Contacts of the helix formed by residues 56 - 67 (chain A) in PDB entry 2O1S
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 56 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52A SER 4.3 2.0 - - - +
53A GLY* 2.8 12.6 + - - -
55A GLY* 1.3 80.1 - - - +
57A VAL* 1.3 56.1 + - - +
58A GLU 3.4 2.2 - - - -
59A LEU* 3.2 13.4 + - + -
60A THR* 2.8 44.9 + - - -
76A TRP* 4.2 11.4 - - + -
81A GLN* 2.9 41.8 + - + -
84A PRO* 3.6 4.9 - - - +
179A ASN* 3.5 31.0 - - - +
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Residues in contact with VAL 57 (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 CYS* 3.5 35.0 - - - +
35A LEU* 3.9 16.2 - - + +
36A ARG* 3.5 31.0 - - - +
39A LEU* 4.7 4.5 - - + -
53A GLY 3.4 10.0 + - - +
54A LEU* 3.4 20.3 + - - +
55A GLY 3.6 0.8 - - - -
56A THR* 1.3 78.2 - - - +
58A GLU* 1.3 71.3 + - - +
60A THR* 3.3 2.3 + - - -
61A VAL* 3.2 21.3 + - - +
84A PRO* 4.5 16.4 - - + -
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Residues in contact with GLU 58 (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 CYS* 3.7 29.4 - - + +
33A ASP* 5.5 0.3 - - - +
36A ARG* 2.9 37.1 + - - -
56A THR 3.4 0.2 - - - -
57A VAL* 1.3 75.9 - - - +
59A LEU* 1.3 64.1 + - - +
61A VAL 3.4 0.7 + - - -
62A ALA* 3.0 25.3 + - - +
256A GLY 3.7 13.2 + - - +
257A HIS* 2.6 56.3 + - - +
258A ASP 4.5 0.2 - - - +
259A VAL* 3.9 17.9 - - + +
262A LEU* 4.4 2.2 - - + -
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Residues in contact with LEU 59 (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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55A GLY 5.3 0.7 - - - +
56A THR* 3.2 21.5 + - + +
58A GLU* 1.3 78.7 - - - +
60A THR* 1.3 57.6 + - - +
62A ALA* 3.5 1.3 + - - +
63A LEU* 2.9 48.8 + - + +
76A TRP* 4.3 7.6 - - + -
149A VAL* 4.0 31.6 - - + -
177A ILE* 4.2 16.6 - - + -
179A ASN* 4.9 1.3 - - - -
256A GLY 4.2 4.8 + - - +
262A LEU* 4.1 19.5 - - + -
266A LEU* 4.6 6.7 - - + -
278A LEU* 6.2 0.2 - - + -
280A ILE* 3.7 34.1 - - + -
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Residues in contact with THR 60 (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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56A THR* 2.8 28.9 + - - -
57A VAL 3.7 4.3 - - - -
59A LEU* 1.3 71.4 - - - +
61A VAL* 1.3 66.5 + - - +
63A LEU* 3.3 2.9 + - - +
64A HIS* 3.1 39.7 + - + +
76A TRP* 3.3 23.9 - - + -
84A PRO* 3.9 14.8 - - - +
85A HIS* 3.6 32.5 + - + +
88A LEU* 3.8 13.0 - - + -
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Residues in contact with VAL 61 (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 LEU* 4.1 7.0 - - + +
28A LEU* 4.0 28.5 - - + -
31A LEU* 4.1 19.3 - - + -
32A CYS* 3.8 19.7 - - - -
35A LEU* 4.0 11.0 - - + -
57A VAL 3.2 13.9 + - - +
58A GLU 3.9 6.3 - - - +
60A THR* 1.3 76.5 - - - +
62A ALA* 1.3 64.1 + - - +
64A HIS* 3.9 0.5 - - - -
65A TYR* 3.0 26.9 + - + +
88A LEU* 3.8 22.2 - - + -
259A VAL* 4.1 12.3 - - + -
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Residues in contact with ALA 62 (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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58A GLU 3.0 18.1 + - - +
59A LEU* 3.7 5.2 - - - +
61A VAL* 1.3 77.7 - - - +
63A LEU* 1.3 57.9 + - - +
65A TYR* 3.4 0.9 + - - +
66A VAL* 3.0 35.0 + - - +
259A VAL* 4.2 4.7 - - + +
262A LEU* 3.9 16.8 - - + -
263A ILE* 3.9 25.4 - - + -
266A LEU* 3.8 17.0 - - + -
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Residues in contact with LEU 63 (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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59A LEU* 2.9 48.5 + - + +
60A THR* 3.7 3.4 - - - +
62A ALA* 1.3 76.6 - - - +
64A HIS* 1.3 58.5 + - - +
67A TYR* 2.8 51.8 + - + +
69A THR* 5.7 0.7 - - - -
74A LEU* 4.5 16.6 - - + -
76A TRP* 4.1 14.4 - - + -
147A VAL* 4.0 21.1 - - + -
149A VAL* 3.9 18.6 - - + -
177A ILE* 3.8 20.6 - - + -
266A LEU* 4.1 11.2 - - + -
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Residues in contact with HIS 64 (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 THR* 3.4 20.9 - - + +
20A LEU* 3.7 15.9 - - + +
21A ARG* 2.8 32.4 + - - +
60A THR* 3.1 33.7 + - + +
63A LEU* 1.3 76.3 - - - +
65A TYR* 1.3 57.8 + - - +
67A TYR 3.4 3.4 - - - +
69A THR* 2.9 35.9 + - + +
74A LEU* 3.7 16.7 - - + +
85A HIS* 2.8 44.0 + + - -
88A LEU* 4.7 5.0 - - + +
89A THR* 3.8 12.4 - - + +
115A TYR* 4.6 1.0 - - - -
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Residues in contact with TYR 65 (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 LEU* 3.6 25.1 - - + -
21A ARG* 3.4 33.2 + - - +
23A LEU 3.2 27.7 + - - -
24A PRO* 4.5 0.7 - - - +
25A LYS* 3.6 27.4 + - + +
28A LEU* 3.8 31.2 - - + -
61A VAL* 3.0 20.4 + - + +
62A ALA* 3.8 4.7 - - - +
64A HIS* 1.3 79.4 - - - +
66A VAL* 1.3 63.4 + - + +
263A ILE* 3.7 26.5 - - + -
267A LYS* 4.5 9.1 - - - -
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Residues in contact with VAL 66 (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 ARG* 5.2 1.2 - - - -
62A ALA 3.0 20.2 + - - +
63A LEU 4.1 0.9 - - - +
65A TYR* 1.3 79.9 - - - +
67A TYR* 1.3 76.2 + - + +
68A ASN 3.9 0.9 + - - -
263A ILE* 3.5 44.4 - - + +
266A LEU* 4.0 10.3 - - + -
267A LYS* 3.7 38.4 - - + +
270A ARG* 4.0 21.7 + - - +
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Residues in contact with TYR 67 (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 ARG* 3.1 19.4 + - - -
63A LEU* 2.8 44.5 + - + +
64A HIS 3.4 6.4 - - - +
66A VAL* 1.3 85.9 - - + +
68A ASN* 1.3 56.8 + - - +
69A THR* 3.1 23.9 + - + -
72A ASP* 3.8 16.4 - - + +
74A LEU* 6.2 0.7 - - + -
145A ARG* 3.9 11.2 - - + -
146A THR 4.5 4.1 + - - -
147A VAL* 3.8 28.7 - - + -
175A LEU* 3.3 29.3 - - + +
266A LEU* 4.6 11.2 - - + -
270A ARG* 3.3 51.0 - - + +
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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