Contacts of the helix formed by residues 116 - 123 (chain C) in PDB entry 3CMM
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 116 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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752A LYS* 5.2 7.3 - - - +
753A PRO 4.8 6.1 - - - +
755A VAL* 4.2 16.3 + - - +
114C LEU* 4.2 5.6 - - - +
115C ASP* 1.3 79.8 + - - +
117C VAL* 1.3 63.8 + - - +
118C THR* 2.9 48.2 + - - +
119C GLN* 3.1 42.7 + - - +
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Residues in contact with VAL 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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723A TYR* 4.2 33.7 - - + +
755A VAL* 5.2 11.7 - - + +
114C LEU* 5.2 6.9 - - + -
115C ASP 3.1 9.7 + - - +
116C ASP* 1.3 69.6 + - - +
118C THR* 1.3 58.7 + - - +
119C GLN 3.2 0.4 - - - -
120C LEU* 3.1 39.6 + - + +
139C LYS* 5.5 0.7 - - + -
140C ILE* 4.4 29.4 - - + +
143C PHE* 3.4 35.4 - - + -
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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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728A PHE* 4.3 19.4 - - - -
729A HIS* 5.3 4.9 + - - -
752A LYS* 5.4 12.6 - - + -
753A PRO* 5.4 9.6 + - + +
755A VAL* 4.8 2.5 - - - +
116C ASP* 2.9 28.0 + - - +
117C VAL* 1.3 76.4 - - - +
119C GLN* 1.3 63.7 + - - +
120C LEU 3.1 2.5 - - - -
121C SER* 3.0 24.7 + - - +
143C PHE* 4.0 16.9 - - - -
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Residues in contact with GLN 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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111C LEU* 3.8 20.8 - - + +
113C SER* 3.2 34.8 + - - +
114C LEU* 4.1 8.8 - - + +
115C ASP* 4.3 0.8 + - - +
116C ASP* 3.1 47.1 + - + +
118C THR* 1.3 76.7 - - - +
120C LEU* 1.3 65.3 + - + +
121C SER 3.0 0.5 + - - -
122C GLN* 2.8 38.3 + - - +
123C PHE* 3.9 3.4 - - - -
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Residues in contact with LEU 120 (chain C).
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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40C LEU* 3.6 30.3 - - + -
42C LEU* 5.4 1.1 - - + -
111C LEU* 5.9 0.2 - - + -
114C LEU* 4.0 22.0 - - + -
117C VAL* 3.1 33.0 + - + +
118C THR 3.1 0.2 - - - -
119C GLN* 1.3 79.6 - - + +
121C SER* 1.3 57.6 + - - +
122C GLN 2.9 7.6 + - - -
123C PHE* 3.0 22.9 + - + +
126C VAL* 4.6 9.9 - - + -
140C ILE* 3.8 31.0 - - + +
143C PHE* 3.7 14.1 - - + -
144C CYS* 4.0 14.6 - - - -
149C ILE* 3.6 12.4 - - + +
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Residues in contact with SER 121 (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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118C THR* 3.0 17.7 + - - +
119C GLN 3.0 1.1 + - - -
120C LEU* 1.3 77.8 - - - +
122C GLN* 1.3 62.7 + - - +
123C PHE 3.4 5.4 + - - +
124C GLN* 5.6 0.5 + - - -
143C PHE* 3.9 15.0 - - - -
147C SER* 5.5 1.6 - - - -
149C ILE* 3.6 16.3 - - - +
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Residues in contact with GLN 122 (chain C).
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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38C ASN* 3.9 13.0 + - - +
111C LEU* 5.6 4.1 - - - +
119C GLN* 2.8 33.3 + - - +
120C LEU 2.9 1.4 + - - -
121C SER* 1.3 82.9 + - - +
123C PHE* 1.3 83.7 + - + +
124C GLN* 3.7 13.1 + - - -
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Residues in contact with PHE 123 (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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38C ASN* 3.6 20.2 - - + +
39C VAL 4.1 10.5 - - - -
40C LEU* 3.6 37.2 - - + -
62C SER* 5.8 0.7 - - - -
64C THR* 3.6 35.2 - - + -
111C LEU* 4.6 12.8 - - + -
119C GLN* 3.9 8.7 - - + -
120C LEU* 3.0 22.1 + - + +
121C SER 4.0 2.8 - - - +
122C GLN* 1.3 105.0 - - + +
124C GLN* 1.3 64.9 + - - +
125C VAL 3.9 11.4 - - - +
126C VAL* 4.2 6.3 - - + -
149C ILE* 3.4 23.3 - - - +
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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