Contacts of the helix formed by residues 83 - 91 (chain B) in PDB entry 2CMG
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 83 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55B LEU* 6.1 0.5 - - - +
58B GLU* 4.6 12.5 - - - +
59B SER* 4.7 7.8 - - - -
62B LEU* 5.3 2.6 - - - +
81B GLY 3.5 1.8 - - - -
82B PHE* 1.3 73.0 - - - +
84B LEU* 1.3 60.1 + - - +
85B GLU* 3.3 13.5 + - - +
86B LEU* 2.7 47.6 + - - +
87B ALA 3.9 1.6 + - - -
99B PHE* 3.4 16.2 - - - -
114B PHE* 4.3 9.5 - - - -
146B LEU* 3.8 21.6 - - + +
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Residues in contact with LEU 84 (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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82B PHE 2.8 5.7 + - - -
83B ASP* 1.3 69.6 - - - +
85B GLU* 1.3 65.5 + - - +
86B LEU 3.1 1.8 - - - -
87B ALA* 3.1 7.7 + - + +
88B HIS 3.1 17.7 + - - -
99B PHE* 3.5 31.0 - - + -
107B LEU* 4.1 18.4 - - + +
114B PHE* 3.8 19.9 - - + -
116B HIS 6.3 0.2 - - - -
117B PHE* 3.7 36.6 - - + -
120B VAL* 3.4 27.4 - - + +
121B LYS* 4.0 12.1 - - + -
126B PHE* 3.7 26.0 - - + -
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Residues in contact with GLU 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B LEU* 4.2 20.9 - - + +
56B HIS* 5.7 1.2 + - - -
59B SER* 3.6 24.7 + - - +
83B ASP* 3.3 10.7 - - - +
84B LEU* 1.3 77.0 - - - +
86B LEU* 1.3 63.0 + - - +
88B HIS* 3.3 6.1 + - - +
89B GLN* 3.2 21.7 + - - +
114B PHE* 3.5 26.2 - - + +
115B PRO* 3.2 14.1 - - - +
116B HIS* 2.7 59.6 + - - +
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Residues in contact with LEU 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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59B SER* 3.7 15.5 - - - +
62B LEU* 4.2 10.3 - - + -
63B ALA* 3.6 33.0 - - + +
78B ILE* 4.2 13.5 - - + -
83B ASP* 2.7 31.2 + - - +
84B LEU 3.1 0.2 - - - -
85B GLU* 1.3 79.6 - - - +
87B ALA* 1.3 56.9 + - - +
89B GLN* 3.3 2.8 + - - +
90B LEU* 3.0 37.3 + - + +
144B PHE* 3.8 31.6 - - + -
146B LEU* 3.9 18.4 - - + -
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Residues in contact with ALA 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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78B ILE* 5.8 1.3 - - + +
83B ASP 3.9 2.1 + - - +
84B LEU* 3.1 16.6 + - - +
86B LEU* 1.3 76.6 - - - +
88B HIS* 1.3 60.6 + - - +
90B LEU* 2.9 9.5 + - - +
91B PHE* 2.8 28.5 + - + -
97B ILE* 3.3 32.4 - - + +
99B PHE* 4.7 5.4 - - + -
120B VAL* 4.0 17.5 - - + -
126B PHE* 4.5 7.2 - - + -
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Residues in contact with HIS 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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84B LEU 3.1 7.6 + - - +
85B GLU* 3.5 10.3 - - - +
86B LEU 3.3 0.2 - - - -
87B ALA* 1.3 76.5 - - - +
89B GLN* 1.3 78.1 + - + +
91B PHE* 2.9 27.3 + - - +
92B LYS* 3.8 23.3 + - + +
116B HIS* 3.2 57.4 + + + +
119B GLU* 3.7 24.2 + - - +
120B VAL* 3.5 21.9 - - + +
233B SER* 5.7 0.4 + - - -
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Residues in contact with GLN 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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56B HIS* 5.4 2.6 - - - +
59B SER* 3.7 24.1 + - - +
60B GLU* 3.3 24.2 + - - +
63B ALA* 3.5 21.8 - - + -
64B HIS* 2.8 36.4 + - - +
85B GLU* 3.2 15.3 + - - +
86B LEU 3.7 2.2 - - - +
87B ALA 3.3 0.2 - - - -
88B HIS* 1.3 92.0 + - + +
90B LEU* 1.3 60.2 + - - +
92B LYS* 2.8 51.2 + - - +
93B TYR* 4.2 2.6 - - - -
116B HIS* 5.4 2.2 + - - -
233B SER 4.9 1.6 + - - -
234B VAL* 3.7 0.3 - - - +
235B ARG* 5.2 3.8 - - - +
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Residues in contact with LEU 90 (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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63B ALA* 4.0 29.8 - - + +
73B LEU* 4.9 0.9 - - + -
76B VAL* 4.2 9.4 - - + -
78B ILE* 4.1 19.7 - - + -
86B LEU* 3.0 35.8 + - + +
87B ALA* 2.9 12.7 + - - +
89B GLN* 1.3 72.4 - - - +
91B PHE* 1.3 58.4 + - - +
92B LYS 3.0 9.4 + - - -
93B TYR* 3.3 22.9 + - + +
95B THR* 3.3 18.8 - - + +
97B ILE* 3.6 11.0 - - + -
142B LEU* 4.6 11.4 - - + -
144B PHE* 3.8 26.2 - - + -
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Residues in contact with PHE 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 ALA 2.8 17.6 + - - -
88B HIS* 2.9 17.5 + - - +
90B LEU* 1.3 77.0 - - - +
92B LYS* 1.3 55.9 + - - +
93B TYR 3.0 12.9 + - - +
95B THR* 3.6 22.0 - - + -
97B ILE* 3.2 32.3 - - + -
119B GLU 6.0 0.2 - - - -
120B VAL* 4.1 13.7 - - + -
123B ASN* 3.2 49.8 - - + +
125B ASN* 3.7 10.5 - - + -
126B PHE* 3.6 27.1 - + + -
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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