Contacts of the strand formed by residues 23 - 30 (chain A) in PDB entry 3ORO
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 SER 23 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19A PHE* 3.2 6.1 - - - +
20A GLY 3.0 24.9 + - - -
22A MET* 1.3 76.1 - - - +
24A GLU* 1.3 60.0 + - - +
25A VAL* 5.0 1.3 - - - -
40A LYS* 3.6 18.8 - - - +
41A VAL 3.2 13.7 - - - -
43A ARG* 3.5 7.1 - - - +
56A PHE* 3.2 22.7 - - - -
340A AGS 2.6 36.8 + - - +
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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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16A ILE* 4.1 10.3 - - + -
18A GLY 3.6 9.0 - - - +
19A PHE* 4.3 3.8 - - + +
23A SER* 1.3 73.3 - - - +
25A VAL* 1.3 64.5 + - - +
26A HIS* 2.6 25.8 + - - +
39A VAL 3.7 1.2 - - - +
40A LYS* 3.4 2.3 - - - -
41A VAL* 2.8 49.3 + - + +
42A LEU 3.8 6.3 - - - +
43A ARG* 3.6 6.9 - - + +
44A ALA* 3.1 22.7 + - - +
334A NHE 2.8 46.3 + - + +
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Residues in contact with VAL 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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16A ILE* 3.4 4.3 - - - +
17A LEU* 2.7 34.3 + - + +
18A GLY 3.0 9.1 + - - -
24A GLU* 1.3 81.5 - - - +
26A HIS* 1.3 58.0 + - - +
38A ALA* 3.8 27.8 - - + -
39A VAL 3.3 7.2 - - - +
40A LYS* 3.9 19.3 - - + -
92A MET* 4.1 4.7 - - + -
340A AGS 3.3 64.4 - - + +
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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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13A LEU* 3.7 33.0 - - + +
14A GLY 4.7 4.0 + - - -
15A GLU 3.7 5.3 - - - +
16A ILE* 3.8 25.0 + - + +
17A LEU* 3.9 4.0 - - - -
24A GLU* 2.6 36.3 + - + +
25A VAL* 1.3 84.6 - - - +
27A LEU* 1.3 62.5 + - - +
28A ALA 3.8 0.2 + - - -
38A ALA* 3.4 4.0 - - - -
39A VAL* 2.7 45.9 + - + +
41A VAL* 4.6 8.2 - - + +
334A NHE 3.5 26.7 - - - -
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Residues in contact with LEU 27 (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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13A LEU* 3.6 4.0 - - - +
14A GLY* 2.6 34.5 + - - -
15A GLU* 2.8 29.1 + - + +
17A LEU* 3.7 18.1 - - + +
26A HIS* 1.3 72.8 - - - +
28A ALA* 1.3 59.7 + - - +
36A ASP* 3.9 21.1 - - + +
37A VAL 3.6 16.8 - - - +
94A TYR* 3.8 42.6 - - + +
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Residues in contact with ALA 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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11A TYR* 4.4 14.4 - - + -
12A GLU 3.3 11.4 - - - +
13A LEU* 4.1 9.2 - - + -
14A GLY* 4.2 0.7 - - - +
26A HIS 3.8 0.2 + - - -
27A LEU* 1.3 79.6 - - - +
29A ARG* 1.3 60.5 + - - +
30A ASP 4.0 0.2 - - - -
36A ASP* 3.5 8.2 - - - +
37A VAL* 2.9 38.7 + - + +
39A VAL* 3.7 27.1 - - + -
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Residues in contact with ARG 29 (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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10A ARG 3.5 0.2 - - - +
11A TYR* 3.3 7.6 - - - -
12A GLU* 2.9 51.5 + - + +
28A ALA* 1.3 72.7 - - - +
30A ASP* 1.3 66.0 + - - +
31A LEU* 3.4 25.5 + - + +
34A HIS* 4.2 12.2 + - - +
35A ARG* 3.6 20.8 + - - +
36A ASP* 2.8 34.5 + - - +
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Residues in contact with ASP 30 (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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10A ARG* 2.8 40.7 + - - +
11A TYR* 3.8 23.1 - - + -
28A ALA 4.0 1.4 + - - -
29A ARG* 1.3 70.7 - - - +
31A LEU* 1.3 54.0 + - - +
32A ARG 3.0 14.9 + - - -
33A ASP* 3.3 9.7 + - - +
34A HIS* 2.7 36.9 + - - -
35A ARG* 2.8 47.5 + - + +
37A VAL* 4.2 3.1 - - + +
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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