Contacts of the helix formed by residues 32 - 42 (chain A) in PDB entry 1O0W
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 32 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30A LEU 3.5 2.6 + - - +
31A CYS* 1.3 75.9 - - - +
33A SER* 1.3 83.9 + - - +
34A SER* 2.8 31.9 + - - +
35A TYR* 3.0 14.0 + - - +
36A ALA* 3.2 9.2 + - - +
50A ASN* 4.5 12.5 - - - +
107A LEU* 5.9 0.7 - - + -
108A PHE 3.0 21.0 + - - +
109A LEU* 3.5 14.6 - - + -
113A GLU* 3.9 13.7 - - + +
124A ILE* 3.5 43.1 - - + +
127A ASP* 6.0 3.4 - - + -
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Residues in contact with SER 33 (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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31A CYS 3.7 1.4 + - - -
32A HIS* 1.3 89.9 + - - +
34A SER* 1.3 66.1 + - - +
36A ALA* 3.7 1.7 - - - +
37A ASN* 2.9 40.6 + - - -
49A SER* 3.6 15.0 - - - -
50A ASN* 4.8 2.0 + - - -
51A GLU* 3.9 28.8 + - - +
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Residues in contact with SER 34 (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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32A HIS* 2.8 25.9 + - - -
33A SER* 1.3 83.0 + - - +
35A TYR* 1.3 56.5 + - - +
37A ASN* 3.7 6.7 + - - +
38A GLU* 3.2 26.7 + - - +
109A LEU* 3.8 2.3 - - - -
110A GLY* 2.9 30.6 + - - -
113A GLU* 3.3 23.6 - - - +
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Residues in contact with TYR 35 (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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2A ASN* 4.5 2.9 + - - -
4A SER* 5.1 1.9 + - - -
5A GLU* 2.5 38.4 + - - +
27A PHE* 4.1 11.7 - + - -
31A CYS* 3.8 11.0 - - - -
32A HIS 3.0 4.7 + - - +
34A SER* 1.3 80.3 + - - +
36A ALA* 1.3 66.0 + - - +
38A GLU* 3.3 12.1 + - - +
39A GLN* 2.9 52.0 + - + +
44A ARG* 4.1 3.1 + - - -
47A VAL* 4.1 3.6 - - + -
108A PHE* 3.4 49.9 - + + +
109A LEU 3.5 22.4 - - - -
110A GLY* 3.7 4.5 - - - +
111A LYS* 6.4 1.3 - - - -
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Residues in contact with ALA 36 (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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31A CYS* 5.3 0.7 - - + -
32A HIS 3.2 4.7 + - - +
33A SER* 3.8 6.3 - - - +
35A TYR* 1.3 81.0 - - - +
37A ASN* 1.3 57.9 + - - +
39A GLN 3.8 0.3 - - - -
40A ASN* 2.8 40.6 + - - +
47A VAL* 3.9 19.5 - - + +
48A GLU* 3.8 6.7 - - - -
49A SER* 3.5 37.7 - - - +
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Residues in contact with ASN 37 (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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33A SER* 2.9 32.0 + - - +
34A SER* 4.0 6.4 - - - +
36A ALA* 1.3 78.3 - - - +
38A GLU* 1.3 58.0 + - - +
40A ASN* 3.8 9.9 - - - +
41A GLN* 2.9 52.5 + - - +
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Residues in contact with GLU 38 (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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34A SER 3.2 17.1 + - - +
35A TYR* 3.6 18.3 - - - +
37A ASN* 1.3 77.8 - - - +
39A GLN* 1.3 84.6 + - - +
41A GLN* 3.2 11.9 + - - +
42A ALA* 3.0 21.5 + - + +
109A LEU 4.4 0.9 - - - +
110A GLY* 3.5 4.0 - - - -
111A LYS* 2.8 53.8 + - - +
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Residues in contact with GLN 39 (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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2A ASN* 5.0 0.9 + - - -
35A TYR* 2.9 51.6 + - + +
36A ALA 3.9 2.2 - - - +
38A GLU* 1.3 99.3 + - - +
40A ASN* 1.3 63.4 + - - +
42A ALA* 3.0 16.8 + - - +
43A GLY 3.2 0.2 + - - -
44A ARG* 2.8 63.1 + - + +
47A VAL* 4.0 20.4 - - + -
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Residues in contact with ASN 40 (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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36A ALA* 2.8 30.7 + - - +
37A ASN* 3.8 10.9 + - - +
38A GLU 3.3 0.2 - - - -
39A GLN* 1.3 73.0 - - - +
41A GLN* 1.3 57.5 + - + +
43A GLY* 2.8 24.1 + - - -
44A ARG 2.8 30.3 + - - -
45A LYS* 3.6 26.6 + - + +
47A VAL* 2.9 26.7 + - - +
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Residues in contact with GLN 41 (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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37A ASN* 2.9 39.9 + - - +
38A GLU* 3.6 8.0 - - - +
40A ASN* 1.3 78.5 - - + +
42A ALA* 1.3 57.1 + - - +
43A GLY 3.1 2.6 + - - -
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Residues in contact with ALA 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 GLU* 3.0 14.4 + - + +
39A GLN* 3.0 20.3 + - - +
41A GLN* 1.3 75.2 - - - +
43A GLY* 1.3 60.2 + - - +
44A ARG* 3.4 7.1 + - + +
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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
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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