Contacts of the helix formed by residues 134 - 146 (chain B) in PDB entry 2VGO
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 VAL 134 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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104B PHE* 3.6 42.0 - - + -
128B GLN 6.0 0.2 - - - +
129B LEU* 3.6 40.6 + - + +
130B GLU 6.0 0.2 - - - -
131B LYS 4.1 16.3 + - - +
135B GLU* 1.3 60.6 + - - +
136B HIS* 3.3 4.8 - - - +
137B GLN* 3.0 21.4 + - - +
138B LEU* 2.6 34.9 + - + +
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Residues in contact with GLU 135 (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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129B LEU* 3.9 14.9 + - + +
130B GLU* 4.0 25.1 + - - +
134B VAL* 1.3 79.3 - - - +
136B HIS* 1.3 79.5 + - + +
138B LEU* 3.6 0.6 + - - -
139B ARG* 3.3 18.7 + - - +
837C PHE* 3.5 60.7 - - + +
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Residues in contact with HIS 136 (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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134B VAL 3.3 2.1 - - - +
135B GLU* 1.3 93.4 + - + +
137B GLN* 1.3 65.4 + - - +
139B ARG* 3.5 16.6 + - - +
140B ARG* 3.2 22.2 + - - +
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Residues in contact with GLN 137 (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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103B LYS* 6.0 0.3 - - - +
104B PHE* 3.5 27.9 - - + -
134B VAL* 3.0 25.2 + - + +
136B HIS* 1.3 75.8 - - - +
138B LEU* 1.3 64.5 + - - +
140B ARG* 3.5 7.4 + - - +
141B GLU* 3.1 24.1 + - - +
236B GLY* 3.3 31.8 - - - +
237B TRP* 4.0 31.0 + - + -
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Residues in contact with LEU 138 (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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104B PHE* 4.5 11.8 - - + -
122B LYS* 5.7 0.9 - - - +
124B LEU* 3.7 32.5 - - + -
129B LEU* 3.8 16.4 - - + -
134B VAL* 2.6 23.4 + - + +
135B GLU* 3.8 4.9 - - - +
137B GLN* 1.3 72.0 - - - +
139B ARG* 1.3 58.0 + - - +
141B GLU* 3.2 14.8 + - + +
142B ILE* 2.9 57.2 + - + +
166B ILE* 3.9 9.6 - - + -
168B LEU* 4.5 8.5 - - + -
837C PHE* 3.7 26.7 - - + -
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Residues in contact with ARG 139 (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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135B GLU* 3.3 10.1 + - - +
136B HIS* 3.7 20.0 + - - +
137B GLN 3.3 0.2 - - - -
138B LEU* 1.3 79.5 - - - +
140B ARG* 1.3 57.9 + - - +
142B ILE* 3.6 5.1 + - - +
143B GLU* 3.0 29.9 + - + +
833C LEU* 3.9 31.1 - - + +
834C GLU* 3.7 35.2 + - - +
837C PHE* 3.5 46.3 - - + +
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Residues in contact with ARG 140 (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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136B HIS 3.2 15.0 + - - +
137B GLN* 3.8 6.5 - - - +
139B ARG* 1.3 77.4 - - - +
141B GLU* 1.3 59.5 + - - +
143B GLU* 3.3 12.7 + - - +
144B ILE* 3.0 48.6 + - + +
215B ARG* 3.9 5.3 - - - +
237B TRP 6.1 0.2 - - - -
238B SER 3.4 17.7 + - - +
239B VAL* 3.7 19.9 - - - +
240B HIS 5.5 0.4 - - - +
246B ARG* 3.7 17.0 - - - +
248B TPO 2.9 27.5 + - - -
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Residues in contact with GLU 141 (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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103B LYS* 5.3 1.8 - - - +
104B PHE* 3.8 23.9 - - - -
122B LYS* 4.0 17.4 + - - -
137B GLN* 3.1 18.2 + - - +
138B LEU* 3.2 12.6 + - + +
140B ARG* 1.3 77.8 - - - +
142B ILE* 1.3 57.6 + - - +
144B ILE* 3.5 3.8 + - - +
145B GLN* 3.0 40.4 + - - +
156B MET* 5.3 2.0 - - + +
168B LEU* 5.6 2.3 - - - +
234B ASP* 4.7 6.6 - - - +
235B PHE* 3.6 37.1 + - + +
236B GLY* 3.5 22.8 - - - -
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Residues in contact with ILE 142 (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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138B LEU* 2.9 54.3 + - + +
139B ARG* 4.0 3.4 - - - +
141B GLU* 1.3 68.7 - - + +
143B GLU* 1.3 59.1 + - - +
146B SER* 2.7 38.8 + - - -
156B MET* 4.0 14.8 - - + -
159B TYR* 3.7 36.1 - - + -
166B ILE* 4.6 1.6 - - + -
168B LEU* 3.8 24.0 - - + -
833C LEU* 3.8 13.9 - - + -
836C LEU* 4.0 22.0 - - + -
837C PHE* 4.6 1.8 - - + -
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Residues in contact with GLU 143 (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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139B ARG 3.0 19.3 + - - +
140B ARG* 3.5 13.1 - - - +
142B ILE* 1.3 77.2 - - - +
144B ILE* 1.3 79.3 + - - +
146B SER* 3.2 2.8 + - - -
147B HIS* 3.0 35.6 - - + +
240B HIS* 4.3 18.9 + - - +
833C LEU* 3.9 20.1 - - + +
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Residues in contact with ILE 144 (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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140B ARG* 3.0 23.8 + - + +
141B GLU* 4.0 5.2 - - - +
143B GLU* 1.3 91.4 - - - +
145B GLN* 1.3 67.0 + - - +
147B HIS* 3.2 14.8 + - - +
148B LEU* 3.5 23.3 - - + +
212B VAL* 3.7 29.8 - - + -
235B PHE* 4.3 11.4 - - + +
238B SER* 3.4 38.1 - - - +
239B VAL* 3.6 12.6 - - - +
240B HIS* 3.9 10.8 - - + +
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Residues in contact with GLN 145 (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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141B GLU* 3.0 29.8 + - - +
144B ILE* 1.3 77.5 - - - +
146B SER* 1.3 61.6 + - - +
147B HIS 3.1 2.0 + - - -
148B LEU* 3.2 25.9 + - - +
153B ILE* 5.3 2.2 - - + -
154B LEU* 3.0 35.0 + - - +
156B MET* 3.8 33.4 + - + +
170B LEU* 4.3 14.3 - - - +
233B ALA 3.9 19.3 + - - +
235B PHE* 3.9 29.1 + - + +
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Residues in contact with SER 146 (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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142B ILE 2.7 24.0 + - - -
143B GLU* 3.2 2.4 + - - -
144B ILE 3.2 0.2 - - - -
145B GLN* 1.3 77.2 - - - +
147B HIS* 1.3 82.1 + - - +
148B LEU 5.1 0.8 - - - +
149B ARG* 5.0 11.6 + - - +
155B ARG* 6.1 0.3 - - - -
156B MET* 4.1 26.9 - - - +
158B ASN* 6.4 0.4 - - - -
159B TYR* 4.0 26.2 + - - -
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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