Contacts of the helix formed by residues 103 - 109 (chain C) in PDB entry 2CMH
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 103 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26C SER* 2.9 27.0 + - - -
28C HIS* 4.2 4.5 - - + +
29C ASN* 2.8 27.8 + - - +
82C PHE* 3.9 3.8 - - + -
101C GLN* 2.9 23.3 + - - +
102C ALA* 1.3 73.0 - - - +
104C GLU* 1.3 61.7 + - - +
105C LYS* 3.5 9.5 + - - +
106C ILE* 2.8 38.9 + - - +
107C LEU* 3.0 19.9 + - - +
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Residues in contact with GLU 104 (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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101C GLN 4.9 1.8 - - - +
102C ALA 3.1 12.4 + - - +
103C ASP* 1.3 68.1 - - - +
105C LYS* 1.3 68.2 + - - +
107C LEU* 3.1 7.3 + - - -
108C ASP* 2.8 41.2 + - - +
128C HIS* 4.1 26.0 + - - +
130C LYS* 5.6 10.2 - - + +
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Residues in contact with LYS 105 (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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24C VAL* 4.9 14.4 - - + -
25C ARG 2.4 32.1 + - - -
26C SER* 3.1 23.3 + - - +
27C GLU* 4.7 1.8 + - - +
103C ASP* 3.5 7.6 + - - +
104C GLU* 1.3 80.4 - - - +
106C ILE* 1.3 69.2 + - + +
108C ASP* 4.0 4.4 - - - +
109C SER* 2.9 25.1 + - - +
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Residues in contact with ILE 106 (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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24C VAL* 3.2 36.6 - - + +
25C ARG 4.6 0.2 - - - -
26C SER* 3.9 6.7 - - - -
29C ASN* 3.6 23.8 - - + +
31C LEU* 4.0 9.4 - - + -
45C LEU* 3.9 21.3 - - + -
82C PHE* 3.7 20.4 - - + -
103C ASP* 2.8 39.1 + - - +
105C LYS* 1.3 73.6 - - + +
107C LEU* 1.3 66.4 + - - +
109C SER* 2.8 22.5 + - - -
110C PHE* 3.5 12.6 - - + -
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Residues in contact with LEU 107 (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 PHE* 3.7 26.6 - - + +
84C LEU* 3.4 38.1 - - + -
99C PHE* 4.2 13.2 - - + -
101C GLN* 4.3 3.8 - - + -
103C ASP 3.0 18.3 + - - +
104C GLU* 3.4 5.4 - - - +
106C ILE* 1.3 76.3 - - - +
108C ASP* 1.3 68.0 + - - +
110C PHE* 3.1 27.4 + - + +
114C PHE* 4.9 0.2 - - + -
117C PHE* 3.8 3.7 - - + -
121C LYS* 5.2 6.5 - - + +
126C PHE* 6.1 0.4 - - + -
128C HIS* 3.5 41.3 - - + +
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Residues in contact with ASP 108 (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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104C GLU* 2.8 33.9 + - - +
105C LYS* 4.0 3.7 - - - +
107C LEU* 1.3 70.7 - - - +
109C SER* 1.3 56.9 + - - +
110C PHE 3.0 10.9 + - - -
111C ILE* 3.0 24.2 + - - +
117C PHE* 3.9 8.6 - - + -
121C LYS* 2.8 31.7 + - - -
128C HIS* 6.1 0.5 - - - -
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Residues in contact with SER 109 (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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22C LEU* 3.6 26.1 - - - +
24C VAL* 3.3 38.4 - - - +
31C LEU* 4.1 10.1 - - - +
33C ILE* 4.6 4.2 - - - +
105C LYS* 2.9 19.4 + - - +
106C ILE 2.8 13.4 + - - -
108C ASP* 1.3 75.9 - - - +
110C PHE* 1.3 58.4 + - - +
111C ILE* 3.2 7.8 + - - +
112C SER 5.0 0.3 + - - -
113C PHE* 5.5 0.5 + - - +
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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