Contacts of the helix formed by residues 59 - 70 (chain B) in PDB entry 4CQM
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 59 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56B ASP* 3.1 20.4 + - + +
58B ALA* 1.3 78.5 - - - +
60B GLU* 1.3 66.1 + - - +
61B HIS* 3.3 1.5 + - + +
62B ASP* 3.2 35.7 + - - +
63B VAL* 3.3 13.3 - - - +
113B LEU* 4.1 0.9 - - - -
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Residues in contact with GLU 60 (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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58B ALA 3.6 3.4 + - - -
59B LYS* 1.3 73.8 - - - +
61B HIS* 1.3 93.7 + - + +
63B VAL* 3.8 3.6 + - - +
64B GLN* 3.5 22.2 + - - +
113B LEU* 3.7 14.8 - - + +
97C THR* 2.8 46.8 + - + +
98C GLU* 5.0 8.2 - - - +
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Residues in contact with HIS 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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59B LYS* 3.3 1.6 - - + +
60B GLU* 1.3 104.8 + - + +
62B ASP* 1.3 67.6 + - - +
63B VAL 3.2 1.6 - - - -
64B GLN* 3.9 18.1 + - - +
65B ASN* 2.8 44.5 + - - +
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Residues in contact with ASP 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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54B SER 5.1 0.4 - - - +
55B CYS* 3.2 6.0 - - - -
56B ASP* 3.4 40.6 + - - +
59B LYS* 3.2 22.0 + - - +
60B GLU 3.5 0.2 - - - -
61B HIS* 1.3 81.8 - - - +
63B VAL* 1.3 54.6 + - - +
65B ASN* 4.1 4.8 + - - +
66B THR* 2.3 36.4 + - - -
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Residues in contact with VAL 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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8B PHE* 4.8 1.3 - - + -
55B CYS* 3.7 9.2 - - - -
56B ASP 3.7 7.6 - - - +
57B VAL* 3.7 24.5 - - - +
59B LYS 3.3 16.6 + - - +
60B GLU 4.0 6.3 - - - +
61B HIS 3.2 0.6 - - - -
62B ASP* 1.3 75.4 - - - +
64B GLN* 1.3 60.5 + - - +
66B THR* 3.1 2.5 + - - -
67B PHE* 2.9 59.0 + - + -
113B LEU* 3.9 30.3 - - + +
114B THR* 4.0 11.0 - - + -
117B ALA* 4.3 2.9 - - + -
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Residues in contact with GLN 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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60B GLU* 3.5 14.2 + - - +
61B HIS* 3.6 21.1 + - - +
62B ASP 3.5 0.2 - - - -
63B VAL* 1.3 79.4 - - - +
65B ASN* 1.3 62.5 + - - +
67B PHE* 3.5 7.3 + - + +
68B GLU* 3.2 26.3 + - - +
116B LYS* 5.1 5.9 + - - -
117B ALA* 5.1 6.7 - - + -
120B ARG* 4.2 21.1 + - - +
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Residues in contact with ASN 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 HIS* 2.8 33.4 + - - +
62B ASP* 4.3 5.5 + - - +
64B GLN* 1.3 81.2 - - - +
66B THR* 1.3 58.6 + - - +
68B GLU* 3.6 7.8 + - - +
69B GLU* 3.2 24.1 + - - +
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Residues in contact with THR 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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8B PHE* 4.9 2.2 - - + -
32B ILE* 3.9 20.9 - - + -
53B PHE* 3.8 30.7 - - + -
54B SER 3.9 5.9 + - - +
55B CYS* 3.2 24.2 - - + +
62B ASP 2.3 26.9 + - - -
63B VAL* 3.1 5.9 + - - -
65B ASN* 1.3 75.7 - - - +
67B PHE* 1.3 56.6 + - - +
68B GLU 3.1 2.0 - - - -
69B GLU* 3.2 4.2 + - - +
70B LEU* 2.7 33.7 + - - +
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Residues in contact with PHE 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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6B ALA* 5.3 2.7 - - + -
8B PHE* 3.4 38.1 - + - -
32B ILE* 6.2 0.2 - - + -
63B VAL* 2.9 37.5 + - + +
64B GLN* 3.5 5.4 + - - +
66B THR* 1.3 75.6 - - - +
68B GLU* 1.3 56.9 - - - +
70B LEU* 4.0 7.3 - - + +
71B GLU* 3.3 24.8 + - - +
77B VAL* 5.0 21.0 - - + +
80B LEU* 4.2 6.5 - - + -
114B THR* 3.2 22.7 - - - -
117B ALA* 3.5 30.5 - - + +
118B ALA* 3.5 26.2 - - + -
121B THR* 4.6 8.8 + - - +
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Residues in contact with GLU 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 GLN 3.2 15.9 + - - +
65B ASN* 3.8 9.9 - - - +
66B THR 3.1 0.6 - - - -
67B PHE* 1.3 80.2 - - - +
69B GLU* 1.3 60.3 + - - +
71B GLU* 3.8 5.1 + - - +
72B LYS* 3.6 20.8 + - - +
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Residues in contact with GLU 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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53B PHE* 3.7 20.7 - - + -
65B ASN 3.2 16.2 + - - +
66B THR* 3.2 6.8 + - - +
68B GLU* 1.3 75.4 - - - +
70B LEU* 1.3 61.8 + - - +
71B GLU 3.1 2.0 - - - -
72B LYS* 3.3 5.4 + - - -
73B HIS* 2.7 37.0 + - + +
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Residues in contact with LEU 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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30B ALA* 5.1 4.0 - - + -
32B ILE* 5.4 3.8 - - + -
53B PHE* 3.6 27.1 - - + -
66B THR* 2.7 24.4 + - + +
67B PHE* 4.4 6.5 - - + -
68B GLU 3.5 0.2 - - - -
69B GLU* 1.3 72.3 - - - +
71B GLU* 1.3 57.7 + - - +
72B LYS 3.4 0.2 - - - -
73B HIS 4.2 0.4 - - - -
74B LEU* 3.3 37.2 + - + +
75B GLY 3.7 2.6 - - - +
77B VAL* 4.8 15.7 - - + +
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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