Contacts of the helix formed by residues 131 - 145 (chain H) in PDB entry 3VON
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 THR 131 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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126H VAL* 4.4 0.7 - - - -
129H GLY 3.8 2.1 + - - -
130H PHE* 1.3 75.2 - - - +
132H GLU* 1.3 71.3 + - + +
133H PHE* 3.6 35.2 - - + -
134H THR* 3.3 28.9 + - - +
135H ILE* 3.6 10.2 + - - +
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Residues in contact with GLU 132 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122H LYS* 2.8 28.6 + - - +
126H VAL* 3.6 31.8 - - + +
130H PHE 3.8 1.8 + - - -
131H THR* 1.3 73.1 - - + +
133H PHE* 1.3 61.0 + - + +
134H THR 2.8 10.4 + - - -
135H ILE* 3.2 4.3 + - - +
136H GLU* 3.2 30.0 + - - +
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Residues in contact with PHE 133 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131H THR* 3.7 22.4 - - + -
132H GLU* 1.3 77.9 - - + +
134H THR* 1.3 75.5 + - - +
136H GLU* 3.8 26.0 + - - +
137H ASP* 4.0 7.6 - - - +
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Residues in contact with THR 134 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131H THR* 3.3 31.1 + - - -
132H GLU 2.8 2.4 + - - -
133H PHE* 1.3 91.6 - - + +
135H ILE* 1.3 61.6 + - + -
136H GLU 3.2 4.8 + - - -
137H ASP* 4.4 2.4 - - - +
138H PHE* 3.3 27.5 - - + -
177H LEU* 5.6 0.4 - - - +
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Residues in contact with ILE 135 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122H LYS* 3.8 23.8 - - + +
125H LEU* 3.8 26.5 - - + -
126H VAL* 3.7 24.9 - - + -
130H PHE* 4.1 26.7 - - + -
131H THR 3.9 6.1 - - - +
132H GLU 3.2 9.8 + - - +
134H THR* 1.3 80.5 - - + +
136H GLU* 1.3 66.3 + - - +
137H ASP 3.4 0.8 + - - -
138H PHE* 3.5 9.3 + - - +
139H HIS* 3.0 23.6 + - - +
174H TYR* 4.4 8.9 - - + -
177H LEU* 3.9 24.7 - - + -
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Residues in contact with GLU 136 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122H LYS* 3.8 29.1 + - - +
132H GLU* 3.2 18.4 + - - +
133H PHE* 3.8 30.5 + - - +
134H THR 3.2 0.4 - - - -
135H ILE* 1.3 77.7 - - - +
137H ASP* 1.3 67.0 + - - +
139H HIS* 3.2 3.3 + - - +
140H ASN* 2.8 39.8 + - - +
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Residues in contact with ASP 137 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133H PHE 4.0 14.4 - - - +
134H THR 4.4 5.4 - - - +
135H ILE 3.5 0.6 - - - -
136H GLU* 1.3 82.2 - - - +
138H PHE* 1.3 65.4 + - + +
140H ASN* 3.3 10.7 + - - +
141H THR* 2.9 30.2 + - - -
170H TYR* 3.8 22.8 - - + -
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Residues in contact with PHE 138 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134H THR* 3.3 28.7 - - + -
135H ILE* 4.1 7.4 - - - +
136H GLU 3.3 0.2 - - - -
137H ASP* 1.3 81.9 - - + +
139H HIS* 1.3 60.7 + - - +
140H ASN 3.4 0.2 - - - -
141H THR* 3.9 3.8 + - - -
142H PHE* 3.3 17.7 + - - +
170H TYR* 3.4 63.4 - + - +
171H LEU* 5.1 0.2 - - - -
173H VAL* 3.7 33.7 - - + -
174H TYR* 3.4 31.7 - - + +
177H LEU* 4.7 3.8 - - + -
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Residues in contact with HIS 139 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118H SER 3.4 19.4 + - - -
119H ALA* 4.0 7.1 - - + -
122H LYS* 3.3 43.1 - - + +
135H ILE 3.0 19.6 + - - +
136H GLU 3.4 4.0 - - - +
138H PHE* 1.3 76.5 - - - +
140H ASN* 1.3 64.8 + - - +
141H THR 3.3 0.2 - - - -
142H PHE* 3.2 3.3 + - + +
143H MET* 2.9 53.0 + - + +
174H TYR* 3.2 38.5 - + + -
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Residues in contact with ASN 140 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122H LYS* 5.2 1.7 - - - -
136H GLU* 2.8 37.1 + - - +
137H ASP* 3.4 13.2 - - - +
139H HIS* 1.3 84.4 + - - +
141H THR* 1.3 56.6 + - - +
143H MET* 3.5 5.4 + - - +
144H ASP* 3.0 31.1 + - - +
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Residues in contact with THR 141 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137H ASP 2.9 17.0 + - - -
138H PHE 4.0 4.9 - - - -
139H HIS 3.3 0.2 - - - -
140H ASN* 1.3 76.7 - - - +
142H PHE* 1.3 61.3 + - - +
144H ASP* 3.4 7.6 + - + +
145H LEU* 3.2 27.4 + - + +
167H THR* 3.5 43.3 - - + +
170H TYR* 3.4 27.7 - - + -
171H LEU* 4.4 3.8 - - - +
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Residues in contact with PHE 142 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96H PHE* 6.1 0.2 - + - -
97H GLY* 6.5 0.2 - - - -
101H LEU* 6.2 2.5 - - + -
114H PHE* 4.3 18.6 - + - -
118H SER* 3.3 29.4 - - - -
138H PHE 3.3 16.1 + - - +
139H HIS* 3.2 6.4 + - + +
141H THR* 1.3 76.5 - - - +
143H MET* 1.3 75.7 + - + +
144H ASP 3.1 0.4 - - - -
145H LEU* 3.3 10.6 + - - +
146H ILE* 3.4 23.9 + - + +
171H LEU* 3.4 34.3 - - + +
174H TYR* 3.7 31.4 - + + -
175H LEU* 4.0 26.7 - - + -
178H LEU* 4.5 8.7 - - + -
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Residues in contact with MET 143 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115H LYS* 4.6 18.9 + - + +
118H SER* 3.3 47.6 - - - +
119H ALA* 3.9 17.3 - - - -
139H HIS* 2.9 42.5 + - + +
140H ASN* 4.0 5.4 - - - +
142H PHE* 1.3 81.5 - - + +
144H ASP* 1.3 57.3 + - - +
146H ILE* 3.5 18.4 + - + +
147H GLU* 3.2 26.3 + - - +
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Residues in contact with ASP 144 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140H ASN 3.0 18.6 + - - +
141H THR* 3.6 10.5 - - + +
142H PHE 3.1 0.4 - - - -
143H MET* 1.3 78.9 - - - +
145H LEU* 1.3 58.9 + - + +
146H ILE 3.4 1.6 - - - -
147H GLU* 3.8 16.5 + - - +
148H GLN* 3.4 24.4 + - - +
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Residues in contact with LEU 145 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101H LEU* 3.4 29.5 - - + +
141H THR* 3.2 16.8 + - + +
142H PHE 3.3 4.4 + - - +
143H MET 3.3 0.6 - - - -
144H ASP* 1.3 76.4 - - + +
146H ILE* 1.3 61.4 + - - +
147H GLU 3.6 0.2 - - - -
148H GLN* 4.1 22.1 - - + +
149H VAL* 3.5 10.7 + - - +
158H LEU* 4.9 4.2 - - + +
161H SER* 3.7 29.6 - - - +
162H PHE* 3.8 28.3 - - + -
167H THR* 4.3 19.5 - - + +
168H SER* 5.7 1.1 - - - -
171H LEU* 3.8 28.3 - - + -
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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