Contacts of the helix formed by residues 114 - 124 (chain A) in PDB entry 3VZC
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 ASN 114 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79A SER 3.2 23.4 - - - +
80A GLY* 3.7 2.9 - - - -
81A ASP* 3.8 4.3 - - - +
109A PRO* 3.5 30.7 - - + +
110A ALA 3.5 3.6 + - - -
111A GLY 3.3 24.3 + - - -
112A SER* 3.7 7.1 - - - +
113A GLY* 1.3 76.9 - - - +
115A ALA* 1.3 58.4 + - - +
116A LEU 3.3 2.2 - - - -
117A ALA* 4.0 6.5 - - + -
118A ALA* 2.9 29.2 + - - +
134A LEU* 4.5 8.3 - - + +
269A GLY* 5.3 0.8 - - - -
270A SER* 4.5 14.7 + - - +
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Residues in contact with ALA 115 (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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81A ASP* 2.9 14.7 + - - +
113A GLY* 3.6 0.6 - - - -
114A ASN* 1.3 74.1 - - - +
116A LEU* 1.3 55.9 + - - +
118A ALA* 3.3 3.1 + - - +
119A SER* 2.7 39.2 + - - -
167A LEU* 3.5 15.9 - - + -
267A HIS* 3.2 20.7 - - - +
268A LEU 3.3 22.7 - - - +
269A GLY* 3.9 10.0 - - - +
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Residues in contact with LEU 116 (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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81A ASP* 2.9 18.7 + - + +
84A MET* 3.7 35.7 - - + -
107A SER* 4.3 8.7 - - - +
115A ALA* 1.3 77.5 - - - +
117A ALA* 1.3 63.6 + - - +
119A SER* 3.2 5.3 + - - -
120A LEU* 3.1 29.4 + - + +
166A VAL* 4.1 18.2 - - + +
167A LEU* 3.9 9.3 - - + +
265A HIS* 3.5 40.4 - - + +
359A PHE* 5.4 1.1 - - + -
361A MET* 3.8 30.1 - - + -
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Residues in contact with ALA 117 (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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81A ASP* 4.6 0.2 + - - -
107A SER* 4.0 20.7 + - - +
109A PRO* 3.8 32.1 - - + -
114A ASN* 3.5 10.1 + - + +
115A ALA 3.4 0.6 - - - -
116A LEU* 1.3 78.6 - - - +
118A ALA* 1.3 57.8 + - - +
120A LEU* 3.4 5.4 + - - +
121A ASN* 3.0 29.8 + - - +
134A LEU* 4.5 1.8 - - + -
138A CYS* 3.7 20.6 - - - -
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Residues in contact with ALA 118 (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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114A ASN 2.9 18.1 + - - +
115A ALA 3.5 4.9 - - - +
117A ALA* 1.3 76.9 - - - +
119A SER* 1.3 57.4 + - - +
121A ASN* 3.3 9.0 + - - +
122A HIS* 2.9 28.4 + - - +
128A GLN* 6.2 0.4 - - + -
129A VAL 6.0 0.2 - - - +
134A LEU* 4.3 8.6 - - + +
267A HIS* 4.0 11.2 + - + -
269A GLY 4.0 8.1 - - - +
270A SER* 3.6 31.0 - - - +
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Residues in contact with SER 119 (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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115A ALA 2.7 22.1 + - - -
116A LEU 3.2 4.9 + - - -
118A ALA* 1.3 74.3 - - - +
120A LEU* 1.3 52.1 + - - +
122A HIS* 3.2 5.0 + - - +
123A TYR* 2.7 46.5 + - - -
265A HIS* 3.3 26.8 - - - +
266A SER* 3.6 17.5 - - - -
267A HIS* 3.1 22.3 + - - +
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Residues in contact with LEU 120 (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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106A CYS* 6.3 0.2 - - - -
107A SER* 4.6 17.7 - - - +
116A LEU* 3.1 22.2 + - + +
117A ALA* 3.8 5.6 - - - +
119A SER* 1.3 74.3 - - - +
121A ASN* 1.3 65.4 + - - +
123A TYR* 3.3 22.6 + - + +
124A ALA* 3.1 24.4 + - - +
138A CYS* 5.6 2.5 - - - -
141A LEU* 3.9 10.8 - - + +
150A MET* 4.3 5.2 - - - -
265A HIS* 5.5 0.7 - - + -
279A ARG* 6.0 0.4 - - - +
361A MET* 3.7 38.1 - - + -
362A VAL 3.9 14.1 - - - +
363A SER* 3.5 30.1 - - - +
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Residues in contact with ASN 121 (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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117A ALA 3.0 17.9 + - - +
118A ALA 3.3 5.8 + - - +
120A LEU* 1.3 74.8 - - - +
122A HIS* 1.3 60.7 + - - +
124A ALA* 3.4 8.0 + - - +
125A GLY 3.5 0.3 + - - -
126A TYR* 3.0 52.6 + - - +
127A GLU 3.0 24.8 - - - +
128A GLN* 4.5 2.1 - - - -
129A VAL* 3.9 7.1 + - - +
134A LEU* 3.7 19.9 - - + +
137A ASN* 3.2 24.0 - - - +
138A CYS* 4.6 3.3 - - - -
141A LEU* 4.4 8.6 - - - +
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Residues in contact with HIS 122 (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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118A ALA 2.9 8.2 + - - +
119A SER 3.3 6.7 - - - +
121A ASN* 1.3 72.9 + - - +
123A TYR* 1.3 76.8 + + - +
124A ALA 3.0 2.0 - - - -
125A GLY* 3.0 15.6 + - - -
126A TYR 4.3 11.7 - - - -
128A GLN* 5.9 1.8 - - + -
266A SER* 3.5 16.6 + - - -
267A HIS* 3.6 24.7 - + + -
273A PHE* 3.5 37.9 - + - -
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Residues in contact with TYR 123 (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 MET* 5.4 7.3 - - - +
119A SER* 2.7 29.9 + - - -
120A LEU* 3.3 26.4 + - + +
122A HIS* 1.3 82.9 - + - +
124A ALA* 1.3 61.6 - - - +
125A GLY* 3.1 1.8 + - - -
150A MET* 5.0 0.4 - - + -
264A LEU 4.3 1.0 + - - -
265A HIS* 2.7 55.0 + + - +
266A SER* 3.2 22.9 + - - -
279A ARG* 3.9 64.8 - - + +
280A CYS 5.6 0.7 + - - -
363A SER* 5.7 2.5 - - - -
364A GLY 3.8 9.8 - - - +
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Residues in contact with ALA 124 (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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120A LEU 3.1 16.2 + - - +
121A ASN 3.7 6.5 - - - +
122A HIS 3.0 1.0 - - - -
123A TYR* 1.3 76.6 - - - +
125A GLY* 1.3 58.7 + - - +
126A TYR* 3.6 12.3 - - + -
141A LEU* 3.8 25.4 - - + -
364A GLY 3.4 29.6 + - - +
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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