Contacts of the helix formed by residues 62 - 74 (chain B) in PDB entry 2P1A
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 62 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60B GLY 4.5 5.4 - - - +
61B SER* 1.3 77.1 - - - +
63B GLU* 1.3 65.4 + - - +
64B LYS* 3.7 11.2 + - - +
65B GLU* 3.1 25.8 + - - +
66B LEU* 3.1 21.8 + - - +
111B TYR* 4.1 6.3 - - - -
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Residues in contact with GLU 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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62B THR* 1.3 71.8 - - - +
64B LYS* 1.3 54.5 + - - +
66B LEU* 2.9 4.9 + - - -
67B HIS* 2.8 64.8 + - + +
111B TYR* 3.6 47.9 + - + +
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Residues in contact with LYS 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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62B THR* 3.7 10.9 + - - +
63B GLU* 1.3 78.6 - - - +
65B GLU* 1.3 57.1 + - - +
67B HIS* 3.4 8.2 + - - +
68B THR* 2.9 38.5 + - - +
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Residues in contact with GLU 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B LEU* 4.4 13.5 - - + +
61B SER* 2.8 34.7 + - - +
62B THR* 3.1 20.6 + - - +
64B LYS* 1.3 81.0 - - - +
66B LEU* 1.3 53.1 + - + +
68B THR* 3.4 6.8 + - - -
69B PHE* 2.7 35.5 + - + +
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Residues in contact with LEU 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B ALA* 3.8 39.7 - - + +
56B LEU* 4.4 7.2 - - + -
57B ILE* 4.0 24.5 - - + -
61B SER* 3.4 28.9 - - - +
62B THR 3.1 22.7 + - - +
63B GLU* 2.9 9.2 + - - +
65B GLU* 1.3 75.0 - - + +
67B HIS* 1.3 62.9 + - + +
69B PHE* 3.1 8.3 + - + +
70B TYR* 2.8 50.7 + - + -
111B TYR* 4.2 12.6 - - + +
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Residues in contact with HIS 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B GLU* 2.8 51.4 + - + +
64B LYS* 3.6 11.2 - - - +
66B LEU* 1.3 77.8 - - + +
68B THR* 1.3 56.2 + - - +
70B TYR* 3.6 5.0 + + - +
71B LYS* 2.9 30.2 + - - +
111B TYR* 4.9 5.6 + - - -
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Residues in contact with THR 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 LYS* 2.9 25.7 + - - +
65B GLU* 3.7 7.3 - - - -
67B HIS* 1.3 72.4 - - - +
69B PHE* 1.3 56.7 + - - +
71B LYS* 3.5 6.8 - - + +
72B GLU* 2.8 58.6 + - + +
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Residues in contact with PHE 69 (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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49B LEU* 4.0 29.6 - - + -
52B HIS* 3.5 30.5 - + + -
53B ALA* 4.0 24.2 - - + -
56B LEU* 3.8 24.5 - - + -
65B GLU* 2.7 23.1 + - + +
66B LEU* 3.1 10.0 + - + +
68B THR* 1.3 73.3 - - - +
70B TYR* 1.3 70.5 + + - +
72B GLU* 4.6 4.7 - - - -
73B GLN* 2.8 75.2 + - + +
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Residues in contact with TYR 70 (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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46B HIS* 3.7 40.6 + + - -
49B LEU* 3.4 38.1 + - + +
50B ILE* 4.7 4.0 + - - +
53B ALA* 3.2 32.8 - - + +
54B ASP* 5.1 2.1 + - - -
66B LEU* 2.8 42.2 + - + +
67B HIS* 4.1 5.6 - + - +
69B PHE* 1.3 73.1 - + - +
71B LYS* 1.3 65.6 + - - +
74B THR* 2.6 30.7 + - - +
128B HIS* 5.4 3.5 - - - -
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Residues in contact with LYS 71 (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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67B HIS 2.9 20.0 + - - +
68B THR* 3.5 9.4 - - + +
70B TYR* 1.3 78.5 - - - +
72B GLU* 1.3 59.3 + - + +
74B THR* 4.9 2.4 + - - -
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Residues in contact with GLU 72 (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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68B THR* 2.8 42.4 + - + +
69B PHE* 4.8 1.0 - - - -
71B LYS* 1.3 74.5 - - + +
73B GLN* 1.3 83.9 + - + +
74B THR 3.9 0.9 - - - -
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Residues in contact with GLN 73 (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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49B LEU* 3.8 10.1 - - + +
69B PHE* 2.8 59.1 + - + +
72B GLU* 1.3 103.4 + - + +
74B THR* 1.3 65.5 + - - +
75B PRO* 3.2 10.0 - - - +
80B GLN* 5.4 2.0 + - - -
84B THR* 5.2 2.3 + - - +
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Residues in contact with THR 74 (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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42B GLU* 5.2 3.6 - - + +
45B ALA* 3.4 33.2 - - + -
46B HIS* 4.7 1.8 - - - +
49B LEU* 3.5 15.1 - - + +
70B TYR* 2.6 30.8 + - - +
71B LYS 4.9 2.0 + - - -
72B GLU 3.9 1.3 - - - +
73B GLN* 1.3 74.8 - - - +
75B PRO* 1.4 70.6 - - + +
76B GLU* 3.6 12.3 + - - +
80B GLN* 4.6 1.8 + - - -
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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