Contacts of the helix formed by residues 109 - 128 (chain A) in PDB entry 2ZU6
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 109 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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107A ALA* 3.3 2.3 - - - +
108A PRO* 1.3 94.4 - - + +
110A ARG* 1.3 65.3 + - - +
111A GLU* 3.8 5.9 + - - +
112A LEU* 3.0 19.1 + - - +
113A ALA* 3.0 21.1 + - - +
158A THR* 3.8 11.7 - - - -
190A ARG* 3.7 19.5 - - - +
210B GLU* 3.4 36.8 - - - +
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Residues in contact with ARG 110 (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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109A THR* 1.3 72.2 - - - +
111A GLU* 1.3 64.1 + - - +
113A ALA* 3.1 7.8 + - - +
114A GLN* 2.9 20.7 + - - +
134A CYS 4.7 2.7 - - - +
135A ILE* 3.3 56.1 + - + +
136A GLY 5.6 1.0 - - - -
137A GLY* 5.6 3.2 - - - +
158A THR* 3.7 4.4 - - + +
161A ARG* 4.5 2.4 - - - +
206B SER* 5.2 9.7 + - - -
210B GLU* 2.9 29.3 + - - +
250B LEU* 4.3 21.8 - - - +
253B ASP* 2.6 40.1 + - - +
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Residues in contact with GLU 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A THR* 3.1 6.6 + - - +
110A ARG* 1.3 78.3 - - - +
112A LEU* 1.3 64.6 + - - +
114A GLN* 3.1 17.1 + - + +
115A GLN* 3.2 32.7 + - + +
173B GLN* 3.3 22.7 - - - +
207B LEU* 6.4 1.3 - - - -
210B GLU* 3.8 6.5 + - - +
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Residues in contact with LEU 112 (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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79A GLY* 5.7 0.7 - - - -
81A GLY* 5.1 0.7 - - - -
82A LYS* 3.7 20.4 - - + +
107A ALA* 3.8 9.4 - - + -
108A PRO* 3.5 30.7 - - + -
109A THR* 3.0 19.5 + - - +
111A GLU* 1.3 77.7 - - - +
113A ALA* 1.3 61.9 + - - +
115A GLN* 3.2 23.5 + - - +
116A ILE* 3.0 28.3 + - + +
182A ASP* 3.5 22.9 - - - +
183A GLU* 3.8 17.0 - - - +
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Residues in contact with ALA 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A ALA* 4.1 6.3 - - + +
109A THR 3.0 11.5 + - - +
110A ARG* 3.3 13.5 - - - +
112A LEU* 1.3 78.4 - - - +
114A GLN* 1.3 60.7 + - - +
116A ILE 3.4 0.5 + - - -
117A GLN* 3.0 20.4 + - - +
133A ALA* 3.8 6.2 - - + +
135A ILE* 4.7 2.5 - - + -
156A VAL* 3.6 34.3 - - + +
157A GLY* 3.9 19.7 - - - -
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Residues in contact with GLN 114 (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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110A ARG 2.9 12.1 + - - +
111A GLU* 3.1 10.1 + - + +
113A ALA* 1.3 70.0 - - - +
115A GLN* 1.3 57.8 + - + +
117A GLN* 3.1 21.1 + - - -
118A LYS* 2.6 56.5 + - - +
132A HIS* 6.0 1.4 - - - -
133A ALA* 3.9 17.5 - - - +
135A ILE* 4.3 25.9 - - + +
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Residues in contact with GLN 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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82A LYS* 3.2 47.9 + - + +
111A GLU* 3.2 28.6 + - + +
112A LEU* 3.5 18.1 - - - +
114A GLN* 1.3 76.0 - - + +
116A ILE* 1.3 66.5 + - - +
118A LYS* 3.0 19.7 + - - +
119A VAL* 3.0 27.7 + - + +
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Residues in contact with ILE 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 GLY* 3.2 32.5 + - - +
82A LYS* 4.8 0.2 - - - +
86A PHE* 3.9 17.3 - - + -
90A ILE* 5.9 0.2 - - + -
105A VAL* 4.3 16.6 - - + -
107A ALA* 4.1 12.6 - - + -
112A LEU* 3.0 31.2 + - + +
113A ALA 3.7 6.1 - - - +
115A GLN* 1.3 75.3 - - - +
117A GLN* 1.3 63.9 + - - +
119A VAL* 3.3 2.4 + - - +
120A VAL* 3.0 36.2 + - + +
131A CYS* 6.0 0.2 - - - -
154A ILE* 6.5 0.7 - - + -
156A VAL* 4.2 15.9 - - + -
182A ASP* 3.4 24.7 - - - +
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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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113A ALA 3.0 14.7 + - - +
114A GLN* 3.1 19.7 + - - +
116A ILE* 1.3 75.8 - - - +
118A LYS* 1.3 81.8 + - - +
119A VAL 3.1 0.2 + - - -
120A VAL* 3.2 1.2 + - - +
121A MET* 2.9 44.9 + - - +
131A CYS* 2.7 49.2 + - - +
132A HIS* 4.7 0.4 - - - +
133A ALA* 3.8 20.6 - - + +
156A VAL* 3.9 5.4 - - + -
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Residues in contact with LYS 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 GLN* 2.6 43.7 + - - +
115A GLN* 3.3 21.1 - - - +
117A GLN* 1.3 79.6 + - - +
119A VAL* 1.3 59.8 + - + +
121A MET* 3.5 2.9 + - - +
122A ALA* 3.0 29.1 + - - +
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Residues in contact with VAL 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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81A GLY 5.0 1.6 - - - +
82A LYS* 3.1 38.1 - - + +
83A THR 3.8 18.4 - - - +
84A ALA* 4.3 5.8 - - + +
87A ALA* 4.1 9.4 - - + -
115A GLN* 3.0 18.9 + - + +
116A ILE* 3.8 3.8 - - - +
118A LYS* 1.3 74.9 - - + +
120A VAL* 1.3 68.8 + - + +
122A ALA* 3.4 9.8 + - + +
123A LEU* 3.3 23.6 + - + +
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Residues in contact with VAL 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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81A GLY 5.7 0.2 - - - +
86A PHE* 5.4 2.0 - - + -
87A ALA* 4.0 26.0 - - + +
90A ILE* 5.5 4.5 - - + -
91A LEU* 3.7 22.9 - - + +
116A ILE* 3.0 30.9 + - + +
117A GLN 3.6 3.1 - - - +
119A VAL* 1.3 77.2 - - + +
121A MET* 1.3 64.3 + - + +
123A LEU* 3.1 6.4 + - - +
124A GLY* 2.8 22.9 + - - -
131A CYS* 3.9 29.8 - - + -
154A ILE* 4.1 12.6 - - + -
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Residues in contact with MET 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 GLN* 2.9 46.8 + - - +
118A LYS* 4.0 3.6 - - - +
120A VAL* 1.3 88.7 - - + +
122A ALA* 1.3 68.3 + - - +
123A LEU 3.0 1.8 - - - -
124A GLY* 2.9 24.9 + - - -
125A ASP* 3.3 33.0 + - - +
129A ALA* 3.1 32.1 - - + +
130A SER* 4.2 1.3 - - - -
131A CYS* 3.9 17.9 - - + +
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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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118A LYS 3.0 14.8 + - - +
119A VAL* 3.5 13.9 - - + +
121A MET* 1.3 74.7 - - - +
123A LEU* 1.3 64.1 + - + +
125A ASP* 5.4 0.2 - - - +
126A TYR* 3.3 24.9 + - - -
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Residues in contact with LEU 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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84A ALA* 4.1 21.5 - - + -
87A ALA* 3.8 12.3 - - + -
88A ILE* 3.6 27.8 - - + -
91A LEU* 3.8 16.3 - - + +
119A VAL* 3.3 15.8 + - + +
120A VAL 3.1 8.5 + - - +
121A MET 3.0 0.6 - - - -
122A ALA* 1.3 81.9 - - + +
124A GLY* 1.3 59.5 + - - +
125A ASP 3.7 0.9 - - - -
126A TYR* 3.9 18.6 - - + +
127A MET* 4.2 7.3 - - - +
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Residues in contact with GLY 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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91A LEU* 4.2 9.0 - - - -
120A VAL 2.8 7.6 + - - -
121A MET* 2.9 19.1 + - - -
123A LEU* 1.3 77.4 - - - +
125A ASP* 1.3 60.8 + - - +
126A TYR 3.2 2.6 + - - -
127A MET* 3.4 4.8 + - - -
128A GLY 2.9 7.8 + - - -
129A ALA* 2.8 38.4 + - - +
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Residues in contact with ASP 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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121A MET* 3.3 30.0 + - - +
123A LEU 3.7 0.2 - - - -
124A GLY* 1.3 74.1 - - - +
126A TYR* 1.3 75.9 + - + +
128A GLY* 3.4 9.6 + - - +
129A ALA 4.8 2.3 - - - +
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Residues in contact with TYR 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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122A ALA 3.3 27.3 + - - -
123A LEU* 3.9 15.3 - - + +
124A GLY 3.2 0.2 - - - -
125A ASP* 1.3 84.7 - - + +
127A MET* 1.3 70.8 + - + +
128A GLY* 2.8 2.4 + - - -
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Residues in contact with MET 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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62A ALA* 5.9 5.8 - - + +
91A LEU* 4.4 31.2 - - + +
92A GLN* 4.9 8.7 - - + -
96A LEU* 2.9 41.4 - - + +
123A LEU 4.2 14.8 - - - +
124A GLY* 3.4 7.4 + - - +
126A TYR* 1.3 78.2 - - + +
128A GLY* 1.3 57.7 + - - +
129A ALA* 4.2 5.8 - - + +
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Residues in contact with GLY 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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96A LEU* 4.4 6.7 - - - +
124A GLY 2.9 5.1 + - - -
125A ASP* 3.4 9.1 + - - -
126A TYR 2.8 8.2 + - - -
127A MET* 1.3 75.7 - - - +
129A ALA* 1.3 61.4 + - - +
130A SER* 5.1 1.4 - - - -
153A HIS* 3.9 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