Contacts of the helix formed by residues 104 - 117 (chain F) in PDB entry 1VQ4
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 ALA 104 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19F ALA* 4.1 8.7 - - + +
22F VAL* 3.4 28.7 - - + -
23F ALA 4.8 0.7 - - - +
101F ALA* 4.3 6.1 - - + -
102F GLY 2.9 6.0 - - - +
103F GLU* 1.3 81.0 - - - +
105F ASP* 1.3 58.3 + - - +
106F ALA* 2.9 5.3 + - - +
107F ASP* 2.9 13.7 + - - +
108F VAL* 2.7 47.6 + - + +
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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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46F GLU* 4.9 4.9 - - - +
100F ASP* 5.3 0.3 - - - -
101F ALA* 3.8 21.9 + - - +
102F GLY* 3.8 5.5 + - - -
103F GLU* 3.7 16.6 + - - -
104F ALA* 1.3 77.8 - - - +
106F ALA* 1.3 61.4 + - - +
108F VAL* 4.0 6.7 - - - +
109F GLU* 3.0 27.4 + - - +
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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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103F GLU 5.4 1.1 - - - -
104F ALA* 2.9 2.1 + - - -
105F ASP* 1.3 79.0 - - - +
107F ASP* 1.3 68.0 + - - +
109F GLU* 3.4 8.7 - - - +
110F ASP* 2.7 35.9 + - - +
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Residues in contact with ASP 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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15F ASP* 5.9 0.7 - - + +
19F ALA* 4.7 9.5 - - + +
22F VAL* 5.8 1.0 - - - +
103F GLU 4.4 4.0 - - - +
104F ALA* 2.9 18.7 + - - +
106F ALA* 1.3 78.4 - - - +
108F VAL* 1.3 64.5 + - - +
110F ASP* 2.8 12.1 + - - +
111F ILE* 2.7 35.6 + - + +
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Residues in contact with VAL 108 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19F ALA* 4.2 14.1 - - + +
46F GLU* 4.9 13.9 - - + -
47F LEU* 4.1 30.7 - - + +
98F VAL* 5.0 8.7 - - + -
101F ALA* 4.0 17.5 - - + -
104F ALA* 2.7 35.0 + - + +
105F ASP* 4.0 5.2 - - - +
107F ASP* 1.3 71.5 - - - +
109F GLU* 1.3 67.3 + - - +
111F ILE* 2.8 13.7 + - - +
112F ALA* 2.8 24.5 + - + +
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Residues in contact with GLU 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 3.0 19.2 + - - +
106F ALA* 3.4 8.4 - - - +
108F VAL* 1.3 81.5 - - - +
110F ASP* 1.3 60.2 + - - +
112F ALA* 3.4 7.8 + - - +
113F ASP* 2.5 44.7 + - - +
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Residues in contact with ASP 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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106F ALA* 2.7 24.8 + - - +
107F ASP* 2.8 10.6 + - - +
109F GLU* 1.3 77.6 - - - +
111F ILE* 1.3 56.2 + - + +
113F ASP* 3.0 12.8 + - - +
114F LYS* 2.6 49.6 + - + +
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Residues in contact with ILE 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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12F LEU* 3.9 22.0 - - + -
15F ASP* 4.0 15.9 - - + +
16F ALA* 3.7 28.9 - - + +
19F ALA* 4.0 16.6 - - + -
47F LEU* 4.3 15.7 - - + -
75F ILE* 4.0 16.6 - - + -
107F ASP* 2.7 28.6 + - + +
108F VAL* 2.8 11.4 + - - +
110F ASP* 1.3 71.9 - - + +
112F ALA* 1.3 63.3 + - - +
114F LYS* 3.0 11.2 + - + +
115F VAL* 2.9 30.4 + - + +
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Residues in contact with ALA 112 (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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46F GLU 5.7 0.2 - - - +
47F LEU* 4.6 11.4 - - + +
73F PRO* 4.0 31.2 - - + +
108F VAL* 2.8 13.2 + - + +
109F GLU* 3.5 12.8 - - - +
111F ILE* 1.3 76.3 - - - +
113F ASP* 1.3 61.2 + - - +
115F VAL* 3.6 7.5 + - - +
116F GLU* 3.2 27.5 + - - +
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Residues in contact with ASP 113 (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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109F GLU* 2.5 34.6 + - - +
110F ASP* 3.0 15.7 + - - +
112F ALA* 1.3 77.7 - - - +
114F LYS* 1.3 64.9 + - - +
116F GLU* 3.3 8.8 + - - +
117F GLU* 3.1 37.1 + - - +
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Residues in contact with LYS 114 (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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12F LEU* 4.5 26.3 - - + +
15F ASP* 4.3 15.7 + - - +
110F ASP* 2.6 31.6 + - + +
111F ILE* 3.6 9.0 - - + +
113F ASP* 1.3 74.1 - - + +
115F VAL* 1.3 57.3 + - - +
117F GLU* 3.4 15.1 + - - +
118F LEU* 3.0 25.0 + - - +
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Residues in contact with VAL 115 (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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6F PHE* 4.2 24.9 - - + -
8F VAL* 6.0 0.2 - - + -
12F LEU* 4.8 8.1 - - + -
47F LEU* 5.8 2.0 - - + -
74F PHE 3.7 21.5 - - - +
75F ILE* 4.2 28.3 - - + -
111F ILE* 2.9 25.5 + - + +
112F ALA* 3.7 8.5 - - - +
113F ASP 3.1 0.2 - - - -
114F LYS* 1.3 72.5 - - - +
116F GLU* 1.3 60.2 + - - +
117F GLU 3.0 1.1 - - - -
118F LEU* 2.6 37.7 + - + +
119F ARG* 3.2 5.7 + - - -
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Residues in contact with GLU 116 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73F PRO* 6.5 0.7 - - + -
112F ALA 3.2 15.8 + - - +
113F ASP* 3.6 11.7 - - - +
115F VAL* 1.3 79.2 - - + +
117F GLU* 1.3 58.9 - - + +
119F ARG* 2.9 24.4 + - - +
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Residues in contact with GLU 117 (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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113F ASP* 3.1 28.3 + - - +
114F LYS* 3.5 14.9 + - - +
115F VAL 3.0 0.6 - - - -
116F GLU* 1.3 73.2 - - + +
118F LEU* 1.3 57.0 + - - +
119F ARG* 2.9 11.4 + - - +
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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