Contacts of the helix formed by residues 105 - 116 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103B LEU 4.4 2.0 - - - +
104B PRO* 1.4 87.2 - - + +
106B LYS* 1.3 65.5 + - - +
107B ALA* 3.4 4.0 + - + +
108B ALA* 3.5 11.0 + - + +
109B ALA* 3.0 19.9 + - - +
120B PRO* 4.3 12.8 - - + -
121B ALA 5.8 1.6 - - - +
123B GLU* 6.1 1.6 - - - +
639B GLU* 3.5 26.0 - - + +
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Residues in contact with LYS 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104B PRO 3.5 2.8 + - - -
105B PRO* 1.3 71.4 - - - +
107B ALA* 1.3 57.1 + - - +
109B ALA* 3.2 0.9 + - - +
110B LEU* 2.8 37.6 + - + +
361B TYR* 3.7 30.5 - - + -
529B ASP* 2.7 28.3 + - - +
531B ASP* 3.2 22.7 + - - -
535B LEU* 3.7 12.3 - - + -
637B ARG* 3.0 33.5 - - - +
639B GLU* 3.2 9.6 + - - +
673B ASP* 2.6 38.6 + - - +
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Residues in contact with ALA 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B PRO* 3.4 2.9 + - + +
106B LYS* 1.3 78.2 - - - +
108B ALA* 1.3 58.0 + - - +
110B LEU* 3.5 5.3 + - - +
111B ALA* 3.0 30.4 + - - +
639B GLU* 4.9 1.4 + - - -
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Residues in contact with ALA 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B PRO* 3.5 13.6 + - + +
107B ALA* 1.3 75.8 - - - +
109B ALA* 1.3 64.1 + - - +
111B ALA* 4.0 5.3 - - - +
112B HIS* 3.2 23.6 + - - +
117B SER* 5.6 0.2 - - - -
118B PRO 4.7 4.0 - - - +
120B PRO* 3.7 31.8 - - + +
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Residues in contact with ALA 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B LEU* 3.6 20.2 - - + +
60B PHE* 4.4 2.0 - - + -
104B PRO* 4.3 10.1 - - + -
105B PRO 3.0 16.7 + - - +
106B LYS 3.4 2.7 - - - +
108B ALA* 1.3 78.1 - - - +
110B LEU* 1.3 61.3 + - - +
112B HIS* 3.4 3.8 + - - +
113B LEU* 3.2 28.2 + - - +
120B PRO* 4.1 5.5 - - - +
361B TYR* 3.4 30.3 - - + +
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Residues in contact with LEU 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106B LYS* 2.8 41.0 + - + +
107B ALA* 4.1 5.2 - - - +
109B ALA* 1.3 70.8 - - - +
111B ALA* 1.3 58.2 + - - +
113B LEU* 3.0 7.1 + - + +
114B ASP* 2.7 46.8 + - - +
115B ARG* 4.9 1.3 - - - +
358B ARG* 3.4 39.3 - - - +
361B TYR* 4.1 17.3 - - + -
531B ASP* 5.1 1.1 - - - +
535B LEU* 3.7 36.1 - - + -
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Residues in contact with ALA 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107B ALA 3.0 18.0 + - - +
108B ALA* 4.0 7.0 - - - +
110B LEU* 1.3 76.2 - - - +
112B HIS* 1.3 58.4 + - - +
115B ARG* 3.0 55.1 + - - +
117B SER* 3.3 25.7 + - - +
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Residues in contact with HIS 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B LEU* 4.0 20.9 - - + -
108B ALA 3.2 13.2 + - - +
109B ALA 3.6 8.1 - - - +
110B LEU 3.1 0.6 - - - -
111B ALA* 1.3 76.8 - - - +
113B LEU* 1.3 66.1 + - + +
116B GLY* 3.1 26.2 + - - -
117B SER* 2.6 30.9 + - - +
118B PRO* 4.2 0.9 - - + +
119B PRO* 3.6 38.4 - - + +
120B PRO* 4.6 1.8 - - + -
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Residues in contact with LEU 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B LEU* 3.8 17.0 - - + -
60B PHE* 3.9 28.5 - - + -
109B ALA 3.2 17.7 + - - +
110B LEU* 3.0 16.0 + - + +
112B HIS* 1.3 87.8 - - + +
114B ASP* 1.3 69.4 + - - +
116B GLY 5.0 0.2 + - - -
329B ARG* 5.4 3.6 - - - +
351B ASP* 4.2 17.9 - - + +
353B ARG* 3.9 29.6 + - - +
358B ARG* 4.3 7.6 - - - +
361B TYR* 5.3 0.7 - - + -
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Residues in contact with ASP 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110B LEU* 2.7 29.4 + - - +
113B LEU* 1.3 80.7 - - - +
115B ARG* 1.3 83.7 + - - +
116B GLY 3.5 0.6 + - - -
353B ARG* 5.5 0.7 + - - -
358B ARG* 2.6 34.5 + - - -
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Residues in contact with ARG 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110B LEU* 5.7 1.0 - - - +
111B ALA* 3.0 45.6 + - - +
114B ASP* 1.3 100.3 + - - +
116B GLY* 1.3 63.5 + - - +
117B SER* 3.4 13.8 + - - +
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Residues in contact with GLY 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112B HIS* 3.1 24.4 + - - -
113B LEU 5.0 0.2 + - - -
114B ASP 3.5 2.0 + - - -
115B ARG* 1.3 77.5 - - - +
117B SER* 1.3 64.6 + - - +
118B PRO* 3.8 1.9 - - - +
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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