Contacts of the helix formed by residues 114 - 124 (chain D) in PDB entry 3ZNG
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 SER 114 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80D GLY* 3.9 14.4 + - - -
82D LEU* 4.9 1.6 - - - +
109D ALA 3.7 1.1 + - - +
112D SER* 3.0 17.0 + - - -
113D GLY* 1.3 74.0 - - - +
115D TRP* 1.3 64.3 + - - +
116D ASP* 3.6 8.0 + - - +
117D CYS* 3.1 36.1 + - - +
118D VAL* 3.0 24.4 + - - +
149D CYS* 4.4 1.1 - - - -
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Residues in contact with TRP 115 (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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113D GLY 3.0 7.8 + - - +
114D SER* 1.3 71.7 - - - +
116D ASP* 1.3 84.8 + - - +
118D VAL* 4.5 1.3 - - + -
119D ASN* 2.9 61.8 + - + +
148D GLU* 3.5 44.8 + - + +
149D CYS* 4.0 15.3 - - - -
152D SER* 2.8 23.9 + - - -
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Residues in contact with ASP 116 (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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82D LEU* 3.6 33.0 - - + +
114D SER* 3.1 6.8 + - - +
115D TRP* 1.3 105.1 - - - +
117D CYS* 1.3 56.6 + - - +
119D ASN* 3.9 1.7 + - - +
120D LEU* 2.9 31.2 + - - +
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Residues in contact with CYS 117 (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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77D CYS* 5.1 3.1 - - - +
80D GLY* 3.9 16.2 - - - -
82D LEU* 3.9 31.6 - - - -
85D VAL* 4.0 19.7 - - + +
109D ALA* 4.1 14.1 - - + -
114D SER* 3.1 37.4 + - - +
116D ASP* 1.3 74.3 - - - +
118D VAL* 1.3 60.1 + - - +
120D LEU* 3.3 3.3 + - - +
121D LEU* 2.9 37.9 + - + +
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Residues in contact with VAL 118 (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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106D LEU* 4.0 13.6 - - + +
109D ALA* 3.7 28.9 - - + -
110D CYS* 4.0 11.7 - - - -
114D SER 3.0 19.2 + - - +
115D TRP* 3.8 4.3 - - + +
117D CYS* 1.3 76.1 - - - +
119D ASN* 1.3 65.2 + - - +
121D LEU* 3.1 4.5 + - - +
122D LEU* 3.0 44.6 + - + +
149D CYS* 3.8 28.7 - - + +
152D SER* 4.3 12.8 - - - -
153D LEU* 5.0 4.5 - - + -
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Residues in contact with ASN 119 (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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115D TRP* 2.9 58.7 + - + +
116D ASP* 4.0 3.1 - - - +
118D VAL* 1.3 79.0 - - - +
120D LEU* 1.3 57.8 + - - +
122D LEU* 3.3 7.7 + - - +
123D GLN* 3.0 57.0 + - - +
152D SER* 4.3 4.7 + - - +
156D TYR* 4.1 17.5 + - - -
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Residues in contact with LEU 120 (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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82D LEU* 3.8 15.3 - - + -
85D VAL* 3.9 17.0 - - + -
86D LYS* 3.7 34.8 - - + +
89D LEU* 4.0 12.6 - - + -
116D ASP 2.9 20.3 + - - +
117D CYS 3.5 4.9 - - - +
118D VAL 3.2 0.2 - - - -
119D ASN* 1.3 74.2 - - - +
121D LEU* 1.3 65.5 + - - +
123D GLN* 3.3 19.4 + - - +
124D HIS* 3.1 46.7 + - + -
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Residues in contact with LEU 121 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73D LEU* 4.5 6.5 - - + -
77D CYS* 3.7 20.4 - - - -
85D VAL* 4.4 13.0 - - + -
89D LEU* 4.5 8.1 - - + -
95D VAL* 4.6 14.5 - - + +
105D PRO* 3.5 36.1 - - + +
106D LEU* 3.7 13.7 - - + -
109D ALA* 3.6 16.4 - - + -
117D CYS 2.9 21.8 + - - +
118D VAL 3.6 3.6 - - - +
120D LEU* 1.3 76.9 - - - +
122D LEU* 1.3 58.8 + - - +
124D HIS* 2.9 20.5 + - - +
125D GLY 3.1 0.5 + - - -
126D ALA* 3.0 30.0 + - + +
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Residues in contact with LEU 122 (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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106D LEU* 3.9 27.8 - - + -
118D VAL* 3.0 38.2 + - + +
119D ASN* 3.6 5.8 - - - +
121D LEU* 1.3 73.8 - - - +
123D GLN* 1.3 66.4 + - - +
125D GLY* 3.0 13.3 + - - -
126D ALA 4.0 14.7 - - - +
128D VAL* 4.5 9.6 - - + -
152D SER* 3.9 18.6 - - - +
153D LEU* 4.5 2.9 - - + +
156D TYR* 3.6 59.6 - - + -
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Residues in contact with GLN 123 (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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119D ASN* 3.0 45.7 + - - +
120D LEU* 3.4 23.5 - - - +
122D LEU* 1.3 76.5 - - - +
124D HIS* 1.3 64.0 + - + +
125D GLY* 3.1 3.7 + - - -
156D TYR* 3.6 17.9 + - - +
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Residues in contact with HIS 124 (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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89D LEU* 3.8 42.9 + - + +
90D LYS* 6.0 0.4 - - - -
95D VAL* 3.8 25.2 - - + +
120D LEU* 3.1 36.0 + - + +
121D LEU* 2.9 11.2 + - - +
123D GLN* 1.3 81.5 - - + +
125D GLY* 1.3 59.7 + - - +
126D ALA 3.4 0.4 + - - -
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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