Contacts of the helix formed by residues 66 - 77 (chain B) in PDB entry 2R6C
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 ASP 66 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97A PRO* 6.1 3.4 - - + -
98A THR* 4.0 10.8 - - + +
101A ASN* 2.8 36.6 + - - +
105A TYR* 2.4 25.2 + - - -
25B PHE* 4.0 21.5 - - - +
28B PRO* 5.7 1.6 - - + -
64B PRO* 4.8 2.7 - - + +
65B VAL* 1.3 78.8 - - - +
67B LEU* 1.3 70.1 + - - +
68B VAL 4.4 0.2 - - - -
69B THR* 2.8 16.4 + - - +
70B VAL* 2.9 15.8 + - - +
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Residues in contact with LEU 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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25B PHE* 3.6 27.8 + - + +
66B ASP* 1.3 73.7 - - - +
68B VAL* 1.3 68.3 + - + +
70B VAL* 3.2 1.4 + - - +
71B THR* 2.9 34.2 + - + +
86B VAL* 5.2 0.7 - - + +
89B LEU* 3.7 38.4 - - + +
90B SER* 3.5 24.2 - - - +
93B ALA* 4.6 10.5 - - + -
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Residues in contact with VAL 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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15A GLU* 3.4 40.6 - - + +
16A ALA* 3.5 17.5 - - + +
19A ALA* 4.2 7.4 - - + -
96A VAL* 5.6 5.6 - - + -
105A TYR* 3.0 34.2 + - + +
66B ASP* 3.3 2.6 + - - -
67B LEU* 1.3 82.4 - - + +
69B THR* 1.3 61.6 + - - +
71B THR* 3.0 8.1 + - - -
72B ALA* 2.9 27.5 + - + +
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Residues in contact with THR 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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104A TYR* 2.0 39.1 + - - -
105A TYR* 3.2 5.3 + - - -
108A ILE* 4.6 3.3 - - - +
58B VAL* 3.5 19.0 - - + +
63B GLU* 3.6 4.5 + - - +
64B PRO 3.1 15.5 + - - +
65B VAL* 3.4 3.8 - - - -
66B ASP* 2.8 49.5 + - - +
68B VAL* 1.3 78.4 - - - +
70B VAL* 1.3 60.3 + - + +
72B ALA* 3.6 8.1 - - - +
73B GLU* 3.4 13.3 + - - +
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Residues in contact with VAL 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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25B PHE* 4.1 25.1 - - + -
51B ILE* 4.8 6.7 - - + +
54B ALA* 4.4 11.9 - - + -
55B MET* 4.4 15.5 - - + +
58B VAL* 4.5 7.9 - - + -
65B VAL* 3.6 29.4 - - + -
66B ASP 2.9 18.0 + - - +
67B LEU 3.9 2.2 - - - +
69B THR* 1.3 77.5 - - + +
71B THR* 1.3 56.8 + - - +
72B ALA 2.9 4.3 - - - -
73B GLU* 2.7 22.2 + - - +
74B LEU* 2.9 32.5 + - + +
89B LEU* 4.8 0.7 - - + -
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Residues in contact with THR 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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15A GLU* 2.9 40.4 + - - +
67B LEU* 2.9 35.8 + - + +
68B VAL* 3.0 11.8 + - - -
70B VAL* 1.3 76.4 - - - +
72B ALA* 1.3 59.8 + - - +
74B LEU* 3.9 5.0 - - - +
75B ALA* 3.0 29.6 + - - +
80B LEU* 3.9 5.8 - - - +
86B VAL* 3.9 13.0 - - + -
89B LEU* 3.3 30.7 - - + -
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Residues in contact with ALA 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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15A GLU* 5.6 1.8 - - + -
16A ALA* 5.4 2.2 - - + -
108A ILE* 4.0 29.6 - - + -
112A LYS* 4.6 6.3 + - - +
68B VAL* 2.9 17.2 + - + +
69B THR 3.6 8.1 - - - +
70B VAL 2.9 0.6 - - - -
71B THR* 1.3 82.2 + - - +
73B GLU* 1.3 58.3 + - - +
75B ALA* 3.9 5.1 - - - +
76B ALA* 3.1 26.5 + - - +
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Residues in contact with GLU 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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54B ALA* 4.1 20.9 - - + +
57B ARG* 4.2 22.5 + - + +
58B VAL* 3.5 26.0 - - + +
61B ARG* 3.1 37.5 + - - -
69B THR 3.4 2.0 + - - +
70B VAL 2.7 11.2 + - - +
72B ALA* 1.3 71.8 - - - +
74B LEU* 1.3 68.3 + - - +
76B ALA* 3.2 6.4 + - - +
77B SER* 3.0 31.5 + - - +
134D ASP* 4.6 10.0 - - - +
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Residues in contact with LEU 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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50B LYS 3.7 26.9 - - - +
51B ILE* 4.3 6.5 - - + -
54B ALA* 3.7 9.9 - - + -
70B VAL* 2.9 34.4 + - + +
71B THR* 3.9 4.0 - - - +
73B GLU* 1.3 77.3 - - - +
75B ALA* 1.3 56.8 + - - +
77B SER* 3.4 4.9 + - - +
78B GLU 2.9 22.5 + - - -
79B GLN* 2.9 27.9 + - + -
80B LEU* 3.9 15.9 - - - +
83B ILE* 3.4 32.3 - - + -
89B LEU* 3.8 19.1 - - + -
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Residues in contact with ALA 75 (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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15A GLU* 5.5 2.0 - - - +
112A LYS* 6.0 1.3 - - - +
71B THR 3.0 19.8 + - - +
72B ALA* 3.9 6.3 - - - +
73B GLU 3.2 0.2 - - - -
74B LEU* 1.3 75.0 - - - +
76B ALA* 1.3 66.4 + - - +
78B GLU* 3.0 17.2 + - - +
80B LEU* 3.9 24.8 - - + +
133D GLU* 4.5 5.8 - - - +
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Residues in contact with ALA 76 (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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112A LYS* 4.0 13.7 - - - +
72B ALA 3.1 19.1 + - - +
73B GLU* 3.2 12.3 + - - +
75B ALA* 1.3 78.1 - - - +
77B SER* 1.3 57.8 + - - +
78B GLU* 3.2 10.4 + - - +
132D ARG 4.0 9.4 - - - +
133D GLU* 4.1 13.5 - - - +
134D ASP* 3.6 35.1 - - - +
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Residues in contact with SER 77 (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 ALA* 6.0 1.0 - - - +
73B GLU* 3.0 25.3 + - - +
74B LEU* 3.5 3.5 + - - +
76B ALA* 1.3 73.3 - - - +
78B GLU* 1.3 67.3 + - - +
79B GLN* 2.7 42.0 + - - +
134D ASP* 3.8 16.1 + - - -
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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