Contacts of the helix formed by residues 129 - 138 (chain D) in PDB entry 3ZWG
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 ASP 129 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51D TYR* 3.7 18.7 - - + +
89D VAL* 5.5 0.2 - - - +
127D ARG* 4.1 8.5 - - + +
128D ALA* 1.3 76.4 - - - +
130D GLN* 1.3 69.3 + - - +
131D ARG* 3.4 18.1 - - - +
132D MET* 2.7 32.0 + - - +
133D TYR 3.0 9.0 + - - -
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Residues in contact with GLN 130 (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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51D TYR* 2.8 48.8 + - + +
53D ARG* 3.4 27.7 + - - +
129D ASP* 1.3 73.9 - - - +
131D ARG* 1.3 64.2 + - - +
133D TYR* 3.2 12.1 + - - +
134D GLU* 2.7 58.0 + - - +
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Residues in contact with ARG 131 (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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129D ASP* 3.4 19.2 - - - +
130D GLN* 1.3 81.0 - - - +
132D MET* 1.3 64.2 + - + +
134D GLU* 3.3 24.8 + - - +
135D GLU* 3.2 44.7 + - - +
139D HIS* 6.2 1.8 - - - -
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Residues in contact with MET 132 (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 VAL* 3.8 15.9 - - + -
91D ALA* 5.0 1.6 - - - -
99D THR* 4.9 1.3 - - + -
101D ALA* 3.8 24.7 - - + -
122D TYR* 4.0 27.4 - - + +
126D LYS* 3.7 31.0 - - + +
127D ARG 3.6 19.7 - - - +
128D ALA* 4.0 9.2 - - - -
129D ASP* 2.7 27.8 + - - +
131D ARG* 1.3 71.4 - - + +
133D TYR* 1.3 64.5 + - - +
135D GLU* 3.2 9.9 + - - +
136D LEU* 2.9 36.6 + - + +
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Residues in contact with TYR 133 (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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51D TYR* 4.0 11.0 - - + -
53D ARG* 3.8 31.3 + - + +
87D VAL* 3.4 33.6 - - + +
88D GLY 5.4 1.1 - - - -
89D VAL* 3.8 19.6 - - + +
103D LEU* 4.2 12.1 - - + -
105D SER* 5.3 0.2 + - - -
129D ASP 3.0 9.3 + - - +
130D GLN* 3.4 28.9 - - - +
132D MET* 1.3 78.5 - - - +
134D GLU* 1.3 64.4 + - - +
136D LEU* 3.9 1.2 - - - +
137D TYR* 2.9 59.7 + + + +
138D TYR* 4.2 21.2 + + - -
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Residues in contact with GLU 134 (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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130D GLN* 2.7 52.3 + - - +
131D ARG* 3.5 25.9 + - - +
132D MET 3.2 0.2 - - - -
133D TYR* 1.3 79.8 - - + +
135D GLU* 1.3 65.1 + - + +
138D TYR* 2.9 48.1 + - + -
139D HIS* 3.6 12.5 + - + -
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Residues in contact with GLU 135 (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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122D TYR* 2.7 42.6 + - - +
126D LYS* 5.9 0.9 - - - -
131D ARG* 3.2 45.5 + - - +
132D MET* 3.2 11.9 + - - +
134D GLU* 1.3 80.7 - - + +
136D LEU* 1.3 63.6 + - - +
139D HIS* 3.2 17.8 + - + +
140D ARG* 3.0 37.9 + - + +
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Residues in contact with LEU 136 (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 VAL* 3.8 30.1 - - + -
101D ALA* 4.0 12.6 - - + +
103D LEU* 3.5 31.9 - - + +
118D ASN* 2.8 36.1 + - + +
120D ARG* 3.5 33.2 - - + +
122D TYR* 3.8 13.9 - - + +
132D MET* 2.9 29.6 + - + +
133D TYR* 4.0 3.4 - - - +
135D GLU* 1.3 74.0 - - - +
137D TYR* 1.3 60.3 + - - +
140D ARG* 4.1 5.9 - - + +
142D PRO* 3.5 8.8 - - - +
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Residues in contact with TYR 137 (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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103D LEU* 3.8 13.7 - - + -
105D SER* 3.5 33.4 + - - -
107D PRO* 5.9 0.3 - - - +
113D TYR* 4.8 16.3 - - - +
114D SER 5.0 1.0 + - - -
116D TRP* 4.0 30.2 + + + -
133D TYR* 2.9 50.9 + + + +
134D GLU 4.2 0.7 - - - +
136D LEU* 1.3 78.1 - - - +
138D TYR* 1.3 90.5 + + + +
142D PRO* 3.5 20.4 - - + +
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Residues in contact with TYR 138 (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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53D ARG* 5.5 3.8 + - - -
130D GLN* 6.1 0.2 - - - -
133D TYR* 4.2 18.4 + + - -
134D GLU* 2.9 46.8 + - + -
137D TYR* 1.3 107.1 - + - +
139D HIS* 1.3 79.8 + + + +
140D ARG 3.4 1.6 + - - -
141D SER* 3.7 9.7 + - - -
142D PRO* 4.7 0.3 - - - +
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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