Contacts of the helix formed by residues 20 - 28 (chain B) in PDB entry 2OHW
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 THR 20 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18B LEU 3.4 1.3 - - - -
19B GLU* 1.3 98.7 - - + +
21B LYS* 1.3 65.4 + - - +
22B PRO* 3.3 19.1 - - - +
23B ASP* 3.3 21.8 + - - +
24B GLU* 3.2 25.1 + - - +
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Residues in contact with LYS 21 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96A ASP* 5.5 0.6 + - - -
20B THR* 1.3 73.3 - - - +
22B PRO* 1.4 69.2 - - + +
24B GLU* 3.0 9.5 + - - +
25B ARG* 2.9 38.3 + - - +
32B LEU* 3.8 40.8 - - + +
34B GLU* 5.0 5.1 + - - -
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Residues in contact with PRO 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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20B THR* 3.3 16.8 - - - +
21B LYS* 1.4 92.8 - - + +
23B ASP* 1.3 57.9 + - - +
25B ARG* 3.3 9.1 + - + +
26B HIS* 2.8 51.8 + - + -
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Residues in contact with ASP 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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6B MET* 4.9 6.7 - - + +
18B LEU* 3.7 24.3 - - + +
19B GLU* 3.7 23.9 + - - +
20B THR* 3.3 24.9 + - - +
21B LYS 3.2 0.8 - - - -
22B PRO* 1.3 79.9 - - - +
24B GLU* 1.3 62.2 + - - +
26B HIS* 3.4 9.7 + - - +
27B LEU* 3.2 17.8 + - - +
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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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17B PRO* 3.6 8.3 - - - +
18B LEU* 3.0 46.9 + - + +
20B THR 3.2 15.7 + - - +
21B LYS* 3.0 9.6 + - - +
23B ASP* 1.3 73.8 - - - +
25B ARG* 1.3 60.0 + - - +
27B LEU 3.1 1.7 + - - -
28B PHE* 2.8 35.5 + - + -
31B SER 3.4 4.5 - - - +
32B LEU* 3.8 12.8 - - - +
33B ARG* 2.9 44.2 + - + +
34B GLU 4.5 1.2 + - - -
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Residues in contact with ARG 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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96A ASP* 2.5 46.1 + - - -
97A LEU 4.9 1.0 - - - -
98A GLN* 3.2 54.5 + - - +
21B LYS* 2.9 32.4 + - - +
22B PRO* 3.8 7.6 - - + +
24B GLU* 1.3 75.5 - - - +
26B HIS* 1.3 67.1 + - + +
27B LEU 3.4 0.2 + - - -
29B LEU* 3.4 3.6 + - - -
30B GLY* 2.8 57.9 + - - +
31B SER 3.5 10.1 - - - +
32B LEU* 3.7 24.9 - - + +
96B ASP* 4.2 1.9 - - - +
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Residues in contact with HIS 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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22B PRO* 2.8 37.8 + - + +
23B ASP* 3.8 10.0 + - - +
24B GLU 3.2 0.2 - - - -
25B ARG* 1.3 80.7 - - + +
27B LEU* 1.3 58.7 + - - +
96B ASP* 2.6 32.8 - - - +
98B GLN* 3.7 33.3 - - + +
99B PHE* 3.4 32.7 - - + +
101B THR* 3.6 0.5 - - - -
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Residues in contact with LEU 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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6B MET* 4.4 9.9 - - + -
9B TYR* 3.7 21.1 - - + -
10B LEU* 3.8 23.3 - - + -
14B MET* 4.4 1.3 - - - -
18B LEU* 4.0 10.1 - - + -
23B ASP 3.2 11.8 + - - +
24B GLU 3.1 6.7 + - - +
26B HIS* 1.3 79.6 - - - +
28B PHE* 1.3 86.6 + - + +
29B LEU 3.3 5.3 + - - -
99B PHE* 4.4 8.5 - - + -
101B THR* 2.7 36.7 + - - +
102B PRO* 3.8 17.5 - - + -
103B LEU* 3.5 20.9 - - + +
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Residues in contact with PHE 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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9B TYR* 3.7 10.8 - + - -
14B MET* 3.8 15.3 - - + -
18B LEU* 4.7 5.4 - - + -
24B GLU* 2.8 33.3 + - - +
27B LEU* 1.3 92.2 - - + +
29B LEU* 1.3 70.6 + - - +
30B GLY 3.2 2.7 - - - -
31B SER* 3.1 26.5 + - - +
33B ARG* 3.6 40.6 - - + -
36B VAL* 3.9 21.8 - - + -
39B ALA* 4.5 1.6 - - + -
67B LEU* 3.9 2.3 - - - +
103B LEU* 3.5 25.4 - - + -
106B VAL* 3.9 16.6 - - + +
118B ILE* 3.9 15.0 - - + -
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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