Contacts of the helix formed by residues 109 - 122 (chain F) in PDB entry 1VHA
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 HIS 109 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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105F LYS 4.0 20.6 + - - -
106F MSE 3.0 12.4 + - + +
108F PRO* 1.3 85.4 + - + +
110F ILE* 1.3 65.7 + - - +
111F ASP 3.3 2.9 - - - -
112F ALA* 2.9 24.3 + - + +
113F MSE 3.1 25.6 + - + +
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Residues in contact with ILE 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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60E LYS* 5.7 8.1 - - - +
99F ILE* 4.8 2.5 - - + -
106F MSE 3.5 12.0 + - + +
107F ARG* 3.0 34.2 + - + +
109F HIS* 1.3 75.9 - - - +
111F ASP* 1.3 61.7 + - - +
113F MSE 2.8 33.9 + - + +
114F ARG* 2.9 22.3 + - - +
130F VAL* 3.4 50.3 - - + +
131F LYS 5.0 0.9 - - - -
132F ALA* 4.6 15.9 - - + +
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Residues in contact with ASP 111 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C GLU* 3.3 35.9 - - - +
107F ARG 4.8 0.4 + - - -
108F PRO 4.7 5.3 + - - +
109F HIS 3.3 0.4 - - - -
110F ILE* 1.3 82.8 - - - +
112F ALA* 1.3 62.2 + - - +
114F ARG* 3.1 32.5 + - - +
115F ALA* 3.1 23.7 + - - +
125F ILE* 4.0 4.1 - - + +
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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
----------------------------------------------------------
108F PRO 5.3 0.6 + - - +
109F HIS* 2.9 22.1 + - + +
111F ASP* 1.3 78.9 - - - +
113F MSE 1.3 63.0 + - + +
115F ALA* 3.7 5.6 + - - +
116F LYS* 3.3 31.8 + - - +
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Residues in contact with MSE 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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41F ALA* 5.6 5.4 - - - -
99F ILE* 4.1 21.5 - - + -
106F MSE 3.9 30.5 - - + +
109F HIS* 3.1 32.3 + - + +
110F ILE* 2.8 19.8 + - + +
112F ALA* 1.3 76.7 - - + +
114F ARG* 1.3 59.4 + - - +
116F LYS* 3.1 8.4 + - - +
117F ILE* 2.8 43.4 + - + +
130F VAL* 4.2 8.1 - - + -
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Residues in contact with ARG 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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25C GLU* 4.8 4.2 + - - -
54E ALA* 4.4 16.7 + - - +
110F ILE* 2.9 24.9 + - - +
111F ASP* 3.1 31.9 + - - +
112F ALA 3.4 0.2 - - - -
113F MSE 1.3 77.4 - - - +
115F ALA* 1.3 51.9 + - - +
117F ILE* 3.2 2.8 + - - +
118F ALA* 2.7 35.3 + - - +
125F ILE* 2.6 51.1 + - + +
126F GLU* 4.1 6.7 - - - +
128F VAL* 2.5 35.0 + - + +
129F ASN* 4.1 4.5 + - - +
130F VAL* 3.8 25.6 - - + +
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Residues in contact with ALA 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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18C PRO* 5.0 21.5 - - + -
111F ASP 3.1 17.6 + - - +
112F ALA* 3.8 7.0 - - - +
113F MSE 3.2 0.2 - - - -
114F ARG* 1.3 76.3 - - - +
116F LYS* 1.3 59.7 + - + +
118F ALA* 2.8 9.4 + - - +
119F GLU* 2.8 38.2 + - + +
125F ILE* 3.6 15.0 - - + +
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Residues in contact with LYS 116 (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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75F ARG* 3.5 41.8 - - - +
112F ALA* 3.3 17.4 + - - +
113F MSE 3.1 10.6 + - - +
115F ALA* 1.3 80.8 - - + +
117F ILE* 1.3 62.8 + - + +
119F GLU* 3.1 12.8 + - - +
120F ASP* 3.0 29.4 + - - +
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Residues in contact with ILE 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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41F ALA* 5.9 5.2 - - + +
42F LEU* 4.0 26.2 - - + -
45F LEU* 3.5 19.3 - - + -
78F LEU* 4.7 2.2 - - + -
95F VAL* 5.0 0.4 - - + -
97F ILE* 5.8 3.1 - - + -
113F MSE 2.8 30.7 + - + +
114F ARG 3.7 3.6 - - - +
116F LYS* 1.3 74.5 - - + +
118F ALA* 1.3 58.1 + - - +
120F ASP* 4.6 6.1 - - - +
121F LEU* 3.0 53.4 + - + +
128F VAL* 3.9 18.8 - - + -
130F VAL* 4.0 26.9 - - + -
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Residues in contact with ALA 118 (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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114F ARG 2.7 13.7 + - - +
115F ALA* 2.8 15.5 + - - +
117F ILE* 1.3 75.2 - - - +
119F GLU* 1.3 64.5 + - + +
121F LEU 3.7 0.2 - - - -
122F GLN* 2.9 18.5 + - - -
123F CYS* 3.2 35.2 + - - +
124F ASP 4.2 0.7 - - - -
125F ILE* 3.8 24.7 - - + +
128F VAL* 4.4 1.8 - - + +
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Residues in contact with GLU 119 (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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16C ASP* 4.1 27.8 - - + +
18C PRO* 5.6 5.0 - - - +
75F ARG* 3.3 21.6 + - - +
115F ALA* 2.8 22.6 + - - +
116F LYS* 3.1 13.4 + - - +
118F ALA* 1.3 74.7 - - + +
120F ASP* 1.3 64.5 + - - +
122F GLN* 2.9 21.0 + - - +
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Residues in contact with ASP 120 (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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42F LEU* 5.1 0.2 - - - +
75F ARG* 2.5 53.7 + - - +
78F LEU* 3.5 27.8 - - + +
79F ARG* 2.7 51.8 + - + +
82F PHE* 4.3 10.9 - - - +
116F LYS* 3.0 10.9 + - - +
117F ILE* 4.1 0.8 - - - +
119F GLU* 1.3 79.9 - - - +
121F LEU* 1.3 61.9 + - - +
122F GLN* 3.7 6.8 + - - +
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Residues in contact with LEU 121 (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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45F LEU* 4.0 7.9 - - + -
49F ILE* 3.6 33.0 - - + -
78F LEU* 3.8 16.4 - - + -
82F PHE* 3.3 43.4 - - + -
92F ILE* 4.3 14.6 - - + +
95F VAL* 4.4 10.8 - - + -
117F ILE* 3.0 41.5 + - + +
120F ASP* 1.3 76.2 - - - +
122F GLN* 1.3 73.7 + - - +
123F CYS* 3.4 15.4 + - - +
128F VAL* 4.9 3.4 - - + -
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Residues in contact with GLN 122 (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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37C ASP* 5.8 3.6 - - - +
72C ALA* 4.1 19.9 + - - +
82F PHE* 3.5 27.0 - - + -
83F ARG* 5.6 5.1 - - - +
86F GLN* 3.6 19.2 + - - +
91F LYS* 5.9 2.9 - - - +
118F ALA 2.9 4.6 + - - -
119F GLU 2.9 15.5 + - - +
120F ASP 4.2 4.8 + - - +
121F LEU* 1.3 83.1 - - - +
123F CYS* 1.3 57.2 + - - +
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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