Contacts of the helix formed by residues 148 - 154 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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77D ILE* 4.3 10.3 - - + -
126D THR* 3.4 31.4 - - - +
140D VAL* 3.6 42.6 - - + -
144D ALA* 3.7 27.4 - - + -
146D THR 3.5 0.8 + - - -
147D LEU* 1.3 74.6 - - - +
149D CYS* 1.3 65.6 + - - +
150D LYS 3.5 1.8 - - - -
151D PRO* 3.3 13.5 - - + +
152D TYR* 3.2 22.3 + - - +
161D MSE 4.4 3.4 - - + +
163D LEU* 4.0 11.1 - - + +
196D ILE* 4.0 11.4 - - + -
200D TYR* 4.1 11.0 - - + +
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Residues in contact with CYS 149 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149C CYS* 2.1 53.6 - - + -
150C LYS* 4.0 15.9 - - - -
200C TYR* 3.6 28.1 + - + -
126D THR 5.5 0.2 + - - -
147D LEU 3.0 6.6 + - - +
148D LEU* 1.3 70.7 - - - +
150D LYS* 1.3 61.7 + - - +
152D TYR* 3.3 4.3 + - - +
153D GLU* 3.0 41.6 + - - +
200D TYR* 5.7 6.1 - - + +
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Residues in contact with LYS 150 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149C CYS* 4.3 8.7 - - - -
153C GLU* 2.8 30.7 + - - +
181C ASN* 4.8 10.4 + - - +
126D THR 3.7 6.6 + - - +
127D LEU* 3.4 41.7 - - + +
130D GLU* 5.8 1.4 + - - -
149D CYS* 1.3 76.0 - - - +
151D PRO* 1.3 73.8 - - + +
153D GLU* 3.1 18.6 + - - +
154D GLN* 2.9 32.2 + - - +
200D TYR* 4.4 21.7 - - + -
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Residues in contact with PRO 151 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75D LEU* 4.4 3.1 - - + -
77D ILE* 3.3 28.0 - - + -
125D GLY 4.3 2.0 - - - +
126D THR 3.8 6.5 - - - +
128D GLY* 4.1 10.3 - - - +
138D VAL* 4.1 8.9 - - + +
148D LEU* 3.3 22.0 - - + +
150D LYS* 1.3 93.7 - - + +
152D TYR* 1.3 58.2 + - - +
154D GLN* 3.2 13.6 + - + +
155D LEU* 3.1 23.7 + - - +
161D MSE 3.1 30.5 - - + -
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Residues in contact with TYR 152 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199C LEU* 4.9 2.0 - - + -
200C TYR* 3.7 18.8 - - - +
147D LEU* 4.2 18.2 - - + -
148D LEU 3.2 16.2 + - - +
149D CYS* 3.5 5.4 - - - +
150D LYS 3.1 0.4 - - - -
151D PRO* 1.3 76.9 - - - +
153D GLU* 1.3 57.4 + - + +
155D LEU* 3.4 11.7 + - + +
161D MSE 4.4 7.0 - - - -
176D VAL* 3.9 15.7 - - + -
178D LYS* 2.6 62.3 + - + +
179D LYS 3.2 14.4 + - - -
180D GLY 2.5 29.0 + - - -
181D ASN* 4.6 6.7 - - - -
183D PRO* 2.8 40.1 - - + +
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Residues in contact with GLU 153 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150C LYS* 2.5 36.3 + - - +
153C GLU* 2.9 30.9 - - - +
200C TYR* 5.2 2.2 - - - +
133D LYS* 4.4 18.2 + - - +
149D CYS* 3.0 26.9 + - - +
150D LYS* 3.5 19.9 + - - +
152D TYR* 1.3 75.0 - - + +
154D GLN* 1.3 62.1 + - + +
155D LEU 3.0 8.8 + - - +
178D LYS* 2.8 21.1 + - - +
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Residues in contact with GLN 154 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75D LEU* 3.5 12.8 - - - +
127D LEU 2.8 27.1 + - - -
128D GLY* 4.1 0.4 - - - -
129D TYR 2.7 33.3 + - - +
130D GLU* 3.5 32.4 + - - +
133D LYS* 2.9 35.6 - - + +
134D PRO* 3.8 1.3 - - - +
135D TYR* 3.1 25.0 + - + -
150D LYS* 2.9 25.6 + - - +
151D PRO* 3.2 6.5 + - + +
153D GLU* 1.3 77.4 - - + +
155D LEU* 1.3 57.5 + - - +
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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