Contacts of the helix formed by residues 85 - 96 (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 GLY 85 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80B LEU* 3.6 21.1 - - - +
81B GLU* 4.8 7.0 - - - -
83B ILE* 5.1 1.4 - - - +
84B GLY* 1.3 77.3 + - - -
86B VAL* 1.3 60.4 + - - -
87B SER* 2.9 13.4 - - - -
88B TYR* 3.8 10.4 + - - +
89B LEU* 3.9 10.7 + - - +
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Residues in contact with VAL 86 (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* 3.2 37.0 - - - +
67B LEU* 6.2 0.7 - - + -
71B THR* 3.9 13.9 - - + -
80B LEU* 3.9 15.5 - - + +
85B GLY* 1.3 72.4 - - - -
87B SER* 1.3 59.8 + - - +
88B TYR 3.3 0.2 - - - -
89B LEU* 3.0 8.1 + - - +
90B SER* 2.7 41.3 + - - +
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Residues in contact with SER 87 (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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85B GLY* 4.5 8.0 - - - -
86B VAL* 1.3 85.2 + - - +
88B TYR* 1.3 56.5 + - - +
90B SER* 3.8 4.8 - - - -
91B GLU* 2.8 38.3 + - - +
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Residues in contact with TYR 88 (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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18B GLN* 3.3 29.8 + - - +
45B ARG* 4.0 12.1 + - - -
47B ALA* 5.1 2.0 - - + -
48B HIS* 2.6 41.1 + + - -
51B ILE* 4.4 0.9 - - + -
83B ILE* 3.7 24.0 - - + -
84B GLY* 3.4 25.1 - - - +
85B GLY 3.8 3.8 - - - +
86B VAL 3.3 0.4 - - - -
87B SER* 1.3 76.2 - - - +
89B LEU* 1.3 61.9 + - - +
91B GLU* 4.0 20.9 - - + +
92B LEU* 3.0 54.5 + - + +
456G LEU* 4.9 3.6 - - + -
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Residues in contact with LEU 89 (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* 3.4 31.0 - - + -
51B ILE* 3.7 34.8 - - + -
67B LEU* 3.7 14.4 - - + -
70B VAL* 4.8 0.2 - - + -
71B THR* 3.3 33.2 - - + +
74B LEU* 3.8 22.9 - - + -
80B LEU* 4.6 3.8 - - + -
83B ILE* 5.0 2.9 - - + -
85B GLY 3.9 13.7 + - - +
86B VAL* 3.0 9.4 + - - +
88B TYR* 1.3 78.9 - - + +
90B SER* 1.3 58.5 + - - +
92B LEU* 3.2 7.1 + - + +
93B ALA* 3.0 26.5 + - - +
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Residues in contact with SER 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B LEU* 3.5 21.2 - - - +
86B VAL* 2.7 23.5 + - - +
87B SER* 3.9 5.4 - - - -
89B LEU* 1.3 71.1 - - - +
91B GLU* 1.3 66.3 + - - +
93B ALA* 3.0 7.0 + - - -
94B ASP* 2.8 42.2 + - - +
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Residues in contact with GLU 91 (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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87B SER* 2.8 27.5 + - - +
88B TYR* 3.8 23.4 - - + +
90B SER* 1.3 72.0 - - - +
92B LEU* 1.3 56.9 + - - +
94B ASP* 4.1 3.3 - - - +
95B ALA* 2.8 35.3 + - - +
456G LEU* 3.1 45.2 + - + +
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Residues in contact with LEU 92 (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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18B GLN* 3.7 28.5 - - + -
21B LEU* 3.7 33.7 - - + -
22B GLY* 3.4 24.8 - - - +
25B PHE* 4.5 11.2 - - + -
48B HIS* 5.0 0.2 - - - +
51B ILE* 4.1 9.9 - - + -
88B TYR* 3.0 60.1 + - + +
89B LEU* 3.2 7.1 + - + +
91B GLU* 1.3 79.4 - - - +
93B ALA* 1.3 61.7 + - - +
95B ALA* 3.9 1.1 - - - +
96B VAL* 3.5 15.9 + - - +
456G LEU* 4.1 7.9 - - + -
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Residues in contact with ALA 93 (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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22B GLY 4.6 3.6 - - - +
25B PHE* 3.9 30.2 - - + -
26B LEU* 5.1 7.3 - - - +
67B LEU* 4.6 12.8 - - + -
89B LEU 3.0 16.1 + - - +
90B SER* 3.6 7.9 - - - +
92B LEU* 1.3 76.0 - - - +
94B ASP* 1.3 68.2 + - - +
95B ALA 3.6 0.2 + - - -
96B VAL* 3.9 13.7 + - - +
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Residues in contact with ASP 94 (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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90B SER* 2.8 36.7 + - - +
91B GLU* 4.1 3.1 - - - +
93B ALA* 1.3 78.6 - - - +
95B ALA* 1.3 53.2 + - - +
458G PRO* 4.5 8.5 - - + +
459G ALA* 2.8 39.5 + - - +
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Residues in contact with ALA 95 (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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91B GLU 2.8 18.8 + - - +
92B LEU* 3.9 4.5 - - - +
93B ALA 3.3 0.2 - - - -
94B ASP* 1.3 76.0 - - - +
96B VAL* 1.3 65.0 + - + +
97B PRO* 3.5 4.2 - - - +
456G LEU* 3.9 25.4 - - + -
457G LEU 3.1 22.0 + - - +
459G ALA* 3.6 4.7 - - - -
462G ASN* 2.7 26.7 + - - +
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Residues in contact with VAL 96 (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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18B GLN 4.0 7.6 - - - +
19B ALA* 3.8 19.3 - - + +
22B GLY* 3.6 26.7 - - - +
23B ALA* 3.9 17.0 - - + +
26B LEU* 4.1 14.0 - - + +
92B LEU 3.5 8.6 + - - +
93B ALA 3.9 10.6 + - - +
94B ASP 3.4 0.6 - - - -
95B ALA* 1.3 78.7 - - + +
97B PRO* 1.3 66.8 - - + +
98B THR 3.3 29.6 - - - +
459G ALA* 3.5 11.0 - - - +
551G HIS* 4.5 1.0 - - - -
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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