Contacts of the helix formed by residues 126 - 133 (chain O) in PDB entry 6CNB
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 126 (chain O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101O LEU 5.1 0.5 - - - +
102O ARG 4.5 15.6 - - - +
103O CYS* 4.5 2.3 - - - -
123O ASN* 3.8 13.7 - - - -
124O GLU* 4.2 3.8 + - - -
125O GLU* 1.3 75.8 - - - +
127O ILE* 1.3 62.0 + - - +
128O HIS* 3.0 10.6 - - - +
129O ILE* 3.3 32.9 + - - +
130O LEU* 4.1 6.8 + - - +
284O LEU* 4.5 3.5 - - - +
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Residues in contact with ILE 127 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49O TYR* 3.6 30.7 - - + -
52O LEU* 3.5 38.6 - - + -
53O VAL* 5.1 6.7 - - + +
65O ILE* 4.8 13.0 - - + -
103O CYS* 3.5 44.6 - - + +
122O TYR* 6.2 4.0 - - + -
125O GLU 2.5 14.6 + - - +
126O GLY* 1.3 69.8 - - - -
128O HIS* 1.3 54.2 + - - +
129O ILE 3.1 0.9 - - - -
130O LEU* 3.2 17.6 + - + +
131O LEU* 2.6 39.6 + - - +
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Residues in contact with HIS 128 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49O TYR* 5.6 0.8 - - - -
125O GLU* 2.9 38.9 + - + +
126O GLY 3.3 4.8 - - - +
127O ILE* 1.3 78.4 - - - +
129O ILE* 1.3 63.3 + - - +
131O LEU* 3.1 6.0 + - - -
132O TYR* 2.8 56.3 + + - -
136O ILE* 6.3 0.4 - - + -
284O LEU* 3.5 35.6 - - + +
287O PHE* 5.5 1.1 - + - -
288O MET* 4.0 1.9 - - + +
291O ARG* 2.8 28.8 + - - -
648O TRP* 5.2 0.8 + - - -
652O GLN* 3.1 34.0 + - - -
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Residues in contact with ILE 129 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101O LEU* 5.1 4.3 - - + +
102O ARG* 3.8 40.4 - - + +
126O GLY* 3.3 19.7 + - - +
128O HIS* 1.3 77.3 - - - +
130O LEU* 1.3 69.1 + - + +
133O SER* 2.8 24.3 + - - -
136O ILE* 3.6 20.3 - - + +
164O ILE* 3.6 33.7 - - + -
282O ILE* 5.8 9.0 - - + -
284O LEU* 4.0 21.8 - - + -
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Residues in contact with LEU 130 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52O LEU* 5.1 10.1 - - + +
53O VAL* 5.4 2.7 - - - +
56O HIS* 3.3 52.9 - - + +
57O LEU* 5.2 4.9 - - + -
101O LEU* 3.8 37.9 - - + +
103O CYS* 4.4 7.0 - - - -
126O GLY 4.2 12.3 - - - +
127O ILE* 3.2 22.0 + - + +
129O ILE* 1.3 84.6 - - + +
131O LEU* 1.3 62.4 + - - +
133O SER* 2.3 28.8 + - - -
164O ILE* 5.6 0.2 - - + -
58Q TYR* 4.1 5.2 + - - -
61Q PHE* 4.8 6.9 - - + -
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Residues in contact with LEU 131 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48O LEU* 3.6 26.2 - - + -
52O LEU* 3.6 34.8 - - + -
127O ILE* 2.6 23.4 + - - +
128O HIS* 3.1 6.7 + - - +
130O LEU* 1.3 73.2 - - - +
132O TYR* 1.3 67.2 + - + +
581O LEU* 5.3 1.3 - - + -
585O MET* 5.0 18.4 - - + -
641O LEU* 4.2 17.9 - - + +
645O LEU* 3.5 28.2 - - + +
648O TRP* 5.6 5.6 - - + +
58Q TYR* 3.8 11.0 + - - -
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Residues in contact with TYR 132 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128O HIS* 2.8 63.3 + + - +
131O LEU* 1.3 83.6 - - + +
133O SER* 1.3 73.2 + - - +
134O GLY 2.9 4.3 + - - -
135O LEU* 3.3 21.1 + - + +
136O ILE* 3.6 17.3 - - + -
287O PHE* 3.5 16.4 - + + -
291O ARG* 3.0 32.7 + - - -
645O LEU* 3.3 37.5 - - + -
648O TRP* 4.0 10.6 - + - -
649O GLU* 3.9 15.6 - - - +
652O GLN* 3.9 4.5 + - - -
58Q TYR* 3.1 12.3 - - - -
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Residues in contact with SER 133 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56O HIS* 5.6 0.2 - - - -
129O ILE 2.8 15.1 + - - -
130O LEU 2.3 28.5 + - - -
132O TYR* 1.3 73.0 - - - +
134O GLY* 1.3 56.7 + - - -
135O LEU 2.7 1.9 + - - -
136O ILE* 2.4 36.8 + - - +
137O ILE* 2.8 12.4 + - - +
164O ILE* 4.9 8.0 - - - +
58Q TYR* 3.5 12.1 - - - -
61Q PHE* 3.2 37.6 - - - -
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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