Contacts of the strand formed by residues 150 - 155 (chain A) in PDB entry 3VG1
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 PHE 150 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A THR* 4.0 8.5 - - + -
121A LEU* 3.9 39.3 - - + -
137A PHE* 3.9 28.3 - + + -
149A LEU* 1.3 78.0 - - - +
151A SER* 1.3 66.6 + - - +
152A LEU* 4.2 11.4 - - + -
162A MET* 4.9 3.6 - - + -
163A ILE 3.2 13.5 - - - +
164A ILE* 4.1 12.1 - - + -
165A GLY 4.4 0.4 - - - +
166A GLY 5.1 2.5 - - - -
187A TYR* 3.4 24.9 - - - -
332A VAL* 3.7 3.0 - - - +
333A PHE* 2.8 66.7 + + + -
335A ARG* 4.0 7.6 - - - -
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Residues in contact with SER 151 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150A PHE* 1.3 76.0 - - - +
152A LEU* 1.3 67.0 + - - +
153A GLN 4.3 0.4 - - - -
161A SER 4.5 0.2 - - - -
162A MET* 3.3 6.4 - - - +
163A ILE* 2.8 48.1 + - - +
166A GLY 3.8 5.9 + - - -
167A ILE* 5.5 0.2 - - - -
330A TYR* 2.6 42.8 + - - -
331A VAL 3.2 11.0 - - - -
332A VAL* 4.2 8.7 - - - -
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Residues in contact with LEU 152 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A LEU* 4.4 8.7 - - + -
31A VAL* 4.0 17.9 - - + -
33A THR* 3.8 29.2 - - + -
150A PHE* 4.2 8.7 - - + -
151A SER* 1.3 77.7 - - - +
153A GLN* 1.3 60.8 + - - +
154A LEU* 3.8 9.9 + - + +
161A SER 3.4 2.2 - - - +
162A MET* 3.5 35.9 - - + -
217A SER* 4.0 12.6 - - - +
326A MET* 3.9 20.6 - - + +
329A PHE 3.7 3.5 - - - +
330A TYR* 4.4 2.2 - - - -
331A VAL* 2.9 35.3 + - - +
333A PHE* 3.9 9.0 - - + -
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Residues in contact with GLN 153 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A ASP* 4.8 3.5 - - - +
152A LEU* 1.3 72.2 - - - +
154A LEU* 1.3 60.1 + - - +
155A CYS* 3.8 17.0 - - - -
160A GLY* 2.9 9.5 - - - -
161A SER* 2.8 56.7 + - - +
171A LEU* 3.7 36.0 + - + +
329A PHE 4.0 4.7 - - - +
330A TYR* 4.1 12.8 - - + -
345A SER* 3.9 19.3 - - - -
346A ALA* 3.8 20.2 - - - +
347A CYS* 3.9 11.8 - - - +
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Residues in contact with LEU 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A LEU* 3.6 28.5 - - + -
14A TYR* 3.7 41.3 - - + +
31A VAL* 6.2 1.6 - - + -
152A LEU* 3.8 19.6 + - + -
153A GLN* 1.3 74.0 - - - +
155A CYS* 1.3 60.7 + - - +
159A GLY 4.0 2.2 - - - -
217A SER* 4.3 12.3 - - - +
323A ALA* 4.4 8.7 - - + -
326A MET* 4.0 36.5 + - + +
327A GLU* 3.2 11.5 - - + +
328A GLY 3.1 24.6 + - - -
329A PHE 4.4 3.7 + - - +
347A CYS* 3.8 2.6 - - - -
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Residues in contact with CYS 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A TYR* 2.9 14.9 + - - -
153A GLN* 3.8 21.5 - - - -
154A LEU* 1.3 76.3 - - - +
156A GLY* 1.3 66.0 + - - +
158A VAL* 3.1 17.5 - - - +
159A GLY 2.9 20.1 + - - +
160A GLY* 4.1 6.1 - - - -
327A GLU* 4.3 0.4 - - - -
328A GLY 4.8 0.4 - - - +
347A CYS* 2.0 50.5 - - + -
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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