Contacts of the helix formed by residues 106 - 121 (chain C) 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 MSE 106 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99C ILE* 4.1 33.7 - - + -
101C ALA* 4.5 12.6 - - + -
103C ALA* 3.8 28.0 - - + -
104C PRO 2.7 11.3 + - - +
105C LYS* 1.3 76.2 - - - +
107C ARG* 1.3 69.1 + - - +
108C PRO* 3.3 2.7 - - - -
109C HIS* 3.1 19.1 + - + -
110C ILE* 3.2 17.4 + - + +
113C MSE 4.0 18.4 - - + -
132C ALA* 4.6 17.0 - - + -
147C ILE* 6.2 2.9 - - + -
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Residues in contact with ARG 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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57B ASP* 4.3 16.7 + - - -
59B GLY* 5.2 9.5 - - - -
60B LYS* 3.2 31.2 + - - +
103C ALA 4.8 5.9 + - - -
104C PRO* 3.4 21.7 + - - +
106C MSE 1.3 81.1 - - - +
108C PRO* 1.3 68.3 - - + +
109C HIS 2.9 1.7 + - - -
110C ILE* 3.0 29.9 + - + +
111C ASP* 4.3 4.5 + - - +
132C ALA* 3.0 39.1 + - - +
133C THR* 5.1 1.0 - - - +
134C THR* 6.3 0.8 - - - +
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Residues in contact with PRO 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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105C LYS* 4.3 10.3 - - + -
106C MSE 3.4 10.8 - - - +
107C ARG* 1.3 95.2 - - + +
109C HIS* 1.3 70.5 + - + +
111C ASP* 5.0 3.7 + - - +
112C ALA* 5.2 3.6 + - - +
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Residues in contact with HIS 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 LYS* 4.2 19.5 + - + +
106C MSE 3.1 12.3 + - + +
107C ARG 3.0 0.8 - - - -
108C PRO* 1.3 90.1 + - + +
110C ILE* 1.3 65.0 + - - +
111C ASP 3.4 2.5 - - - -
112C ALA* 3.3 14.1 + - + +
113C MSE 3.1 38.1 + - + +
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Residues in contact with ILE 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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57B ASP* 5.1 1.8 - - - +
60B LYS* 4.8 14.1 - - - +
99C ILE* 5.8 0.7 - - + -
106C MSE 3.3 16.6 - - + +
107C ARG* 3.0 36.4 + - + +
109C HIS* 1.3 77.6 - - - +
111C ASP* 1.3 62.6 + - - +
113C MSE 3.1 14.8 + - - +
114C ARG* 3.0 36.2 + - - +
130C VAL* 3.4 44.6 - - + +
131C LYS* 4.6 9.6 - - - -
132C ALA* 4.6 11.7 - - + +
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Residues in contact with ASP 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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60B LYS* 6.1 1.0 - - - -
107C ARG 4.3 4.3 + - - +
108C PRO 5.0 3.3 + - - +
109C HIS 3.4 0.4 - - - -
110C ILE* 1.3 76.9 - - - +
112C ALA* 1.3 66.2 + - - +
114C ARG* 3.2 34.9 + - - +
115C ALA* 3.0 23.6 + - - +
125C ILE* 4.1 7.4 - - + +
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Residues in contact with ALA 112 (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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108C PRO 5.2 2.4 + - - +
109C HIS* 3.3 18.2 + - + +
110C ILE 3.3 0.4 - - - -
111C ASP* 1.3 78.4 - - - +
113C MSE 1.3 61.7 + - - +
115C ALA* 3.4 7.7 + - - +
116C LYS* 3.2 36.4 + - - +
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Residues in contact with MSE 113 (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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41C ALA* 5.4 6.5 - - - -
99C ILE* 4.0 22.2 - - + -
106C MSE 4.0 31.4 - - + +
109C HIS* 3.1 30.8 + - + +
110C ILE* 3.1 11.5 + - - +
112C ALA* 1.3 75.4 - - + +
114C ARG* 1.3 64.9 + - - +
116C LYS* 3.2 8.7 + - - +
117C ILE* 2.9 38.5 + - + +
130C VAL* 4.3 14.4 - - + -
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Residues in contact with ARG 114 (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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54B ALA* 4.3 16.8 + - - +
110C ILE* 3.0 26.7 + - - +
111C ASP* 3.2 33.8 + - - +
113C MSE 1.3 74.9 - - - +
115C ALA* 1.3 53.9 + - - +
117C ILE* 3.3 2.2 + - - +
118C ALA* 2.7 36.7 + - - +
125C ILE* 2.8 54.6 + - + +
126C GLU* 4.2 6.5 - - - +
128C VAL* 2.7 32.7 + - + +
129C ASN* 4.4 4.3 - - - +
130C VAL* 4.0 24.7 - - + +
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Residues in contact with ALA 115 (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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111C ASP 3.0 13.8 + - - +
112C ALA* 3.6 11.7 - - - +
114C ARG* 1.3 76.6 - - - +
116C LYS* 1.3 57.3 + - + +
118C ALA* 3.2 6.4 + - - +
119C GLU* 2.9 30.1 + - - +
125C ILE* 3.8 12.5 - - + +
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Residues in contact with LYS 116 (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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42C LEU* 6.4 0.9 - - + -
75C ARG* 3.5 43.9 + - - +
112C ALA* 3.2 20.4 + - - +
113C MSE 3.2 11.2 + - - +
115C ALA* 1.3 79.5 - - + +
117C ILE* 1.3 64.1 + - + +
119C GLU* 3.2 9.0 + - - +
120C ASP* 3.1 28.5 + - - +
62F PHE* 6.3 0.8 - - - -
80F GLU* 4.9 14.5 + - - -
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Residues in contact with ILE 117 (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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41C ALA* 5.8 5.6 - - + +
42C LEU* 3.9 29.4 - - + -
45C LEU* 3.6 26.2 - - + -
78C LEU* 4.8 6.3 - - + -
95C VAL* 4.6 1.6 - - + -
97C ILE* 5.0 6.3 - - + -
113C MSE 2.9 25.7 + - + +
114C ARG 3.7 3.1 - - - +
116C LYS* 1.3 73.8 - - + +
118C ALA* 1.3 67.0 + - - +
119C GLU 3.0 1.7 + - - -
120C ASP 3.2 1.4 + - - +
121C LEU* 3.0 38.5 + - + +
128C VAL* 3.8 20.0 - - + -
130C VAL* 4.0 26.5 - - + -
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Residues in contact with ALA 118 (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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114C ARG 2.7 22.1 + - - +
115C ALA* 3.2 6.0 + - - +
117C ILE* 1.3 74.1 - - - +
119C GLU* 1.3 60.9 + - - +
121C LEU 4.0 0.2 - - - -
122C GLN* 3.3 2.6 + - - -
123C CYS* 3.1 45.1 + - - +
124C ASP 4.0 1.6 - - - +
125C ILE* 3.7 35.7 - - + +
128C VAL* 4.2 2.4 - - + +
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Residues in contact with GLU 119 (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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75C ARG* 3.7 18.6 + - - +
115C ALA 2.9 13.3 + - - +
116C LYS* 3.4 13.3 - - - +
117C ILE 3.0 0.4 - - - -
118C ALA* 1.3 77.7 - - - +
120C ASP* 1.3 63.8 + - - +
122C GLN* 3.3 18.4 + - - +
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Residues in contact with ASP 120 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75C ARG* 2.8 39.7 + - - +
78C LEU* 3.9 24.0 - - + +
79C ARG* 2.6 54.9 + - + +
82C PHE* 3.7 21.1 - - - +
116C LYS 3.1 14.3 + - - +
117C ILE 4.1 0.7 - - - +
119C GLU* 1.3 76.1 - - - +
121C LEU* 1.3 58.9 + - - +
122C GLN* 3.3 5.2 + - - +
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Residues in contact with LEU 121 (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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45C LEU* 4.3 5.6 - - + -
49C ILE* 3.4 32.3 - - + -
78C LEU* 4.2 13.2 - - + -
82C PHE* 3.3 41.4 - - + -
92C ILE* 3.8 22.7 + - + +
95C VAL* 4.3 12.8 - - + -
117C ILE* 3.0 38.3 + - + +
120C ASP* 1.3 78.1 - - - +
122C GLN* 1.3 73.3 + - - +
123C CYS* 3.1 19.9 + - - +
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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