Contacts of the helix formed by residues 60 - 68 (chain B) in PDB entry 2PCB
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 LYS 60 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36B PHE* 4.6 3.6 - - - +
37B GLY 5.5 1.1 - - - +
58B THR* 3.9 19.3 - - + -
59B TRP* 1.3 75.3 - - - +
61B GLU* 1.3 82.8 + - - +
62B GLU* 4.9 15.7 - - - +
63B THR* 2.7 34.5 + - - +
64B LEU* 2.7 17.1 + - - -
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Residues in contact with GLU 61 (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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36B PHE* 3.9 18.6 - - - -
60B LYS* 1.3 81.0 + - + +
62B GLU* 1.3 71.9 + - + +
64B LEU* 2.8 5.4 + - - +
65B MET* 2.7 22.1 + - + -
95B ILE* 3.1 32.7 - - + +
99B LYS* 2.9 33.6 - - - +
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Residues in contact with GLU 62 (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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60B LYS* 3.5 11.7 - - - +
61B GLU* 1.3 81.4 - - + +
63B THR* 1.3 66.8 + - - +
65B MET* 2.5 44.8 + - + +
66B GLU* 2.9 11.9 + - - +
88B LYS* 4.3 17.5 + - - -
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Residues in contact with THR 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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57B ILE* 3.0 29.4 - - + -
58B THR 3.4 2.1 + - - +
59B TRP* 3.7 7.7 - - + -
60B LYS* 2.7 48.1 + - - +
62B GLU* 1.3 70.3 - - - +
64B LEU* 1.3 62.7 + - - +
66B GLU* 3.3 7.0 + - - +
67B TYR* 3.1 18.2 + - - +
74B TYR* 2.7 29.7 + - - +
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Residues in contact with LEU 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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35B LEU* 4.1 9.9 - - + -
36B PHE* 3.8 31.9 - - + -
59B TRP* 2.9 40.8 - - + -
60B LYS 2.7 20.6 + - - +
61B GLU 2.8 1.5 + - - +
62B GLU 2.8 1.6 + - - -
63B THR* 1.3 66.6 - - - +
65B MET* 1.3 50.7 + - - -
66B GLU 2.4 20.0 + - - -
67B TYR* 2.7 25.7 + - + -
68B LEU* 2.9 19.7 + - + -
95B ILE* 2.9 24.9 - - + -
98B LEU* 4.0 19.3 - - + -
105B HEM 4.6 9.2 - - + -
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Residues in contact with MET 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 GLU* 2.7 13.2 + - + +
62B GLU* 2.5 51.0 + - + +
64B LEU* 1.3 67.9 - - - +
66B GLU* 1.3 49.1 + - - +
88B LYS* 4.3 21.4 - - + +
91B ARG* 2.6 54.8 + - - +
92B GLU* 2.9 58.3 - - + -
95B ILE* 2.7 18.9 - - + +
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Residues in contact with GLU 66 (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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62B GLU 2.9 7.5 + - - +
63B THR* 3.5 5.8 - - - +
64B LEU 2.4 13.3 + - - -
65B MET* 1.3 67.2 - - - +
67B TYR* 1.3 55.3 + - - +
68B LEU 3.1 0.9 - - - -
69B GLU* 2.7 35.4 + - - +
70B ASN 3.6 2.3 + - - -
73B LYS* 6.0 1.7 - - - +
74B TYR* 2.5 48.8 + - + +
91B ARG* 4.5 1.6 - - - +
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Residues in contact with TYR 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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52B ASN* 5.4 2.3 + - - -
59B TRP* 3.6 28.0 - + + -
63B THR 3.3 10.3 - - - +
64B LEU* 2.7 12.7 + - + +
66B GLU* 1.3 76.4 - - - +
68B LEU* 1.3 76.0 + - + +
70B ASN 2.9 4.0 + - - -
71B PRO* 2.9 56.7 - - + +
74B TYR* 3.9 22.6 - + + -
75B ILE* 4.0 17.3 - - + +
78B THR* 5.5 3.3 + - - +
80B MET* 3.2 39.6 - - + +
105B HEM 3.6 42.8 - + + +
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Residues in contact with LEU 68 (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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64B LEU* 2.9 20.9 + - + +
67B TYR* 1.3 100.6 - - + +
69B GLU* 1.3 50.9 + - - +
71B PRO* 4.6 0.7 - - - -
80B MET* 4.9 5.6 - - + -
82B PHE* 5.0 8.1 - - + -
84B GLY* 2.8 7.2 - - - -
85B ILE* 2.5 39.4 + - + +
91B ARG* 3.1 30.1 - - + +
94B LEU* 4.6 22.7 - - + -
95B ILE* 3.8 30.1 - - + -
98B LEU* 5.6 0.4 - - + -
105B HEM 4.2 24.2 - - + -
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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