Contacts of the helix formed by residues 100 - 111 (chain C) in PDB entry 2VHW
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 SER 100 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76C GLU* 6.0 2.9 - - - -
82C TYR* 4.8 0.5 + - - -
95C LEU 5.8 0.2 - - - -
96C HIS 3.7 6.1 + - - -
97C LEU 3.0 10.5 + - - +
98C ALA 3.4 0.4 - - - -
99C ALA* 1.3 81.2 - - - +
101C ARG* 1.3 57.0 + - - +
102C ALA* 3.6 11.4 + - - +
103C CYS* 3.2 29.5 + - - +
104C THR* 2.8 30.8 + - - -
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Residues in contact with ARG 101 (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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99C ALA 4.2 0.4 - - - -
100C SER* 1.3 68.9 - - - +
102C ALA* 1.3 65.6 + - - +
104C THR* 3.8 0.4 - - - -
105C ASP* 3.0 64.9 + - - -
359C LEU* 3.2 61.9 + - + +
360C GLY 4.1 10.7 + - - -
361C VAL* 4.3 14.8 - - - +
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Residues in contact with ALA 102 (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 TYR* 3.5 21.5 + - + +
100C SER* 3.6 8.5 - - - +
101C ARG* 1.3 79.9 - - - +
103C CYS* 1.3 62.9 + - - +
105C ASP* 3.4 6.5 + - - +
106C ALA* 3.2 21.0 + - - +
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Residues in contact with CYS 103 (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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76C GLU* 4.0 22.4 - - + -
77C PRO* 3.8 32.1 - - - +
82C TYR* 3.3 16.1 + - - +
95C LEU* 4.8 1.8 - - - +
97C LEU* 4.1 17.0 - - + -
100C SER* 3.2 23.2 + - - +
102C ALA* 1.3 75.9 - - - +
104C THR* 1.3 66.0 + - - +
106C ALA* 3.2 3.8 + - - +
107C LEU* 3.0 27.0 + - - +
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Residues in contact with THR 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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97C LEU* 3.1 35.0 + - + +
100C SER 2.8 18.8 + - - -
101C ARG 3.8 3.8 - - - -
102C ALA 3.3 0.2 - - - -
103C CYS* 1.3 76.1 - - - +
105C ASP* 1.3 65.0 + - - +
107C LEU* 3.2 5.8 + - - +
108C LEU* 3.0 44.9 + - + +
345C THR* 5.3 0.4 - - + -
350C LEU* 4.1 25.4 - - + -
355C VAL* 4.6 0.4 - - + -
359C LEU* 3.6 18.2 - - + +
361C VAL* 5.7 0.9 - - + -
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Residues in contact with ASP 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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101C ARG* 3.0 48.4 + - - +
102C ALA* 3.6 6.9 - - - +
104C THR* 1.3 77.5 - - - +
106C ALA* 1.3 56.7 + - - +
108C LEU* 3.5 13.2 + - - +
109C ASP* 2.9 44.2 + - - +
361C VAL* 5.5 4.0 - - - +
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Residues in contact with ALA 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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82C TYR* 3.5 48.1 - - + +
85C LEU* 3.7 9.5 - - + +
102C ALA 3.2 8.6 + - - +
103C CYS 3.4 8.5 - - - +
104C THR 3.2 0.6 - - - -
105C ASP* 1.3 74.7 - - - +
107C LEU* 1.3 64.2 + - - +
109C ASP* 3.9 5.1 - - - +
110C SER* 3.0 27.2 + - - -
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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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77C PRO* 4.3 5.8 - - + -
85C LEU* 3.8 21.8 - - + -
91C LEU* 3.8 24.0 - - + -
95C LEU* 4.0 14.6 - - + -
97C LEU* 3.6 34.8 - - + -
103C CYS* 3.0 18.1 + - - +
104C THR 3.6 6.5 - - - +
106C ALA* 1.3 76.5 - - - +
108C LEU* 1.3 61.1 + - - +
110C SER* 2.8 19.8 + - - -
111C GLY* 3.4 4.3 + - - -
112C THR* 3.7 16.7 + - + +
114C SER* 3.8 17.7 - - - +
345C THR* 3.8 18.9 + - + +
348C GLY 5.2 0.5 + - - -
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Residues in contact with LEU 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 THR* 3.0 39.9 + - + +
105C ASP* 3.8 13.0 - - - +
107C LEU* 1.3 76.0 - - - +
109C ASP* 1.3 66.5 + - - +
111C GLY* 3.1 11.4 + - - -
345C THR* 3.9 15.9 - - + -
348C GLY* 3.4 42.4 - - - +
349C ALA 3.6 23.3 - - - +
350C LEU* 3.7 15.3 - - + +
361C VAL* 5.0 10.3 - - + -
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Residues in contact with ASP 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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105C ASP* 2.9 28.6 + - - +
106C ALA* 4.0 5.7 - - - +
108C LEU* 1.3 78.4 - - - +
110C SER* 1.3 61.2 + - - +
111C GLY 3.6 0.2 + - - -
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Residues in contact with SER 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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82C TYR 5.1 2.0 - - - -
85C LEU* 3.3 33.2 - - - +
86C ARG* 3.9 1.6 - - - -
87C HIS* 3.4 21.7 + - - +
106C ALA 3.0 15.9 + - - -
107C LEU 2.8 16.6 + - - -
109C ASP* 1.3 78.8 - - - +
111C GLY* 1.3 54.9 + - - +
112C THR* 3.1 20.4 + - - +
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Residues in contact with GLY 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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87C HIS* 3.7 23.8 - - - -
88C GLY 4.7 0.9 + - - -
107C LEU 3.4 1.2 + - - -
108C LEU 3.1 14.9 + - - -
109C ASP 3.3 0.6 - - - -
110C SER* 1.3 77.7 + - - +
112C THR* 1.3 60.8 + - - +
113C THR* 4.8 0.7 + - - -
347C GLU* 3.1 25.0 + - - +
348C GLY* 3.8 12.3 - - - -
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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