Contacts of the helix formed by residues 148 - 154 (chain B) in PDB entry 1VBF
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 LEU 148 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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77B ILE* 5.2 2.2 - - + -
126B THR* 4.1 27.4 - - - +
140B VAL* 3.7 39.7 - - + -
144B ALA* 3.8 24.2 - - + -
146B THR 3.3 1.7 + - - +
147B LEU* 1.3 74.7 - - - +
149B CYS* 1.3 64.0 - - - +
150B LYS 3.6 0.4 - - - -
151B PRO* 3.7 19.9 - - + +
152B TYR* 3.2 24.3 + - - +
161B MSE 4.3 6.4 - - + +
163B LEU* 4.0 10.0 - - + +
196B ILE* 4.0 11.9 - - + -
200B TYR* 4.3 17.0 - - + +
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Residues in contact with CYS 149 (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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149A CYS* 2.1 53.2 - - + -
150A LYS* 4.2 17.5 - - - -
153A GLU* 4.0 0.2 - - - -
200A TYR* 3.8 22.7 - - + -
126B THR 5.6 0.6 + - - -
147B LEU 3.1 4.4 + - - +
148B LEU* 1.3 69.5 - - - +
150B LYS* 1.3 60.6 + - - +
152B TYR* 3.4 2.1 + - - +
153B GLU* 2.8 51.2 + - - +
200B TYR* 5.5 6.4 - - + +
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Residues in contact with LYS 150 (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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149A CYS* 4.2 9.4 - - - -
153A GLU* 2.7 31.3 + - - +
181A ASN* 5.0 8.9 - - - +
126B THR 3.5 13.6 + - - +
127B LEU* 3.1 38.1 - - - +
130B GLU* 5.8 3.8 - - + +
149B CYS* 1.3 73.0 - - - +
151B PRO* 1.3 73.5 - - + +
153B GLU* 3.0 18.5 + - - +
154B GLN* 2.8 33.2 + - - +
200B TYR* 4.3 21.0 + - + -
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Residues in contact with PRO 151 (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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75B LEU* 4.4 9.0 - - + -
77B ILE* 4.6 5.6 - - + -
125B GLY 4.4 7.9 - - - +
126B THR 3.9 6.5 - - - +
128B GLY* 4.2 13.2 - - - -
138B VAL* 4.1 13.0 - - + +
148B LEU* 3.5 29.6 - - + +
150B LYS* 1.3 93.8 - - + +
152B TYR* 1.3 64.0 + - - +
154B GLN* 2.9 19.9 + - + +
155B LEU* 2.9 14.4 + - - +
161B MSE 3.2 27.8 - - + -
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Residues in contact with TYR 152 (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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150A LYS* 6.2 0.4 - - - -
199A LEU* 5.1 2.0 - - + -
200A TYR* 3.5 22.2 - - - +
147B LEU* 4.1 17.0 - - + -
148B LEU 3.2 18.3 + - - +
149B CYS 3.6 4.3 - - - +
151B PRO* 1.3 79.6 - - - +
153B GLU* 1.3 65.0 + - + +
155B LEU* 3.3 19.7 + - + +
161B MSE 4.2 7.0 - - - -
176B VAL* 3.8 22.9 - - + -
178B LYS* 3.1 49.2 + - + +
179B LYS 3.4 5.2 + - - -
180B GLY 2.6 29.3 + - - -
181B ASN* 4.8 5.6 - - - -
183B PRO* 3.0 32.2 - - + +
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Residues in contact with GLU 153 (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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150A LYS* 2.6 34.5 + - - +
153A GLU* 2.8 31.2 - - - +
130B GLU* 5.2 6.2 - - - +
133B LYS* 4.4 9.4 + - - -
149B CYS* 2.8 31.1 + - - +
150B LYS* 3.0 22.9 + - - +
152B TYR* 1.3 82.0 - - + +
154B GLN* 1.3 61.4 + - + +
155B LEU 3.5 1.0 - - - +
178B LYS* 3.0 20.8 + - - +
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Residues in contact with GLN 154 (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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75B LEU* 3.8 2.1 - - - +
127B LEU 2.9 24.6 + - - -
128B GLY* 3.5 3.8 - - - -
129B TYR 2.5 36.5 + - - +
130B GLU* 3.6 33.1 + - - +
133B LYS* 2.8 41.7 + - + +
134B PRO* 3.6 3.5 - - - +
135B TYR* 3.0 24.7 + - + -
150B LYS* 2.8 26.1 + - - +
151B PRO* 3.4 8.1 - - + +
153B GLU* 1.3 76.9 + - + +
155B LEU* 1.3 60.2 + - - +
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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