Contacts of the helix formed by residues 19 - 24 (chain B) in PDB entry 5M73
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 TYR 19 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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149A A 2.2 35.1 + - - +
150A G 2.9 24.6 - - - -
197A G 3.8 10.0 + - - -
17B CYS* 4.4 6.1 - - + -
18B ILE* 1.3 82.3 - - - +
20B PRO* 1.3 74.3 - - + +
21B ALA 3.1 0.9 + - - -
22B TYR* 3.0 48.3 + + + +
23B LEU* 4.6 0.3 + - - +
49B ILE* 4.7 1.1 - - - +
67B MET 3.8 11.2 - - - -
68B TYR* 3.5 53.8 - + + -
69B SER 5.0 0.4 - - - -
80B GLY 4.3 7.4 - - - -
81B ARG* 3.2 33.5 + - + -
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Residues in contact with PRO 20 (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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19B TYR* 1.3 87.3 - - + +
21B ALA* 1.3 62.4 - - + +
23B LEU* 2.9 18.9 + - - +
24B ASN* 3.5 8.5 + - + -
44B PRO* 3.5 27.8 - - - +
46B ALA* 4.3 11.2 - - + +
49B ILE* 4.6 11.0 - - + -
68B TYR* 5.2 4.0 - - + +
77B GLN 4.7 4.5 - - - +
78B TYR* 3.6 18.2 - - + +
79B ARG 3.5 24.2 - - - +
80B GLY 3.2 20.4 - - - +
81B ARG* 4.9 0.2 - - - -
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Residues in contact with ALA 21 (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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19B TYR 3.1 0.8 + - - -
20B PRO* 1.3 79.6 - - - +
22B TYR* 1.3 64.4 + - - +
23B LEU 2.8 1.0 + - - -
24B ASN* 3.1 13.9 + - - +
27B LYS* 3.9 30.9 - - + +
31B GLU 4.2 6.3 - - - +
32B GLY 4.4 2.5 - - - -
33B ARG* 3.7 13.5 + - - +
68B TYR* 3.4 35.4 - - + -
71B GLU* 5.2 2.5 - - + +
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Residues in contact with TYR 22 (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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149A A 3.6 0.9 + - - -
150A G 2.0 40.3 + - - -
17B CYS* 4.4 6.4 + - - +
18B ILE* 4.0 11.0 - - + -
19B TYR* 3.0 58.4 + + + +
20B PRO 3.0 1.2 + - - -
21B ALA* 1.3 78.6 - - - +
23B LEU* 1.3 61.9 + - + +
32B GLY 3.6 11.2 - - - -
33B ARG* 4.0 1.8 - - - +
34B ARG* 3.1 62.0 + - + +
35B ILE* 3.3 21.1 + - - +
68B TYR* 4.4 6.1 - + - -
105B MET* 3.9 23.6 - - + -
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Residues in contact with LEU 23 (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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18B ILE* 5.3 2.9 - - + -
19B TYR 5.1 0.7 - - - +
20B PRO 2.9 5.1 + - - +
21B ALA 2.9 0.4 - - - -
22B TYR* 1.3 87.9 - - + +
24B ASN* 1.3 59.3 + - - +
25B ASN 3.1 1.0 + - - -
33B ARG* 5.5 0.9 - - - -
35B ILE* 3.3 27.8 - - + -
40B ALA* 2.9 24.0 - - + +
41B VAL* 3.1 10.2 + - + +
44B PRO* 3.8 14.0 - - + +
49B ILE* 3.8 23.6 - - + -
105B MET* 3.6 34.1 - - + +
108B ALA* 3.6 30.3 - - + -
109B ALA* 4.2 8.1 - - + +
112B ILE* 4.5 5.8 - - + -
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Residues in contact with ASN 24 (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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20B PRO 3.5 7.5 + - - +
21B ALA* 3.1 12.6 + - - +
23B LEU* 1.3 75.0 - - - +
25B ASN* 1.3 58.0 + - - +
26B LYS* 3.0 13.7 + - - +
27B LYS* 2.9 51.4 + - + +
33B ARG* 4.0 5.2 - - - +
40B ALA* 4.4 0.2 - - - -
41B VAL 3.5 1.8 - - - -
42B GLU* 3.9 0.5 - - - -
43B ASN* 2.5 52.9 + - - +
44B PRO* 3.6 7.2 - - + +
78B TYR* 3.7 22.0 + - - -
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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