Contacts of the helix formed by residues 105 - 115 (chain C) in PDB entry 2C10
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 PRO 105 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102C GLN* 6.4 0.2 - - + -
103C LEU 4.3 2.2 - - - +
104C PRO* 1.3 86.6 - - + +
106C LYS* 1.3 65.8 + - - +
107C ALA* 3.4 4.0 - - + +
108C ALA* 3.5 17.3 + - + +
109C ALA* 3.0 20.1 + - - +
120C PRO* 4.6 7.9 - - + -
121C ALA 5.9 1.6 - - - +
123C GLU* 5.6 6.3 - - - +
639C GLU* 3.8 22.0 - - + +
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Residues in contact with LYS 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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104C PRO 3.5 1.6 + - - -
105C PRO* 1.3 69.4 - - - +
107C ALA* 1.3 70.2 + - - +
109C ALA* 3.0 1.9 + - - +
110C LEU* 2.8 33.2 + - + +
361C TYR* 3.6 33.2 - - + +
529C ASP* 2.7 24.3 + - - +
531C ASP* 3.0 34.5 + - - -
535C LEU* 3.7 10.8 - - + -
637C ARG* 3.3 39.5 - - - +
639C GLU* 3.3 9.6 + - - +
673C ASP* 2.8 27.3 + - - +
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Residues in contact with ALA 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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105C PRO* 3.4 2.8 - - + +
106C LYS* 1.3 79.7 - - - +
108C ALA* 1.3 57.3 + - - +
110C LEU* 3.4 8.8 + - - +
111C ALA* 3.0 26.7 + - - +
115C ARG* 4.5 4.0 + - - -
639C GLU* 4.9 0.8 + - - -
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Residues in contact with ALA 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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105C PRO* 3.5 15.6 + - + +
106C LYS 3.2 0.4 - - - -
107C ALA* 1.3 76.0 - - - +
109C ALA* 1.3 65.6 + - - +
111C ALA* 3.6 8.6 - - - +
112C HIS* 3.2 22.5 + - - +
118C PRO 4.7 3.8 - - - +
120C PRO* 4.0 26.8 - - + +
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Residues in contact with ALA 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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59C LEU* 3.5 28.9 - - + +
60C PHE* 4.4 1.6 - - + -
104C PRO* 4.5 4.9 - - + -
105C PRO 3.0 17.8 + - - +
106C LYS 3.0 4.9 + - - +
108C ALA* 1.3 76.7 - - - +
110C LEU* 1.3 56.1 + - - +
112C HIS* 3.3 4.9 + - - +
113C LEU* 3.0 34.3 + - - +
120C PRO* 4.2 5.5 - - - +
361C TYR* 3.6 22.9 - - + +
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Residues in contact with LEU 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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106C LYS* 2.8 36.2 + - + +
107C ALA* 3.6 6.7 - - - +
109C ALA* 1.3 70.8 - - - +
111C ALA* 1.3 60.8 + - - +
113C LEU* 4.4 5.4 - - + +
114C ASP* 2.9 40.3 + - - +
115C ARG* 4.2 8.9 + - - +
358C ARG* 3.5 35.4 - - - +
361C TYR* 3.9 22.0 - - + -
531C ASP* 4.7 2.9 - - - +
535C LEU* 3.9 39.0 - - + -
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Residues in contact with ALA 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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107C ALA 3.0 17.6 + - - +
108C ALA* 3.6 10.5 - - - +
109C ALA 3.3 0.6 - - - -
110C LEU* 1.3 76.4 - - - +
112C HIS* 1.3 57.9 + - - +
115C ARG* 2.9 49.6 + - - +
116C GLY 3.0 7.3 + - - -
117C SER* 3.3 24.3 + - - +
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Residues in contact with HIS 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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59C LEU* 3.4 28.6 - - + +
108C ALA 3.2 10.3 + - - +
109C ALA 3.6 6.7 - - - +
111C ALA* 1.3 77.6 - - - +
113C LEU* 1.3 70.0 + - + +
116C GLY* 3.4 18.9 + - - -
117C SER* 2.8 30.2 + - - +
118C PRO 4.1 6.7 - - - +
119C PRO* 3.7 32.6 - - + +
120C PRO* 4.4 2.9 - - + -
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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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59C LEU* 4.4 18.4 - - + -
60C PHE* 4.1 24.2 - - + -
109C ALA* 3.0 26.0 + - + +
110C LEU* 4.2 8.3 - - + +
112C HIS* 1.3 82.9 - - + +
114C ASP* 1.3 67.4 + - - +
116C GLY 4.7 0.2 - - - -
329C ARG* 4.7 9.4 - - - +
351C ASP* 3.7 21.3 - - + +
353C ARG* 3.7 27.6 + - - +
358C ARG* 4.2 7.9 - - - +
361C TYR* 5.3 1.8 - - + -
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Residues in contact with ASP 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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110C LEU* 2.9 24.9 + - - +
113C LEU* 1.3 85.7 - - - +
115C ARG* 1.3 78.3 + - - +
116C GLY 3.6 0.2 - - - -
353C ARG* 4.8 1.9 + - - -
358C ARG* 2.6 37.3 + - - -
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Residues in contact with ARG 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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107C ALA 4.5 4.2 + - - -
110C LEU* 4.2 14.1 + - - +
111C ALA* 2.9 41.9 + - - +
114C ASP* 1.3 90.5 + - - +
116C GLY* 1.3 61.3 + - - +
117C SER* 4.4 9.1 + - - +
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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