Contacts of the helix formed by residues 119 - 132 (chain B) in PDB entry 2VSH
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 119 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39B LYS* 5.2 4.3 - - - +
117B PHE 3.8 7.4 - - - +
118B ILE* 1.3 77.9 - - - +
120B LEU* 1.3 64.0 + - - +
121B ARG* 3.7 11.5 + - - +
122B MET* 3.0 49.0 + - + +
123B ILE* 3.3 19.1 + - - +
213B GLU* 4.9 6.5 + - + +
215B SER* 5.8 1.6 - - - +
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Residues in contact with LEU 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B LYS* 5.4 3.3 + - - +
42B LEU* 4.3 33.7 - - + +
43B GLU* 3.6 40.8 - - + +
44B PRO* 5.7 0.7 - - + -
119B THR* 1.3 73.0 - - - +
121B ARG* 1.3 53.2 + - - +
123B ILE* 3.1 12.0 + - + +
124B GLN* 2.8 54.4 + - + +
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Residues in contact with ARG 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119B THR* 3.8 8.9 + - - +
120B LEU* 1.3 78.4 - - - +
122B MET* 1.3 77.4 + - - +
124B GLN* 3.2 14.6 + - - +
125B ASP* 2.8 71.8 + - - +
211B LYS* 2.9 47.6 + - - +
212B GLY 3.4 8.1 + - - -
213B GLU* 2.9 29.1 + - - -
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Residues in contact with MET 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117B PHE 4.1 7.4 - - - +
118B ILE* 4.2 16.6 - - + -
119B THR* 3.0 45.8 + - + +
120B LEU 3.3 0.6 - - - -
121B ARG* 1.3 98.3 - - - +
123B ILE* 1.3 60.3 + - - +
125B ASP* 3.5 1.2 + - - +
126B ASN* 2.8 35.7 + - - +
138B THR* 4.9 3.4 - - + -
170B PRO* 4.9 5.8 - - + -
211B LYS 3.7 9.6 - - - +
212B GLY* 4.4 4.3 - - - -
213B GLU* 2.8 47.1 - - + -
216B ASN* 4.5 13.5 - - + -
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Residues in contact with ILE 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B LYS* 3.4 31.0 - - + +
40B PHE* 3.8 34.8 - - + -
43B GLU* 4.2 19.3 - - + -
46B ILE* 4.5 3.1 - - + -
109B VAL* 4.9 3.8 - - + -
118B ILE* 3.6 23.6 - - + -
119B THR 3.3 13.2 + - - +
120B LEU* 3.1 13.3 + - + +
122B MET* 1.3 72.9 - - - +
124B GLN* 1.3 65.5 + - - +
126B ASN* 3.3 7.8 + - - +
127B ILE* 3.1 39.0 + - + +
170B PRO* 5.2 2.0 - - + -
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Residues in contact with GLN 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B GLU* 3.5 19.3 + - - +
120B LEU* 2.8 40.7 + - + +
121B ARG* 3.5 18.6 + - - +
123B ILE* 1.3 76.9 - - - +
125B ASP* 1.3 58.6 + - - +
127B ILE* 3.2 8.7 + - - +
128B GLN* 3.0 47.7 + - - +
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Residues in contact with ASP 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121B ARG* 2.8 59.2 + - - +
122B MET* 3.8 4.3 - - - +
124B GLN* 1.3 75.1 - - - +
126B ASN* 1.3 57.8 + - - +
128B GLN* 3.8 15.9 + - - +
129B LEU* 2.9 47.6 + - + +
210B ALA* 4.6 7.6 - - + -
211B LYS* 5.0 4.3 + - - +
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Residues in contact with ASN 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109B VAL* 4.5 4.0 - - + -
122B MET 2.8 23.1 + - - +
123B ILE* 3.5 10.5 - - - +
125B ASP* 1.3 75.3 - - - +
127B ILE* 1.3 63.2 + - - +
130B ALA* 3.1 25.1 + - - +
136B VAL* 3.6 21.7 - - - +
138B THR* 2.8 29.5 + - - +
170B PRO* 3.4 22.9 + - + +
172B THR* 2.8 36.0 + - + +
210B ALA* 3.6 6.8 - - - +
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Residues in contact with ILE 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2B ILE* 3.7 44.6 - - + -
43B GLU* 4.1 12.6 - - + +
45B SER* 4.0 15.7 - - - +
46B ILE* 4.3 1.6 - - + -
107B ILE* 4.1 10.1 - - + -
109B VAL* 4.0 10.8 - - + -
123B ILE* 3.1 32.0 + - + +
124B GLN* 3.2 7.4 + - - +
126B ASN* 1.3 73.0 - - - +
128B GLN* 1.3 67.4 + - + +
130B ALA* 3.4 8.5 + - - +
131B GLN* 2.9 33.9 + - - +
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Residues in contact with GLN 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124B GLN* 3.0 39.1 + - - +
125B ASP* 3.8 15.1 + - - +
127B ILE* 1.3 78.4 - - + +
129B LEU* 1.3 63.8 + - + +
131B GLN* 3.2 27.5 + - - +
132B ASN* 4.2 2.4 + - - +
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Residues in contact with LEU 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125B ASP* 2.9 29.0 + - + +
128B GLN* 1.3 74.7 - - + +
130B ALA* 1.3 63.9 + - - +
131B GLN 3.1 3.6 + - - -
132B ASN* 3.6 0.7 + - - -
133B HIS* 2.9 48.2 + - + +
136B VAL* 3.5 17.3 - - + -
208B ALA* 4.5 8.3 - - + -
209B LEU 3.6 23.8 - - - +
210B ALA* 3.8 20.2 - - + +
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Residues in contact with ALA 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107B ILE* 4.2 17.9 - - + -
126B ASN 3.1 20.1 + - - +
127B ILE 3.6 6.7 - - - +
128B GLN 3.3 0.2 - - - -
129B LEU* 1.3 74.3 - - - +
131B GLN* 1.3 65.4 + - - +
133B HIS 3.0 20.0 - - - +
134B ASP 6.0 0.2 - - - -
135B ALA* 5.4 1.1 - - - +
136B VAL* 3.3 10.0 - - + +
172B THR* 3.7 23.8 - - + +
173B PHE* 5.0 2.9 - - - +
174B ARG* 3.1 14.1 + - - +
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Residues in contact with GLN 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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0B HIS* 3.7 31.2 + - - -
107B ILE* 4.4 7.3 - - - +
127B ILE* 2.9 28.4 - - + +
128B GLN* 3.2 21.5 - - - +
129B LEU 3.1 0.6 - - - -
130B ALA* 1.3 77.7 - - - +
132B ASN* 1.3 68.4 + - - +
133B HIS 3.6 0.9 + - - -
174B ARG* 2.7 26.3 + - - +
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Residues in contact with ASN 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128B GLN 4.2 2.7 + - - +
129B LEU 3.6 2.6 + - - -
130B ALA 3.5 0.2 - - - -
131B GLN* 1.3 84.0 - - - +
133B HIS* 1.3 80.4 + - + +
206B ASP* 4.7 1.0 - - - +
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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