CYS* 2.9 7.9 - - - -
39B HIS* 1.3 78.4 - - - +
41B ASP* 1.3 57.9 + - - +
43B HIS* 3.1 9.3 + - - +
44B MET* 2.9 30.8 + - - +
49B PHE* 3.9 5.2 - - - -
68B HIS* 3.9 7.4 - - - -
120B ILE* 5.5 0.2 - - - -
272B LEU* 4.4 0.2 - - - +
403B NAD 2.8 29.1 + - - -
600B ETX 2.9 44.0 + - - -
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Residues in contact with ASP 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B GLY 4.6 0.9 - - - +
38B CYS 2.9 22.1 + - - +
40B SER* 1.3 75.1 - - - +
42B VAL* 1.3 60.3 + - - +
43B HIS 3.3 0.2 - - - -
44B MET* 3.7 12.0 - - - +
45B ARG* 3.0 27.9 + - - +
66B LEU* 3.8 20.8 - - + +
67B GLY* 4.2 2.5 + - - -
68B HIS* 3.7 24.0 + - - -
119B GLY 4.7 1.4 - - - +
126B TYR* 2.7 32.0 + - - +
331B ILE* 3.9 27.3 - - + +
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Residues in contact with VAL 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B CYS 4.9 0.2 - - - +
39B HIS* 3.0 31.0 + - + +
41B ASP* 1.3 79.1 - - - +
43B HIS* 1.3 60.5 + - + +
45B ARG* 3.6 3.4 + - - +
46B GLN* 3.2 47.1 + - - +
331B ILE* 3.5 37.0 - - + +
334B LEU* 3.9 12.8 - - + -
335B GLU* 3.8 32.3 - - + +
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Residues in contact with HIS 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B HIS* 3.6 27.0 - + - -
40B SER* 3.1 1.5 + - - +
42B VAL* 1.3 77.5 - - + +
44B MET* 1.3 59.8 + - - +
46B GLN* 3.1 16.0 + - - -
47B GLY 2.8 23.4 + - - -
48B ARG 3.0 29.1 + - - +
49B PHE* 3.4 31.2 - + + -
272B LEU* 3.5 18.7 + - + -
273B PHE* 4.2 11.0 - + - -
403B NAD 2.9 45.7 + - - -
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Residues in contact with MET 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B LEU* 3.4 29.1 - - + +
9B ILE* 3.8 0.7 - - - +
40B SER 2.9 21.8 + - - +
41B ASP* 3.8 17.3 - - - +
42B VAL 3.4 0.2 - - - -
43B HIS* 1.3 76.5 - - - +
45B ARG* 1.3 59.2 + - - +
47B GLY* 2.8 20.5 + - - +
49B PHE* 3.8 25.4 - - + -
54B ILE* 3.8 27.4 - - + +
60B VAL* 4.6 3.4 - - + -
64B VAL* 4.8 0.9 - - + -
66B LEU* 4.4 13.2 - - + -
119B GLY 4.1 4.7 - - - +
120B ILE* 3.6 50.9 - - + +
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Residues in contact with ARG 45 (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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6B LEU* 4.1 10.1 - - + +
9B ILE* 3.9 3.1 - - - -
10B GLY* 2.9 27.2 + - - -
11B LYS 3.3 28.0 + - - +
12B PRO* 4.3 4.2 - - - +
13B LEU* 3.9 19.3 - - + -
41B ASP 3.0 17.7 + - - +
42B VAL 3.8 4.4 + - - +
43B HIS 3.3 0.2 - - - -
44B MET* 1.3 77.3 - - - +
46B GLN* 1.3 58.9 + - + +
47B GLY 3.2 0.6 + - - -
66B LEU* 5.1 0.4 - - - +
328B ASN* 3.0 39.3 + - - +
331B ILE* 3.4 24.8 - - - +
332B ASP* 2.9 29.6 + - - +
335B GLU* 2.7 30.3 + - - -
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Residues in contact with GLN 46 (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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9B ILE* 3.2 12.7 - - - +
10B GLY* 4.5 5.3 - - - +
42B VAL* 3.2 21.0 + - + +
43B HIS* 3.1 23.3 + - - +
45B ARG* 1.3 78.3 - - + +
47B GLY* 1.3 61.0 + - - +
48B ARG* 3.4 36.1 + - + +
335B GLU* 3.1 30.0 - - - +
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Residues in contact with GLY 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B ILE* 3.4 25.9 - - - +
43B HIS 2.8 0.2 + - - -
44B MET 2.8 16.7 + - - -
45B ARG 3.2 1.0 + - - -
46B GLN* 1.3 78.7 - - - +
48B ARG* 1.3 66.7 + - - +
53B ARG* 3.5 7.3 - - - +
54B ILE* 3.1 27.3 + - - +
55B VAL* 4.8 0.3 + - - +
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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