Contacts of the helix formed by residues 100 - 111 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76F GLU* 6.2 2.0 - - - -
82F TYR* 4.4 2.1 + - - -
95F LEU 5.8 0.7 - - - -
96F HIS 3.8 4.7 + - - -
97F LEU 3.0 9.8 + - - +
98F ALA 3.4 0.8 + - - -
99F ALA* 1.3 81.4 - - - +
101F ARG* 1.3 62.3 + - - +
102F ALA* 3.6 8.9 + - - +
103F CYS* 2.9 31.9 + - - +
104F THR* 3.0 23.6 + - - -
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Residues in contact with ARG 101 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99F ALA 4.3 0.2 - - - -
100F SER* 1.3 71.4 - - - +
102F ALA* 1.3 56.5 - - - +
104F THR* 4.8 1.6 - - - -
105F ASP* 2.8 61.7 + - - +
359F LEU* 3.5 57.0 + - + +
360F GLY 5.0 1.8 + - - -
361F VAL* 3.6 19.0 - - - +
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Residues in contact with ALA 102 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82F TYR* 3.6 21.1 + - + +
100F SER* 3.1 6.7 + - - +
101F ARG* 1.3 79.5 + - - +
103F CYS* 1.3 60.9 + - - +
105F ASP* 3.9 6.3 - - - +
106F ALA* 3.1 23.4 + - - +
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Residues in contact with CYS 103 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76F GLU* 4.2 14.4 - - + -
77F PRO* 3.7 38.4 - - - +
82F TYR* 3.4 15.2 + - - +
85F LEU* 6.5 0.2 - - - -
95F LEU* 4.7 2.0 - - - +
97F LEU* 4.0 18.6 - - + -
100F SER* 2.9 26.9 + - - +
102F ALA* 1.3 73.1 - - - +
104F THR* 1.3 64.4 + - - +
106F ALA* 3.3 3.2 + - - +
107F LEU* 3.0 32.9 + - - +
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Residues in contact with THR 104 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97F LEU* 3.3 33.6 + - + +
100F SER 3.0 14.0 + - - -
101F ARG* 3.5 9.6 - - - -
103F CYS* 1.3 76.2 - - - +
105F ASP* 1.3 55.6 + - - +
107F LEU* 3.1 6.5 + - - +
108F LEU* 2.9 56.7 + - + +
345F THR* 5.0 0.6 - - + +
350F LEU* 4.5 19.5 - - + -
355F VAL* 4.7 0.4 - - + -
359F LEU* 3.3 22.7 - - + +
361F VAL* 5.4 2.2 - - + -
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Residues in contact with ASP 105 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101F ARG* 2.8 57.9 + - - +
102F ALA* 3.9 6.9 - - - +
104F THR* 1.3 72.1 - - - +
106F ALA* 1.3 53.7 + - - +
108F LEU* 4.4 13.0 - - - +
109F ASP* 2.8 52.2 + - - +
361F VAL* 5.4 0.9 - - - +
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Residues in contact with ALA 106 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82F TYR* 3.6 42.0 - - + +
85F LEU* 3.5 10.3 - - + +
102F ALA 3.1 15.1 + - - +
103F CYS 3.5 5.4 - - - +
104F THR 3.3 0.2 - - - -
105F ASP* 1.3 78.7 - - - +
107F LEU* 1.3 56.3 + - - +
109F ASP* 4.0 4.9 - - - +
110F SER* 3.1 30.0 + - - -
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Residues in contact with LEU 107 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77F PRO* 4.4 4.0 - - + -
85F LEU* 3.7 20.0 - - + -
91F LEU* 3.5 29.8 - - + -
95F LEU* 3.9 15.0 - - + -
97F LEU* 3.7 36.6 - - + -
103F CYS* 3.0 17.4 + - - +
104F THR* 3.6 4.9 - - - +
106F ALA* 1.3 72.7 - - - +
108F LEU* 1.3 65.1 + - - +
110F SER* 2.9 20.2 + - - -
111F GLY* 3.3 6.4 + - - -
112F THR* 3.7 16.7 + - + +
114F SER* 3.9 13.5 - - - +
345F THR* 4.0 16.0 + - + +
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Residues in contact with LEU 108 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104F THR* 2.9 39.0 + - + +
105F ASP* 3.8 11.7 - - - +
107F LEU* 1.3 76.6 - - - +
109F ASP* 1.3 66.5 + - - +
111F GLY* 3.0 12.0 + - - -
345F THR* 3.7 16.8 - - + -
348F GLY* 3.3 33.9 - - - +
349F ALA 3.5 35.4 - - - +
350F LEU* 3.7 12.8 - - + +
361F VAL* 4.5 13.9 - - + -
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Residues in contact with ASP 109 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105F ASP* 2.8 39.1 + - - +
106F ALA* 4.2 4.8 - - - +
108F LEU* 1.3 75.3 - - - +
110F SER* 1.3 60.8 + - - +
111F GLY* 3.4 0.7 + - - -
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Residues in contact with SER 110 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82F TYR 5.2 1.8 - - - -
85F LEU* 3.5 33.1 - - - +
86F ARG* 4.5 0.3 - - - -
87F HIS* 3.2 24.4 + - - +
106F ALA 3.1 16.9 + - - -
107F LEU 2.9 14.4 + - - -
109F ASP* 1.3 78.6 - - - +
111F GLY* 1.3 55.5 + - - +
112F THR* 3.1 21.7 + - - +
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Residues in contact with GLY 111 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87F HIS* 3.6 21.5 + - - -
88F GLY 4.5 1.2 + - - -
107F LEU 3.3 1.7 + - - -
108F LEU 3.0 16.0 + - - -
109F ASP 3.2 1.3 - - - -
110F SER* 1.3 79.0 + - - +
112F THR* 1.3 65.5 + - - +
113F THR* 3.9 1.0 + - - -
347F GLU* 3.2 22.6 + - - +
348F GLY 3.8 11.9 - - - -
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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