Contacts of the helix formed by residues 106 - 115 (chain P) in PDB entry 6CNC
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 TRP 106 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105P ILE* 1.3 83.2 - - - +
107P SER* 1.3 86.0 + - - +
108P LYS* 3.2 44.0 - - + -
109P THR* 3.0 30.6 - - + +
110P ILE* 3.1 11.2 + - - +
144P THR* 4.0 10.3 + - + -
145P ARG* 2.7 88.4 + - + +
146P LYS 4.3 0.4 - - - -
147P ILE* 3.7 15.3 - - + +
148P TYR* 5.8 2.7 - - - -
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Residues in contact with SER 107 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106P TRP* 1.3 94.9 - - - +
108P LYS* 1.3 61.0 + - - +
110P ILE* 2.8 36.7 + - - +
111P LYS* 3.2 7.2 + - - +
118P GLN* 4.2 21.7 + - - +
121P VAL* 5.4 3.3 - - - +
122P LEU* 5.5 4.3 - - - +
125P LEU* 5.6 5.9 - - - +
145P ARG 4.9 2.9 - - - -
146P LYS 5.1 2.2 + - - -
148P TYR* 5.6 12.5 - - - -
36Y A 4.7 5.8 + - - -
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Residues in contact with LYS 108 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106P TRP* 3.2 29.4 - - + -
107P SER* 1.3 81.0 - - - +
109P THR* 1.3 56.6 + - - +
111P LYS* 2.9 50.4 + - + +
112P ALA* 3.3 9.6 + - + +
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Residues in contact with THR 109 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96P TYR* 4.3 1.9 + - - -
105P ILE* 3.6 14.3 - - + +
106P TRP* 3.0 51.0 - - + +
108P LYS* 1.3 77.0 - - - +
110P ILE* 1.3 57.2 + - - +
112P ALA* 4.4 4.5 + - - +
113P ARG* 3.1 28.2 + - - +
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Residues in contact with ILE 110 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93P VAL* 3.7 30.7 - - + -
96P TYR* 4.2 22.9 - - + -
97P ILE* 3.7 22.4 - - + -
105P ILE* 5.0 8.5 - - + -
106P TRP 3.1 10.7 + - - +
107P SER* 2.8 25.0 + - - +
109P THR* 1.3 78.8 - - - +
111P LYS* 1.3 69.6 + - + +
112P ALA 3.4 0.2 - - - -
113P ARG* 3.3 2.8 + - - -
114P THR* 2.9 34.9 + - + +
121P VAL* 4.7 17.7 - - + -
125P LEU* 5.3 12.3 - - + -
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Residues in contact with LYS 111 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107P SER* 3.2 10.1 + - - +
108P LYS* 2.9 42.0 + - + +
110P ILE* 1.3 79.4 - - - +
112P ALA* 1.3 58.4 + - - +
114P THR* 3.3 8.9 - - - +
115P ASN* 2.8 28.9 + - - -
116P LEU 3.4 12.2 + - - +
117P HIS* 3.9 14.8 - - - +
118P GLN* 3.5 49.3 + - + +
121P VAL* 4.1 10.5 - - + -
35Y G 5.1 4.4 + - - -
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Residues in contact with ALA 112 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315B GLN* 5.7 4.6 + - - +
108P LYS* 3.3 10.3 + - + +
109P THR* 4.9 4.7 - - - +
111P LYS* 1.3 77.6 - - - +
113P ARG* 1.3 67.3 + - + +
115P ASN* 3.3 13.9 + - - +
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Residues in contact with ARG 113 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65P LYS* 3.9 19.8 - - - +
92P LEU* 5.6 4.0 - - - +
96P TYR* 2.5 71.0 + - + +
109P THR* 3.1 21.7 + - - +
110P ILE 3.3 4.5 + - - +
112P ALA* 1.3 80.9 - - + +
114P THR* 1.3 60.9 + - - +
115P ASN* 4.9 0.9 - - - +
380S VAL* 5.8 4.0 - - - +
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Residues in contact with THR 114 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92P LEU* 5.6 10.1 - - - +
93P VAL* 3.8 18.8 - - + +
96P TYR* 6.1 0.8 - - - -
110P ILE* 2.9 26.6 + - + +
111P LYS* 3.3 11.0 - - - +
113P ARG* 1.3 76.0 - - - +
115P ASN* 1.3 72.5 - - - +
116P LEU* 3.4 41.0 - - + +
121P VAL* 3.9 9.0 - - + -
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Residues in contact with ASN 115 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86B ASP* 4.9 12.3 - - - +
315B GLN* 4.3 18.4 - - - +
111P LYS 2.8 12.9 + - - -
112P ALA* 3.3 12.3 + - - +
113P ARG 4.9 0.9 - - - +
114P THR* 1.3 80.9 - - - +
116P LEU* 1.3 65.5 + - - +
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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