Contacts of the helix formed by residues 109 - 122 (chain C) in PDB entry 3CB4
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 GLU 109 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12C HIS* 3.7 30.4 + - + +
106C GLN* 5.0 6.9 - - - +
107C GLY 3.5 16.1 - - - +
108C VAL* 1.3 76.9 - - - +
110C ALA* 1.3 66.1 + - - +
111C GLN* 3.4 25.4 + - - +
112C THR* 2.7 36.1 + - + -
113C LEU* 3.1 13.0 + - - +
409C LEU* 5.7 2.0 - - - -
467C SER* 4.1 15.1 - - - +
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Residues in contact with ALA 110 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109C GLU* 1.3 71.7 - - - +
111C GLN* 1.3 59.5 + - - +
113C LEU* 3.3 13.8 + - + +
114C ALA* 3.1 26.0 + - - +
407C HIS* 4.4 11.7 - - + +
409C LEU* 4.1 18.8 - - + +
467C SER* 3.2 39.3 + - - +
468C LEU 4.3 3.4 - - - +
469C ASP* 4.0 7.2 - - + +
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Residues in contact with GLN 111 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12C HIS* 3.4 31.1 + - + -
80C GLY* 3.4 30.5 - - - +
81C HIS* 5.3 11.2 + - + +
109C GLU* 3.5 25.6 + - - +
110C ALA* 1.3 77.5 - - - +
112C THR* 1.3 69.5 + - + +
113C LEU 3.5 0.3 + - - -
114C ALA* 3.5 9.7 + - - +
115C ASN* 3.6 13.6 + - - +
467C SER* 5.1 5.7 - - - -
468C LEU 4.4 14.6 + - - +
469C ASP* 4.7 8.7 - - - +
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Residues in contact with THR 112 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10C ILE* 3.7 23.4 - - - +
11C ALA* 3.4 32.5 - - - +
12C HIS* 4.2 4.7 - - + -
80C GLY* 6.2 0.4 - - - -
100C LEU* 4.4 9.4 - - - +
108C VAL* 3.9 9.9 - - - +
109C GLU* 2.7 35.4 + - + +
111C GLN* 1.3 93.2 - - + +
113C LEU* 1.3 58.4 + - - +
115C ASN* 4.1 1.6 - - - +
116C CYS* 3.2 24.4 + - - +
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Residues in contact with LEU 113 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100C LEU* 6.1 0.7 - - + -
108C VAL* 3.7 22.2 - - + -
109C GLU* 3.1 17.0 + - - +
110C ALA* 3.4 16.6 - - - +
111C GLN 3.2 0.2 - - - -
112C THR* 1.3 77.8 - - - +
114C ALA* 1.3 54.3 + - - +
116C CYS* 3.1 5.4 + - + +
117C TYR* 2.7 64.6 + - + +
150C ILE* 4.0 15.0 - - + -
151C VAL* 3.6 32.8 - - + -
409C LEU* 3.7 35.4 - - + -
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Residues in contact with ALA 114 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82C VAL* 5.2 3.8 - - + -
110C ALA 3.1 8.5 + - - +
111C GLN 3.8 5.4 - - - +
112C THR 3.5 0.4 - - - -
113C LEU* 1.3 76.1 - - - +
115C ASN* 1.3 57.5 + - - +
117C TYR* 4.1 9.0 - - - +
118C THR* 2.7 37.6 + - - +
469C ASP* 3.3 40.2 - - - +
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Residues in contact with ASN 115 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10C ILE* 3.8 30.5 - - + +
78C THR* 4.2 5.2 - - + +
79C PRO 3.8 5.1 + - - -
80C GLY* 3.2 34.7 - - - -
81C HIS 5.0 1.6 + - - -
85C SER* 5.9 1.0 - - - -
88C VAL* 3.4 29.3 - - + +
92C LEU* 4.0 4.6 - - + +
111C GLN 3.6 10.8 + - - +
112C THR* 4.0 2.6 - - - +
114C ALA* 1.3 79.9 - - - +
116C CYS* 1.3 54.2 + - - +
118C THR* 3.1 8.2 + - - -
119C ALA* 2.8 35.1 + - - +
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Residues in contact with CYS 116 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10C ILE* 4.3 6.0 - - + +
100C LEU* 3.8 28.5 - - + -
112C THR 3.2 15.0 + - - +
113C LEU* 3.1 13.6 + - + +
115C ASN* 1.3 77.2 - - - +
117C TYR* 1.3 63.4 + - + +
119C ALA* 3.0 15.5 + - - +
120C MET* 3.2 21.1 + - - +
126C VAL* 4.1 18.4 - - - -
151C VAL* 3.4 32.1 - - + -
153C ILE* 5.1 1.6 - - - -
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Residues in contact with TYR 117 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113C LEU* 2.7 51.6 + - + +
114C ALA* 4.1 7.6 - - - +
116C CYS* 1.3 72.3 - - - +
118C THR* 1.3 60.1 + - + +
120C MET* 3.3 24.8 + - + +
121C GLU* 3.2 35.4 + - - +
150C ILE* 3.1 43.3 + - - +
151C VAL* 4.1 16.8 - - + -
407C HIS* 6.5 2.0 - + + -
409C LEU* 5.7 1.1 - - + +
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Residues in contact with THR 118 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85C SER* 6.1 0.9 - - - +
88C VAL* 5.4 1.9 - - - +
89C SER* 5.7 8.0 - - - -
92C LEU* 4.4 9.0 - - - +
114C ALA 2.7 24.0 + - - +
115C ASN* 3.1 14.4 + - - -
117C TYR* 1.3 72.7 - - + +
119C ALA* 1.3 58.4 + - - +
120C MET 3.1 6.4 + - - -
121C GLU* 4.0 23.1 - - - +
122C MET* 3.4 32.3 + - - +
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Residues in contact with ALA 119 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10C ILE* 4.2 6.1 - - + -
92C LEU* 4.2 23.8 - - + -
98C ALA* 5.3 1.1 - - + -
115C ASN 2.8 19.4 + - - +
116C CYS* 3.0 12.3 + - - +
118C THR* 1.3 77.0 - - - +
120C MET* 1.3 54.0 + - - +
122C MET* 2.7 19.5 - - - +
124C LEU* 3.3 27.2 + - + +
126C VAL* 4.1 14.7 - - + +
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Residues in contact with MET 120 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116C CYS* 3.2 12.5 + - - +
117C TYR* 3.3 37.4 + - + +
118C THR 3.1 0.2 - - - -
119C ALA* 1.3 80.9 - - - +
121C GLU* 1.3 66.6 + - - +
122C MET 3.0 11.8 + - - -
123C ASP* 3.3 16.3 + - - +
124C LEU 4.7 4.5 - - - +
126C VAL* 4.2 12.8 - - + -
151C VAL* 3.9 14.6 - - + +
152C GLY 5.2 1.3 - - - +
153C ILE* 3.3 32.3 - - - -
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Residues in contact with GLU 121 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117C TYR* 3.2 21.5 + - - +
118C THR* 4.0 23.9 - - - +
120C MET* 1.3 74.6 - - - +
122C MET* 1.3 60.5 + - + +
123C ASP* 3.9 6.2 + - - +
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Residues in contact with MET 122 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89C SER* 3.9 14.6 - - - +
90C ARG* 3.4 30.3 - - - +
92C LEU* 4.4 16.4 - - - +
93C ALA* 3.8 23.1 - - + -
118C THR* 3.4 18.7 + - - +
119C ALA* 2.7 17.8 - - - +
120C MET 3.1 2.7 - - - +
121C GLU* 1.3 76.5 - - + +
123C ASP* 1.3 54.6 + - - +
124C LEU* 2.6 31.4 + - + +
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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