Contacts of the helix formed by residues 20 - 28 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18A LEU* 4.3 2.2 - - - +
19A GLU* 1.3 93.8 - - + +
21A LYS* 1.3 67.1 + - - +
22A PRO* 3.6 13.7 - - - +
23A ASP* 2.9 48.2 + - - +
24A GLU* 3.4 14.1 + - - +
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Residues in contact with LYS 21 (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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20A THR* 1.3 71.0 - - - +
22A PRO* 1.4 75.4 - - + +
24A GLU* 3.0 22.7 + - - +
25A ARG* 3.0 31.1 + - - +
32A LEU* 3.5 38.5 - - + +
34A GLU* 4.6 12.7 + - - +
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Residues in contact with PRO 22 (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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20A THR* 3.6 14.8 - - - +
21A LYS* 1.4 94.7 - - + +
23A ASP* 1.3 62.5 + - - +
25A ARG* 3.2 9.6 + - + +
26A HIS* 2.9 47.5 + - + +
95B SER* 5.8 7.4 - - - +
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Residues in contact with ASP 23 (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 MET* 5.2 6.5 - - + -
18A LEU* 3.9 18.8 - - + +
19A GLU* 3.2 35.0 - - - +
20A THR* 2.9 30.4 + - - +
22A PRO* 1.3 79.0 - - - +
24A GLU* 1.3 63.0 + - - +
26A HIS* 3.3 8.7 + - - +
27A LEU* 3.1 22.2 + - - +
99A PHE* 6.0 0.2 - - - -
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Residues in contact with GLU 24 (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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17A PRO* 3.6 13.5 - - - +
18A LEU* 3.0 46.1 + - + +
20A THR 3.6 11.5 - - - +
21A LYS* 3.0 21.9 + - - +
23A ASP* 1.3 77.6 - - - +
25A ARG* 1.3 56.8 + - - +
27A LEU* 3.1 2.0 + - - -
28A PHE* 2.8 37.3 + - + -
31A SER 3.3 4.0 - - - +
32A LEU* 3.7 13.8 - - - +
33A ARG* 2.8 41.0 + - + +
34A GLU 4.4 1.4 + - - -
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Residues in contact with ARG 25 (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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21A LYS* 3.0 23.7 + - - +
22A PRO* 3.8 9.6 - - + +
24A GLU* 1.3 76.1 - - - +
26A HIS* 1.3 66.0 + - + +
27A LEU 3.4 0.3 + - - -
29A LEU* 3.5 4.2 + - - -
30A GLY* 2.8 56.4 + - - +
31A SER* 3.4 8.0 - - - +
32A LEU* 3.6 42.3 - - + +
91B PHE 5.6 1.0 + - - -
92B LYS* 3.7 49.0 - - - +
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Residues in contact with HIS 26 (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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22A PRO* 2.9 39.8 + - + +
23A ASP* 3.8 8.9 + - - +
24A GLU 3.2 0.2 - - - -
25A ARG* 1.3 82.1 - - + +
27A LEU* 1.3 58.0 + - - +
29A LEU* 4.7 1.6 + - - -
97A LEU* 6.0 1.4 - - - +
98A GLN* 3.5 41.5 + - + -
99A PHE* 3.2 40.8 - - + +
101A THR* 3.7 9.0 - - - +
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Residues in contact with LEU 27 (chain A).
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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6A MET* 4.3 8.1 - - + -
9A TYR* 3.8 20.9 - - + -
10A LEU* 3.8 28.9 - - + -
14A MET* 4.4 0.7 - - - -
18A LEU* 4.3 8.5 - - + -
23A ASP 3.1 10.8 + - - +
24A GLU 3.1 7.4 + - - +
26A HIS* 1.3 77.7 - - - +
28A PHE* 1.3 86.4 + - + +
29A LEU 3.3 6.7 + - - -
99A PHE* 4.5 9.1 - - + -
101A THR* 2.7 33.7 + - - +
102A PRO* 3.9 11.9 - - + -
103A LEU* 3.5 23.0 - - + +
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Residues in contact with PHE 28 (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 TYR* 3.8 10.5 - + - -
14A MET* 3.7 15.5 - - + -
18A LEU* 5.0 1.8 - - + -
24A GLU* 2.8 36.3 + - + +
27A LEU* 1.3 94.4 - - + +
29A LEU* 1.3 70.7 + - - +
30A GLY 3.1 2.7 - - - -
31A SER* 3.1 26.4 + - - +
33A ARG* 3.6 40.2 - - + -
36A VAL* 3.8 22.7 - - + -
39A ALA* 4.5 2.2 - - + -
67A LEU* 3.9 2.6 - - - +
103A LEU* 3.5 26.2 - - + -
106A VAL* 3.9 16.4 - - + +
118A ILE* 3.9 15.5 - - + -
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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