Contacts of the helix formed by residues 72 - 78 (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 GLN 72 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70C PRO* 3.5 11.2 + - + +
71C VAL* 1.3 84.6 - - - +
73C LEU* 1.3 68.5 + - - +
74C ALA* 3.1 7.0 - - + +
75C ASP* 2.9 31.9 + - - +
76C LEU* 4.1 0.7 - - - +
87C ILE* 4.4 4.7 - - + -
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Residues in contact with LEU 73 (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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72C GLN* 1.3 72.0 - - - +
74C ALA* 1.3 62.1 + - - +
76C LEU* 3.1 31.0 + - + +
84C GLU* 3.6 37.2 - - + +
87C ILE* 3.9 21.6 - - + +
414C ASN* 3.4 39.5 - - - +
415C SER* 3.6 13.0 - - - +
416C ARG* 3.7 25.5 - - + +
418C ASP* 6.0 0.4 - - - +
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Residues in contact with ALA 74 (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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45C LYS* 6.0 0.2 - - - +
72C GLN* 2.9 6.4 + - + +
73C LEU* 1.3 76.9 - - - +
75C ASP* 1.3 64.3 + - - +
77C SER* 3.1 22.7 + - - -
415C SER 4.6 8.5 + - - -
416C ARG 4.2 2.7 - - - +
418C ASP* 4.5 13.6 + - + +
419C ASN* 3.6 31.6 + - - +
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Residues in contact with ASP 75 (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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45C LYS* 3.0 35.8 + - + +
46C GLY 5.2 1.6 + - - -
70C PRO 3.8 0.3 - - - +
71C VAL* 3.5 5.4 - - - -
72C GLN* 2.9 35.6 + - - +
74C ALA* 1.3 77.2 - - - +
76C LEU* 1.3 58.1 + - - +
77C SER* 3.0 6.7 + - - -
78C THR* 3.5 2.3 + - - -
79C GLN* 3.5 21.1 + - + +
82C LEU* 3.8 19.3 - - + -
91C ARG* 3.1 29.2 + - - -
358C ASP* 4.4 6.5 - - - +
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Residues in contact with LEU 76 (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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71C VAL* 4.0 21.3 - - + -
72C GLN 4.1 2.0 - - - +
73C LEU* 3.1 32.2 + - + +
75C ASP* 1.3 76.5 - - - +
77C SER* 1.3 63.8 + - - +
78C THR 3.0 1.9 + - - -
79C GLN* 3.8 9.2 + - - +
82C LEU* 3.6 31.2 - - + +
83C THR* 3.7 9.6 - - - +
84C GLU* 3.6 31.9 - - + +
87C ILE* 5.1 2.0 - - + -
416C ARG* 3.2 52.5 + - + +
455C LEU* 3.6 5.7 - - - +
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Residues in contact with SER 77 (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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74C ALA 3.1 16.7 + - - -
75C ASP 3.0 0.4 + - - -
76C LEU* 1.3 77.4 - - - +
78C THR* 1.3 59.3 + - - +
358C ASP* 2.9 36.9 + - - +
360C PRO* 3.9 0.7 - - - +
416C ARG* 3.4 17.2 + - - +
419C ASN* 3.9 12.6 - - - +
420C GLN* 2.9 35.1 + - - +
455C LEU* 3.5 15.8 - - - +
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Residues in contact with THR 78 (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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46C GLY* 2.8 29.5 - - - +
50C GLU* 5.8 0.7 - - - +
75C ASP 3.5 1.4 + - - -
77C SER* 1.3 77.9 + - - +
79C GLN* 1.3 62.9 + - - +
80C PHE* 3.3 13.3 + - - -
358C ASP* 3.3 27.9 + - - +
359C ILE 4.0 0.3 - - - -
360C PRO* 3.7 22.7 - - + +
363C VAL* 3.4 28.9 - - + +
455C LEU* 3.4 19.8 - - + +
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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