Contacts of the helix formed by residues 56 - 67 (chain B) in PDB entry 2OY0
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 56 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37B ARG* 3.0 25.0 + - - +
54B PRO* 4.1 1.7 - - - +
55B VAL* 1.3 82.1 - - - +
57B ARG* 1.3 63.0 + - - +
58B GLY* 2.8 15.1 + - - -
59B THR* 3.5 14.1 - - - +
60B ALA 4.7 1.2 + - - -
84B ARG* 4.7 6.3 - - - -
86B GLY* 3.9 4.5 - - - -
257B ASP* 5.0 1.0 - - - +
302B SAH 2.8 31.5 + - - -
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Residues in contact with ARG 57 (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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29B LYS* 4.8 4.8 - - - +
34B GLU* 3.4 35.2 + - - +
35B VAL* 3.4 40.2 + - + +
37B ARG* 3.7 34.8 - - + +
56B SER* 1.3 72.7 - - - +
58B GLY* 1.3 68.5 + - - +
59B THR 3.6 0.2 - - - -
60B ALA* 3.5 8.0 + - - +
61B LYS* 3.3 21.8 + - + +
211B LEU* 5.6 3.4 - - + +
257B ASP* 5.9 0.2 - - - -
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Residues in contact with GLY 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B SER* 2.8 8.2 + - - -
57B ARG* 1.3 77.2 - - - +
59B THR* 1.3 65.3 + - - +
61B LYS* 2.7 28.8 + - - +
62B LEU 3.3 3.3 + - - -
87B TRP* 3.7 12.4 + - - -
146B ASP* 5.9 0.4 - - - -
302B SAH 3.3 22.9 - - - -
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Residues in contact with THR 59 (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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54B PRO* 3.1 33.0 - - + +
55B VAL 4.3 1.8 - - - +
56B SER 3.5 10.1 - - - +
58B GLY* 1.3 69.4 - - - -
60B ALA* 1.3 63.8 + - - -
62B LEU* 3.0 4.7 + - - +
63B ARG* 2.8 23.0 + - - +
86B GLY* 3.3 42.2 - - - +
87B TRP* 4.4 2.9 - - - -
89B TYR* 5.9 2.5 - - + -
90B TYR* 4.1 16.8 - - - +
258B VAL* 3.6 17.8 - - - +
260B LEU* 4.6 6.5 - - + +
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Residues in contact with ALA 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B VAL* 4.0 33.0 - - + -
56B SER 4.7 0.4 + - - +
57B ARG 3.5 11.6 + - - +
58B GLY 2.9 0.6 + - - -
59B THR* 1.3 81.6 + - - +
61B LYS* 1.3 67.0 + - - +
63B ARG* 3.0 13.9 + - - +
64B TRP* 3.1 12.1 + - - +
211B LEU* 4.6 9.7 - - + +
255B GLU* 5.9 0.4 - - - +
257B ASP* 4.3 4.9 - - - +
258B VAL* 3.9 18.8 - - + -
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Residues in contact with LYS 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B ARG* 3.3 14.8 + - + +
58B GLY* 2.7 17.2 + - - +
60B ALA* 1.3 73.5 - - - +
62B LEU* 1.3 63.0 + - - +
64B TRP* 3.0 21.1 + - - +
65B LEU* 3.4 2.5 + - + -
87B TRP* 4.8 6.3 - - + +
146B ASP* 5.1 5.8 + - - -
182B LYS* 5.2 0.4 - - - +
209B ASN* 3.3 23.7 + - - +
211B LEU* 3.5 44.4 - - + +
212B SER* 3.6 7.7 + - - +
218B GLU* 3.1 21.6 + - - -
220B TYR* 3.0 32.3 + - - -
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Residues in contact with LEU 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B GLY 3.3 1.6 + - - -
59B THR* 3.0 7.0 + - - +
61B LYS* 1.3 79.8 - - - +
63B ARG* 1.3 63.2 + - - +
65B LEU* 3.2 25.7 + - + -
66B VAL* 3.2 23.4 + - + +
71B LEU* 4.3 13.0 - - + -
87B TRP* 3.5 60.7 - - + +
90B TYR* 3.9 4.3 - - + -
91B MET* 3.2 34.8 - - + -
144B LEU* 4.2 5.2 - - + -
180B CYS* 4.5 5.6 - - + -
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Residues in contact with ARG 63 (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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59B THR 2.8 12.0 + - - +
60B ALA* 3.0 13.0 + - - +
62B LEU* 1.3 73.3 - - - +
64B TRP* 1.3 59.5 + - - +
65B LEU 2.7 16.2 + - - -
66B VAL* 3.0 2.1 + - - +
67B GLU* 2.8 62.7 + - + +
90B TYR* 3.8 40.6 + - + -
94B GLN* 5.8 0.8 + - - -
258B VAL* 4.0 34.0 - - + +
259B ASN 5.7 1.4 + - - -
260B LEU* 5.9 0.6 - - - +
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Residues in contact with TRP 64 (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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33B ILE* 5.8 1.6 - - + -
60B ALA 3.1 5.8 + - - +
61B LYS 3.0 14.3 + - - +
63B ARG* 1.3 81.4 - - - +
65B LEU* 1.3 86.5 + - + +
67B GLU* 4.9 0.4 - - - -
68B ARG* 3.0 67.6 + - - +
70B PHE* 3.6 27.1 - + - -
207B VAL* 4.0 15.3 - - + -
208B ARG 4.4 1.8 - - - -
209B ASN* 3.8 12.1 - - - +
210B PRO* 3.4 41.1 - - + +
211B LEU* 4.3 18.2 - - + -
255B GLU* 5.4 5.4 - - - +
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Residues in contact with LEU 65 (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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61B LYS* 3.9 2.0 - - + +
62B LEU* 3.2 25.8 + - + +
63B ARG 2.7 5.3 + - - -
64B TRP* 1.3 97.8 - - + +
66B VAL* 1.3 65.7 + - - +
67B GLU 3.2 1.1 - - - -
68B ARG 3.3 9.5 + - - -
69B ARG 3.4 0.2 + - - -
70B PHE* 3.3 32.7 + - + -
71B LEU* 3.7 8.5 - - + -
87B TRP* 5.1 2.7 - - + -
180B CYS* 3.5 31.9 - - + -
207B VAL* 4.8 7.4 - - + +
209B ASN* 3.8 20.4 - - + +
220B TYR* 4.7 14.1 - - + -
222B VAL* 4.5 12.3 - - + -
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Residues in contact with VAL 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B LEU* 3.2 17.7 - - + +
63B ARG 3.0 3.9 + - - +
65B LEU* 1.3 76.4 - - - +
67B GLU* 1.3 65.4 + - + +
69B ARG* 3.0 25.1 + - - -
71B LEU* 3.2 33.6 - - + +
73B PRO* 4.6 9.4 - - + -
90B TYR* 2.9 39.5 - - + +
91B MET* 4.0 14.6 - - + -
94B GLN* 4.1 13.7 - - - +
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Residues in contact with GLU 67 (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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63B ARG* 2.8 70.3 + - + +
64B TRP* 4.9 0.3 - - - -
66B VAL* 1.3 84.8 - - + +
68B ARG* 1.3 76.9 + - - +
69B ARG* 3.2 9.1 + - - +
90B TYR* 4.7 1.3 - - - +
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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