Contacts of the helix formed by residues 116 - 128 (chain A) in PDB entry 2ZV6
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 116 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114A LEU 4.6 2.0 - - - +
115A PHE* 1.3 70.5 - - - +
117A GLN* 1.3 65.9 + - - +
118A GLU* 4.3 15.3 - - + +
119A TYR* 3.1 17.1 + - - +
120A LEU* 3.3 10.4 + - - +
315A SER 5.4 0.2 - - - +
316A GLY* 3.9 17.9 - - - +
317A MET 2.9 6.5 + - - -
318A THR 3.3 32.8 - - - +
319A GLY* 3.4 14.4 - - - +
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Residues in contact with GLN 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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115A PHE 3.4 3.7 + - - +
116A LEU* 1.3 68.8 - - - +
118A GLU* 1.3 68.4 + - - +
120A LEU* 2.9 33.6 + - - +
121A ASP* 2.9 37.9 + - - +
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Residues in contact with GLU 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A LEU* 3.1 15.1 - - + +
117A GLN* 1.3 76.7 - - - +
119A TYR* 1.3 65.3 + - - +
121A ASP* 2.9 29.2 + - - +
122A ALA* 3.3 9.4 + - - +
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Residues in contact with TYR 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A MET 2.8 22.6 + - - -
43A LEU* 3.6 6.3 - - + -
44A GLY* 3.1 39.0 - - - -
107A LEU* 3.4 10.6 - - + +
115A PHE* 4.5 3.8 - + - -
116A LEU* 3.1 10.6 + - - +
118A GLU* 1.3 77.6 - - - +
120A LEU* 1.3 66.9 + - + +
121A ASP 3.0 1.2 + - - -
122A ALA* 3.1 15.3 + - + +
123A ILE* 3.2 34.2 + - + +
131A VAL* 3.8 28.9 - - + -
316A GLY 3.4 19.0 + - - +
317A MET* 3.3 43.5 - - + +
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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
----------------------------------------------------------
115A PHE* 3.8 30.3 - - + +
116A LEU 3.6 4.5 - - - +
117A GLN* 2.9 39.3 + - - +
119A TYR* 1.3 76.6 - - + +
121A ASP* 1.3 58.6 + - - +
123A ILE* 3.5 6.3 - - + +
124A LYS* 3.1 30.0 + - - +
130A SER* 3.9 9.6 + - - +
131A VAL* 3.5 43.5 - - + +
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Residues in contact with ASP 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A GLN* 2.9 31.9 + - - +
118A GLU* 2.9 20.8 + - - +
120A LEU* 1.3 76.9 - - - +
122A ALA* 1.3 60.8 + - - +
124A LYS* 3.8 2.8 - - - +
125A LYS* 2.9 33.2 + - - +
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Residues in contact with ALA 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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43A LEU* 3.2 30.3 - - + -
118A GLU* 3.3 10.8 + - - +
119A TYR* 3.1 9.5 + - + +
121A ASP* 1.3 79.3 - - - +
123A ILE* 1.3 53.6 + - - +
125A LYS* 4.3 2.7 - - - +
126A PHE* 2.7 53.9 + - + +
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Residues in contact with ILE 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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40A MET* 3.8 26.2 - - + +
43A LEU* 3.4 22.4 - - + -
119A TYR* 3.5 35.7 - - + +
120A LEU* 3.5 13.5 - - - +
122A ALA* 1.3 73.4 - - - +
124A LYS* 1.3 64.0 + - - +
127A TYR* 2.6 39.4 + - - +
128A GLN 3.1 1.2 + - - -
129A THR* 3.4 5.4 - - + +
130A SER* 3.2 36.6 - - - +
131A VAL* 3.7 21.3 - - + +
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Residues in contact with LYS 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 17.2 + - - +
121A ASP* 3.8 3.4 - - - +
123A ILE* 1.3 81.3 - - - +
125A LYS* 1.3 59.9 + - - +
128A GLN* 2.7 57.2 + - + +
129A THR* 3.0 17.1 + - - +
130A SER* 3.7 15.0 + - - +
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Residues in contact with LYS 125 (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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86A GLN* 2.9 29.2 + - - +
121A ASP 2.9 20.1 + - - +
122A ALA* 3.6 2.9 - - - +
124A LYS* 1.3 79.3 - - - +
126A PHE* 1.3 92.1 + - + +
128A GLN* 2.9 18.5 + - - +
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Residues in contact with PHE 126 (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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43A LEU* 4.8 4.7 - - + -
82A HIS* 3.0 42.6 - + + +
83A HIS* 3.7 19.5 - + + -
86A GLN* 2.9 48.7 + - + +
89A LEU* 4.1 2.8 - - - +
122A ALA* 2.7 44.1 + - + +
125A LYS* 1.3 106.9 - - + +
127A TYR* 1.3 78.7 + - + +
128A GLN* 3.6 1.6 + - - -
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Residues in contact with TYR 127 (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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36A SER* 3.1 47.3 - - - -
37A ALA* 5.6 0.2 - - - -
39A GLY* 3.2 22.2 - - - -
40A MET* 3.6 14.8 - - + -
43A LEU* 4.6 3.8 - - + -
81A VAL* 5.0 0.5 - - - +
82A HIS* 2.7 33.6 + - + -
85A PHE* 3.8 25.6 - + + +
89A LEU* 4.1 17.9 - - + +
105A ASN* 5.6 2.9 - - - +
123A ILE* 2.6 25.2 + - - +
126A PHE* 1.3 92.6 - - + +
128A GLN* 1.3 76.1 + - - +
129A THR* 2.8 24.3 + - + +
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Residues in contact with GLN 128 (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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86A GLN* 3.6 19.2 - - - +
89A LEU* 3.7 15.5 - - + +
90A THR* 4.3 12.2 - - - +
93A ASN* 3.5 26.7 + - - +
124A LYS* 2.7 36.4 + - + +
125A LYS 2.9 24.0 + - - +
126A PHE 4.0 0.8 - - - +
127A TYR* 1.3 81.8 - - - +
129A THR* 1.3 56.3 + - - +
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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