Contacts of the helix formed by residues 39 - 47 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A CYS* 1.3 72.3 - - - +
40A SER* 1.3 60.7 + - - +
41A ASP 3.1 0.2 - - - -
42A VAL* 3.0 29.9 + - + +
43A HIS* 3.5 25.6 - - - -
273A PHE* 3.8 12.4 - + - -
334A LEU* 3.2 42.2 + - + +
335A GLU* 4.5 1.7 - - - -
337A PHE* 3.7 21.0 - + - -
403A NAD 2.8 67.4 + - - +
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Residues in contact with SER 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A CYS* 2.9 7.8 - - - -
39A HIS* 1.3 79.5 - - - +
41A ASP* 1.3 58.7 + - - +
43A HIS* 3.1 8.6 + - - +
44A MET* 2.9 30.4 + - - +
49A PHE* 3.9 5.9 - - - -
68A HIS* 3.9 7.9 - - - -
403A NAD 2.9 28.4 + - - -
600A ETX 2.9 43.6 + - - -
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Residues in contact with ASP 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A GLY 4.6 1.0 - - - +
38A CYS 2.9 23.2 + - - +
40A SER* 1.3 75.3 - - - +
42A VAL* 1.3 59.5 + - - +
44A MET* 3.7 11.3 - - - +
45A ARG* 3.1 27.4 + - - +
66A LEU* 3.9 20.2 - - + +
67A GLY* 4.2 1.8 + - - -
68A HIS* 3.5 25.8 + - - -
119A GLY 4.7 0.9 - - - +
126A TYR* 2.7 32.0 + - - +
331A ILE* 3.8 26.9 - - + +
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Residues in contact with VAL 42 (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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38A CYS 4.9 0.2 - - - +
39A HIS* 3.0 31.6 + - + +
41A ASP* 1.3 77.5 - - - +
43A HIS* 1.3 63.8 + - + +
45A ARG* 3.6 4.0 + - - +
46A GLN* 3.1 49.7 + - - +
331A ILE* 3.5 37.5 - - + +
334A LEU* 3.9 13.0 - - + -
335A GLU* 3.8 32.0 - - + +
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Residues in contact with HIS 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A HIS* 3.5 29.6 - + - -
40A SER* 3.1 1.3 + - - +
42A VAL* 1.3 77.0 - - + +
44A MET* 1.3 59.2 - - - +
46A GLN* 3.1 17.3 + - - +
47A GLY 2.8 23.6 + - - -
48A ARG 2.9 29.7 + - - +
49A PHE* 3.4 30.3 - + + -
272A LEU 3.6 18.7 + - - -
273A PHE* 4.1 10.8 - + - -
403A NAD 2.9 45.9 + - - -
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Residues in contact with MET 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A LEU* 3.4 18.9 - - + +
9A ILE* 3.9 0.5 - - - +
40A SER 2.9 21.9 + - - +
41A ASP* 3.8 18.6 - - - +
42A VAL 3.4 0.2 - - - -
43A HIS* 1.3 76.5 - - - +
45A ARG* 1.3 58.1 + - - +
47A GLY* 2.8 21.0 + - - +
49A PHE* 3.9 25.6 - - + -
54A ILE* 3.8 27.7 - - + +
60A VAL* 4.8 1.6 - - + -
64A VAL* 4.8 1.8 - - + -
66A LEU* 4.3 22.7 - - + -
119A GLY 4.0 5.4 - - - +
120A ILE* 3.6 50.5 - - + +
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Residues in contact with ARG 45 (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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6A LEU* 4.1 9.3 - - + +
9A ILE* 3.9 2.8 - - - -
10A GLY* 2.9 27.8 + - - -
11A LYS 3.3 25.4 - - - +
12A PRO* 4.2 4.6 - - - +
13A LEU* 4.1 20.6 - - + +
41A ASP 3.1 15.8 + - - +
42A VAL 3.8 4.4 + - - +
44A MET* 1.3 79.0 - - - +
46A GLN* 1.3 59.9 + - + +
47A GLY 3.2 0.4 + - - -
66A LEU* 5.0 0.6 - - - +
328A ASN* 3.0 38.4 + - - +
331A ILE* 3.3 23.7 - - - +
332A ASP* 2.9 30.1 + - - +
335A GLU* 2.8 28.5 + - - -
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Residues in contact with GLN 46 (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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9A ILE* 3.3 13.9 - - - +
10A GLY* 4.6 5.7 - - - +
42A VAL* 3.1 27.9 + - + +
43A HIS* 3.1 23.5 + - - +
45A ARG* 1.3 78.6 - - + +
47A GLY* 1.3 61.5 + - - +
48A ARG* 3.6 33.1 + - + +
335A GLU* 3.4 25.0 - - - +
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Residues in contact with GLY 47 (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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9A ILE* 3.4 25.6 - - - +
43A HIS 2.8 0.6 + - - -
44A MET 2.8 16.9 + - - -
45A ARG 3.2 0.8 - - - -
46A GLN* 1.3 78.6 - - - +
48A ARG* 1.3 64.8 + - - +
53A ARG* 3.5 5.9 - - - +
54A ILE* 3.1 28.4 + - - +
55A VAL* 4.7 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