Contacts of the helix formed by residues 22 - 31 (chain B) 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 ASN 22 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20B PHE* 3.6 9.4 - - - -
21B LYS* 1.3 75.8 - - + +
23B GLU* 1.3 59.7 + - - +
24B GLU* 3.0 26.1 + - - +
25B LEU* 3.1 40.7 + - + +
139B ASP* 2.7 14.3 + - - +
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Residues in contact with GLU 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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1B MET* 3.8 14.4 - - + +
6B ARG* 2.9 35.9 + - - -
9B VAL* 4.0 12.7 - - + +
10B GLU* 5.4 4.8 - - - +
13B GLN* 2.8 32.3 + - - +
20B PHE* 4.2 19.6 - - + +
21B LYS 3.8 3.4 + - - +
22B ASN* 1.3 68.9 + - - +
24B GLU* 1.3 60.3 + - - +
25B LEU 3.2 0.4 - - - -
26B LEU* 3.2 6.2 + - - +
27B PHE* 3.0 26.7 + - - +
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Residues in contact with GLU 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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-1B HIS* 3.1 42.9 + - - +
1B MET* 4.2 8.8 - - + +
22B ASN* 3.0 17.5 + - - +
23B GLU* 1.3 74.3 - - - +
25B LEU* 1.3 59.6 + - - +
27B PHE* 3.4 9.4 + - - +
28B ARG* 2.9 78.0 + - - +
46B ASP 5.0 1.4 - - - +
48B GLU 5.5 0.3 + - - -
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Residues in contact with LEU 25 (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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70A TYR* 4.4 11.0 - - + +
20B PHE* 4.0 3.4 - - + -
22B ASN* 3.1 33.5 + - + +
24B GLU* 1.3 78.7 - - + +
26B LEU* 1.3 61.9 + - - +
28B ARG* 3.6 11.6 + - - +
29B ALA 3.1 17.8 + - - -
53B LEU* 3.6 12.8 - - + +
135B ALA* 3.5 27.9 - - + +
138B LEU* 4.0 27.4 - - + -
139B ASP* 3.8 34.1 - - + +
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Residues in contact with LEU 26 (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 VAL* 3.9 21.3 - - + +
12B PHE* 3.4 44.9 - - + -
13B GLN* 3.6 22.4 - - + -
20B PHE* 3.9 26.5 - - + -
22B ASN 3.9 0.8 + - - -
23B GLU* 3.2 11.0 + - - +
25B LEU* 1.3 78.6 - - - +
27B PHE* 1.3 63.4 + - - +
29B ALA* 3.3 4.7 + - + +
30B LEU* 3.2 40.7 + - + +
132B LEU* 4.1 13.0 - - + -
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Residues in contact with PHE 27 (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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-1B HIS* 3.1 38.4 - + - -
1B MET* 4.4 5.8 - - + -
5B GLU* 3.7 36.1 - - + -
9B VAL* 4.3 15.9 - - + +
23B GLU 3.0 13.5 + - - +
24B GLU* 3.6 17.3 - - - +
26B LEU* 1.3 76.7 - - - +
28B ARG* 1.3 68.3 + - - +
30B LEU* 3.1 5.8 + - - +
31B CYS* 2.9 45.3 + - - -
35B TYR* 4.0 4.7 - + - -
47B VAL* 4.1 13.2 - - + -
48B GLU 4.8 3.4 - - - -
108B PHE* 3.4 34.5 - + - -
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Residues in contact with ARG 28 (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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70A TYR* 5.4 5.8 + - - -
-1B HIS* 5.9 0.6 - - - +
24B GLU* 2.9 51.8 + - - +
25B LEU* 3.8 9.4 - - - +
27B PHE* 1.3 82.3 - - - +
29B ALA* 1.3 62.2 + - - +
31B CYS* 3.0 11.4 + - - +
46B ASP 4.7 6.1 + - - -
48B GLU* 3.3 54.7 + - - +
49B SER 3.4 16.6 - - - +
50B ASN* 3.1 19.2 + - - +
53B LEU* 3.7 22.3 - - + +
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Residues in contact with ALA 29 (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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25B LEU 3.1 14.6 + - - +
26B LEU* 3.6 9.4 - - - +
27B PHE 3.2 0.2 - - - -
28B ARG* 1.3 75.2 - - - +
30B LEU* 1.3 58.8 - - + +
50B ASN* 3.0 28.7 + - - +
53B LEU* 3.5 8.9 - - + +
128B ALA* 3.8 8.6 - - - +
131B ALA* 3.7 33.0 - - - +
132B LEU* 3.8 16.2 - - + +
135B ALA* 4.1 4.0 - - + -
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Residues in contact with LEU 30 (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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8B ILE* 4.6 4.0 - - + -
9B VAL* 5.0 3.4 - - + -
12B PHE* 4.3 11.2 - - + -
26B LEU* 3.4 36.6 - - + +
27B PHE* 3.1 9.9 + - - +
29B ALA* 1.3 80.5 - - + +
31B CYS* 1.3 58.1 + - - +
32B HIS 3.5 2.1 + - - -
50B ASN* 4.6 0.7 - - - -
103B LEU* 3.7 30.5 - - + -
106B PHE* 3.6 39.5 - - + +
107B LEU* 3.5 16.6 - - + +
108B PHE* 2.8 40.3 + - + -
128B ALA* 5.4 1.8 - - + +
132B LEU* 5.9 2.5 - - + -
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Residues in contact with CYS 31 (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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27B PHE* 2.9 56.9 + - - -
28B ARG 3.0 7.9 + - - +
29B ALA 3.3 0.4 - - - -
30B LEU* 1.3 74.4 - - - +
32B HIS* 1.3 65.6 + - - +
35B TYR* 3.8 15.3 - - + -
36B ALA* 5.1 1.3 - - + -
47B VAL* 4.4 1.8 - - - -
48B GLU 3.4 19.5 - - - +
49B SER* 3.3 2.5 - - - -
50B ASN* 2.7 34.8 + - - -
108B PHE* 3.8 9.4 - - - -
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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