Contacts of the helix formed by residues 83 - 91 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55A LEU* 6.1 0.5 - - - +
58A GLU* 4.7 11.1 - - - +
59A SER* 4.5 9.2 + - - -
62A LEU* 4.9 4.2 - - - +
78A ILE* 5.1 0.3 - - - +
81A GLY 3.7 1.2 - - - -
82A PHE* 1.3 74.1 - - - +
84A LEU* 1.3 58.9 + - - +
85A GLU* 3.2 21.8 + - - +
86A LEU* 2.8 39.2 + - + +
87A ALA 4.0 1.9 + - - -
99A PHE* 3.6 14.0 - - - -
114A PHE* 4.1 10.1 - - - -
146A LEU* 4.0 21.8 - - + +
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Residues in contact with LEU 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A PHE 2.8 12.8 + - - +
83A ASP* 1.3 70.9 - - - +
85A GLU* 1.3 60.3 + - - +
86A LEU 3.3 0.9 - - - -
87A ALA* 3.3 9.2 - - - +
88A HIS 3.1 19.2 + - - -
99A PHE* 4.1 20.4 - - + -
107A LEU* 3.9 11.4 - - + -
114A PHE* 3.8 20.6 - - + -
116A HIS 6.3 0.2 - - - -
117A PHE* 3.3 43.7 - - + +
120A VAL* 3.6 17.3 - - + +
121A LYS* 3.4 17.5 - - + -
126A PHE* 3.8 32.8 - - + -
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Residues in contact with GLU 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A LEU* 3.9 18.8 - - + +
59A SER* 3.7 18.8 + - - +
83A ASP* 3.2 8.4 + - - +
84A LEU* 1.3 76.2 - - - +
86A LEU* 1.3 65.6 + - - +
87A ALA 3.0 1.6 - - - -
88A HIS* 2.9 15.6 + - - +
89A GLN* 2.9 19.2 + - - +
114A PHE* 3.0 45.4 - - + +
115A PRO* 3.9 8.4 - - - +
116A HIS* 2.8 48.4 + - - +
117A PHE 4.1 0.5 + - - -
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Residues in contact with LEU 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A SER* 3.7 10.5 - - - +
62A LEU* 3.8 13.9 - - + -
63A ALA* 3.3 43.8 - - + +
78A ILE* 4.3 10.3 - - + -
83A ASP* 2.8 28.8 + - - +
85A GLU* 1.3 76.4 - - - +
87A ALA* 1.3 61.7 + - - +
89A GLN 3.6 0.2 + - - -
90A LEU* 3.1 34.7 + - + +
144A PHE* 3.8 30.1 - - + -
146A LEU* 3.7 29.4 - - + -
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Residues in contact with ALA 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A ILE* 4.3 10.7 - - + +
83A ASP 4.0 1.7 + - - +
84A LEU* 3.3 18.0 + - - +
85A GLU 3.0 0.2 - - - -
86A LEU* 1.3 77.3 - - - +
88A HIS* 1.3 65.0 + - - +
90A LEU* 3.1 9.2 + - - +
91A PHE* 3.0 27.0 + - - -
97A ILE* 3.4 15.9 - - + +
99A PHE* 5.0 1.3 - - + -
120A VAL* 3.5 19.5 - - + -
126A PHE* 4.3 12.1 - - + -
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Residues in contact with HIS 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A LEU 3.1 8.5 + - - +
85A GLU* 2.9 12.2 + - - +
87A ALA* 1.3 75.6 - - - +
89A GLN* 1.3 85.1 + - - +
91A PHE* 2.9 23.7 + - + +
92A LYS* 3.7 25.1 + - - +
116A HIS* 3.1 60.8 + + + -
119A GLU* 4.6 12.1 + - + -
120A VAL* 3.7 21.5 - - + +
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Residues in contact with GLN 89 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56A HIS* 5.0 5.7 - - - +
59A SER* 3.5 27.4 + - - +
60A GLU* 3.6 20.4 + - - +
63A ALA* 3.5 22.0 - - + -
64A HIS* 3.0 27.9 + - - +
85A GLU* 2.9 18.1 + - - +
88A HIS* 1.3 94.2 + - - +
90A LEU* 1.3 60.8 + - - +
92A LYS* 2.8 51.2 + - - +
93A TYR* 4.0 2.6 - - - -
116A HIS* 5.2 2.6 + - - -
233A SER 5.3 0.8 + - - -
235A ARG* 6.0 0.2 - - - +
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Residues in contact with LEU 90 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63A ALA* 3.6 30.7 - - + +
73A LEU* 4.6 4.7 - - + -
76A VAL* 3.8 18.8 - - + -
78A ILE* 3.8 27.4 - - + -
86A LEU* 3.1 24.4 + - + +
87A ALA* 3.1 10.3 + - - +
88A HIS 3.0 0.6 - - - -
89A GLN* 1.3 72.4 - - - +
91A PHE* 1.3 55.8 + - - +
92A LYS 3.0 9.4 + - - -
93A TYR* 3.1 30.1 + - + +
95A THR* 3.5 10.3 - - + +
97A ILE* 3.5 13.0 - - + -
142A LEU* 4.4 12.3 - - + -
144A PHE* 3.9 18.8 - - + -
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Residues in contact with PHE 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A ALA 3.0 16.6 + - - -
88A HIS* 2.9 16.3 + - + +
90A LEU* 1.3 74.4 - - - +
92A LYS* 1.3 55.8 + - - +
93A TYR 3.0 15.5 + - - +
95A THR 4.1 11.4 - - - -
97A ILE* 3.4 26.9 - - + -
119A GLU 5.2 0.4 - - - -
120A VAL* 3.6 31.0 - - + -
123A ASN* 3.5 42.2 - - + +
125A ASN* 3.7 18.6 - - + -
126A PHE* 3.5 25.4 - + + -
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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