Contacts of the helix formed by residues 101 - 112 (chain X) in PDB entry 5CQM
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 ASN 101 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71X TYR* 3.7 27.0 - - - +
72X PRO* 5.1 3.1 - - - +
100X PHE* 1.3 74.6 - - - +
102X ILE* 1.3 62.1 + - - +
103X ASP* 2.8 33.1 + - - +
104X ILE* 3.1 38.2 + - + +
105X LEU* 3.3 15.1 + - - +
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Residues in contact with ILE 102 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100X PHE* 3.7 22.4 + - + -
101X ASN* 1.3 72.0 - - - +
103X ASP* 1.3 71.6 + - - +
104X ILE 3.3 0.2 - - - -
105X LEU* 3.9 4.5 - - + -
106X ASN* 2.8 52.7 + - - +
219X HIS* 3.6 22.7 - - + +
222X VAL* 4.3 13.0 - - + +
223X GLU* 3.3 27.8 - - - +
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Residues in contact with ASP 103 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69X MET* 3.6 16.2 - - + -
71X TYR* 6.1 1.0 - - + +
101X ASN* 2.8 18.6 + - - +
102X ILE* 1.3 82.4 - - - +
104X ILE* 1.3 63.4 + - - +
106X ASN* 3.5 8.1 + - - +
107X GLU* 3.2 28.1 + - - +
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Residues in contact with ILE 104 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66X LEU* 4.8 13.0 - - + -
69X MET* 3.8 20.2 - - + -
71X TYR* 3.7 37.9 - - + +
101X ASN* 3.1 33.1 - - + +
103X ASP* 1.3 75.1 - - - +
105X LEU* 1.3 65.2 + - + +
107X GLU* 3.2 5.0 + - - +
108X GLN* 3.0 39.6 + - + +
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Residues in contact with LEU 105 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100X PHE* 3.7 33.0 - - + -
101X ASN 3.3 11.9 + - - +
102X ILE* 4.0 5.8 - - + +
104X ILE* 1.3 77.6 - - + +
106X ASN* 1.3 62.7 + - - +
108X GLN* 3.2 21.1 + - - +
109X PHE* 3.0 40.0 + - + -
222X VAL* 3.7 14.6 - - + -
223X GLU* 3.8 26.0 - - + +
317X LYS* 5.5 5.8 - - - +
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Residues in contact with ASN 106 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102X ILE* 2.8 45.6 + - - +
103X ASP* 3.9 8.5 + - - +
104X ILE 3.3 0.2 - - - -
105X LEU* 1.3 73.0 - - - +
107X GLU* 1.3 57.8 + - - +
110X ARG* 2.8 38.8 + - + +
143X VAL 5.2 3.7 + - - +
145X HIS* 2.8 30.7 + - + -
219X HIS* 5.5 3.5 - - - -
222X VAL* 3.7 12.1 + - - +
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Residues in contact with GLU 107 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66X LEU* 3.6 12.8 - - + -
67X PRO* 3.4 32.4 - - - +
69X MET* 3.9 19.5 - - + +
103X ASP 3.2 17.2 + - - +
104X ILE 3.4 8.7 - - - +
106X ASN* 1.3 73.7 - - + +
108X GLN* 1.3 66.0 + - - +
110X ARG* 3.9 4.4 - - - +
111X LEU* 2.9 41.9 + - - +
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Residues in contact with GLN 108 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63X MET* 3.9 17.0 - - + +
66X LEU* 4.0 25.8 - - + +
104X ILE* 3.0 23.1 + - + +
105X LEU* 3.2 31.7 + - - +
107X GLU* 1.3 80.8 - - - +
109X PHE* 1.3 70.6 + - + +
111X LEU* 3.6 5.7 + - - +
112X GLN* 3.6 23.4 + - - +
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Residues in contact with PHE 109 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105X LEU* 3.0 42.1 + - + +
108X GLN* 1.3 82.7 - - + +
110X ARG* 1.3 63.6 - - - +
112X GLN* 3.2 7.5 + - + -
114X THR* 2.7 46.2 + - + +
145X HIS* 4.0 16.2 - - - +
206X TYR* 3.7 22.9 - + - -
222X VAL* 3.6 28.5 - - + -
225X LEU* 3.8 43.1 - - + -
317X LYS* 5.2 2.7 - - - -
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Residues in contact with ARG 110 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106X ASN* 2.8 27.6 + - + +
107X GLU* 4.0 5.4 - - - +
109X PHE* 1.3 70.9 - - - +
111X LEU* 1.3 63.2 + - + +
113X ASN* 2.9 59.5 + - - +
114X THR 4.6 2.0 + - - +
144X GLY 3.4 26.8 + - - -
145X HIS* 3.5 19.7 - - + +
146X ARG* 4.6 15.4 - - - +
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Residues in contact with LEU 111 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63X MET* 4.7 4.0 - - - -
64X VAL* 4.3 29.1 - - + +
65X SER 3.9 17.0 - - - +
66X LEU* 3.9 24.5 - - + -
67X PRO* 4.7 1.8 - - + -
107X GLU* 2.9 33.2 + - - +
108X GLN* 3.9 6.3 - - - +
109X PHE 3.3 0.2 - - - -
110X ARG* 1.3 78.7 - - + +
112X GLN* 1.3 71.1 + - - +
113X ASN* 3.7 0.5 + - - +
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Residues in contact with GLN 112 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61X GLU* 4.2 14.7 - - - +
62X PHE 3.4 16.8 + - - +
63X MET* 2.9 57.3 - - + +
64X VAL 4.4 2.0 - - - +
108X GLN 3.6 6.9 + - - +
109X PHE* 3.2 10.2 + - + +
110X ARG 3.1 1.0 - - - -
111X LEU* 1.3 97.3 + - - +
113X ASN* 1.3 67.5 + - - +
114X THR* 3.2 10.6 + - - +
205X ASP* 4.9 2.4 - - - +
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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