Contacts of the helix formed by residues 107 - 118 (chain B) in PDB entry 1Z6T
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 THR 107 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97B SER* 5.8 0.9 - - - +
101B ASP* 3.8 15.0 - - + +
105B GLY* 3.8 6.1 + - - +
106B ILE* 1.3 78.3 - - - +
108B SER* 1.3 59.4 + - - +
109B TYR* 3.4 3.3 - - - +
110B VAL* 3.2 16.2 + - - +
111B ARG* 3.0 34.2 + - - +
171B HIS* 2.8 44.0 + - + +
274C MET* 4.2 26.2 - - + -
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Residues in contact with SER 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72B TYR* 3.4 20.8 - - - -
73B ASN* 3.4 17.2 + - - -
76B LEU* 3.4 20.0 - - - +
88B HIS* 6.4 0.4 - - - -
101B ASP* 4.5 1.8 + - - -
107B THR* 1.3 71.9 - - - +
109B TYR* 1.3 58.9 + - - +
111B ARG* 3.2 9.0 + - - +
112B THR* 2.9 38.4 + - - -
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Residues in contact with TYR 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107B THR* 3.4 9.1 - - - +
108B SER* 1.3 79.2 - - - +
110B VAL* 1.3 66.6 + - + +
112B THR* 3.4 4.5 + - - -
113B VAL* 3.0 49.5 + - + +
171B HIS* 3.4 30.7 - + + +
174B LEU* 4.0 25.9 + - + +
175B GLU* 3.9 30.5 - - + +
178B PHE 4.6 1.9 + - - -
179B PRO* 4.3 16.1 + - - +
274C MET* 5.9 1.1 - - - -
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Residues in contact with VAL 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105B GLY 3.9 5.6 - - - +
106B ILE* 4.1 8.7 - - + -
107B THR* 3.2 19.9 + - - +
109B TYR* 1.3 76.7 - - + +
111B ARG* 1.3 64.3 + - - +
113B VAL 4.0 0.2 - - - -
114B LEU* 3.0 31.6 + - + +
169B ARG* 3.8 38.6 - - + -
170B ASP 3.6 3.6 - - - -
171B HIS* 3.3 40.6 - - + +
174B LEU* 3.9 13.5 - - + -
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Residues in contact with ARG 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73B ASN* 2.9 57.2 + - - +
76B LEU* 4.0 16.6 - - + +
77B HIS* 3.8 28.5 - - + +
101B ASP* 3.1 33.5 + - - -
106B ILE* 3.6 33.3 + - + +
107B THR 3.0 17.6 + - - +
108B SER* 3.2 7.5 + - - +
110B VAL* 1.3 77.1 - - + +
112B THR* 1.3 61.3 + - - +
114B LEU* 4.1 3.6 - - - +
115B CYS* 3.2 25.8 + - - +
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Residues in contact with THR 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B LEU* 3.7 22.7 - - + +
81B LYS* 4.2 22.7 - - + -
108B SER 2.9 18.6 + - - -
109B TYR* 3.8 4.7 - - - -
111B ARG* 1.3 74.3 - - - +
113B VAL* 1.3 68.1 + - + +
114B LEU 3.3 0.2 + - - -
115B CYS* 3.4 3.6 + - - +
116B GLU* 2.9 42.9 + - - +
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Residues in contact with VAL 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109B TYR* 3.0 50.2 + - + +
110B VAL 4.0 2.2 - - - +
112B THR* 1.3 77.2 - - + +
114B LEU* 1.3 67.9 + - + +
116B GLU* 3.4 15.4 + - - +
117B GLY* 3.1 18.7 + - - -
174B LEU* 3.9 27.4 - - + -
178B PHE 5.7 0.4 - - - +
181B GLY* 4.1 24.7 - - - -
182B VAL* 4.3 8.0 - - - +
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Residues in contact with LEU 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110B VAL* 3.0 24.3 + - + +
111B ARG* 4.1 3.1 - - - +
113B VAL* 1.3 75.7 - - + +
115B CYS* 1.3 62.6 + - - +
117B GLY* 3.2 2.3 + - - -
118B GLY 3.1 4.9 + - - -
119B VAL* 3.0 43.8 + - + +
165B ALA 4.2 4.5 - - - +
168B VAL* 3.7 31.2 - - + +
169B ARG* 3.7 57.2 - - + +
174B LEU* 4.0 10.3 - - + -
182B VAL* 4.0 13.2 - - + -
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Residues in contact with CYS 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76B LEU 4.2 6.7 - - - +
77B HIS 4.6 2.7 - - - +
78B GLU 4.2 1.3 - - - -
79B GLY* 3.1 38.1 - - - -
111B ARG 3.2 18.0 + - - +
112B THR* 3.9 3.1 - - - +
114B LEU* 1.3 76.2 - - - +
116B GLU* 1.3 66.6 + - - +
118B GLY* 3.1 13.3 + - - -
119B VAL 4.9 4.9 - - - +
121B GLN* 4.5 7.0 - - - +
428B ARG 3.9 14.4 - - - -
429B ASN* 3.2 31.7 + - - +
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Residues in contact with GLU 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81B LYS* 3.2 43.6 + - + +
112B THR* 2.9 31.9 + - - +
113B VAL* 3.5 14.6 - - - +
115B CYS* 1.3 74.2 - - - +
117B GLY* 1.3 60.9 + - - +
118B GLY 3.3 0.5 + - - -
183B HIS* 4.6 9.6 + - + -
205B ARG* 5.4 2.9 + - - -
208B GLN* 5.9 1.4 + - - -
429B ASN* 5.2 5.2 + - - +
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Residues in contact with GLY 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113B VAL 3.1 12.4 + - - -
114B LEU 3.2 4.4 + - - -
116B GLU* 1.3 74.6 - - - +
118B GLY* 1.3 58.7 + - - +
119B VAL* 3.4 2.7 - - - -
182B VAL* 3.1 28.0 - - - -
183B HIS* 3.6 7.6 - - - -
184B TRP 2.9 26.9 + - - -
205B ARG* 3.3 13.6 + - - -
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Residues in contact with GLY 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114B LEU 3.1 0.2 + - - -
115B CYS* 3.1 17.2 + - - -
116B GLU 3.2 1.6 + - - -
117B GLY* 1.3 78.2 - - - +
119B VAL* 1.3 63.8 + - - +
120B PRO* 3.5 4.2 - - - +
184B TRP* 3.4 17.9 - - - +
205B ARG* 4.7 5.2 - - - -
394B LYS* 5.4 0.5 + - - -
427B ASP* 4.9 6.2 - - - +
429B ASN* 6.2 2.0 - - - -
434B ARG* 5.1 13.5 + - - -
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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