Contacts of the helix formed by residues 114 - 130 (chain A) in PDB entry 1ZY3
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 MET 114 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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109A SER* 2.7 32.3 + - - +
110A VAL* 4.5 0.4 + - - +
112A LYS* 4.2 13.2 - - + +
113A GLU* 1.3 74.3 - - - +
115A GLU* 1.3 65.2 + - - +
116A VAL* 3.0 20.6 - - + +
117A LEU* 3.1 51.6 + - + +
118A VAL* 3.2 14.9 + - - +
120A GLN* 6.1 0.4 - - - +
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Residues in contact with GLU 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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109A SER 5.1 0.2 - - - -
110A VAL* 5.0 13.4 - - - +
113A GLU* 3.6 3.4 - - - +
114A MET* 1.3 76.2 - - - +
116A VAL* 1.3 58.0 + - + +
118A VAL* 3.6 27.3 - - - +
119A GLY* 2.8 31.9 + - - -
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Residues in contact with VAL 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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113A GLU 5.9 0.4 - - - +
114A MET* 3.0 19.3 - - + -
115A GLU* 1.3 81.4 - - + +
117A LEU* 1.3 61.2 + - - +
119A GLY* 3.6 1.7 + - - -
120A GLN* 3.2 41.7 + - - +
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Residues in contact with LEU 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A GLN* 4.1 23.6 - - + -
76A GLN* 4.0 23.8 - - - +
105A LEU* 5.9 0.7 - - + -
109A SER* 3.6 21.8 - - - +
112A LYS* 6.2 1.1 - - - +
114A MET* 3.1 32.3 + - + +
116A VAL* 1.3 76.3 - - - +
118A VAL* 1.3 61.4 - - - +
120A GLN* 3.0 20.0 + - + +
121A VAL* 2.8 43.8 + - + +
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Residues in contact with VAL 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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106A CYS* 3.8 24.2 - - + +
109A SER* 3.5 21.5 - - - -
110A VAL* 3.9 16.2 - - + -
114A MET 3.2 15.5 - - - +
115A GLU* 3.2 25.8 + - - +
117A LEU* 1.3 76.8 - - - +
119A GLY* 1.3 57.8 + - - +
121A VAL* 3.2 7.3 + - - +
122A GLN* 2.9 51.0 + - + +
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Residues in contact with GLY 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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115A GLU* 2.8 18.4 + - - -
116A VAL 4.1 2.0 - - - -
118A VAL* 1.3 76.6 - - - +
120A GLN* 1.3 57.3 + - - +
122A GLN* 4.0 5.1 - - - +
123A GLU* 3.0 30.9 + - - +
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Residues in contact with GLN 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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76A GLN* 4.8 5.5 + - - -
114A MET* 6.1 0.6 - - - +
116A VAL* 3.2 37.0 + - - +
117A LEU* 3.0 25.9 + - + +
119A GLY* 1.3 74.6 - - - +
121A VAL* 1.3 61.1 + - + +
123A GLU* 3.3 10.6 + - - +
124A TRP* 2.9 45.8 + - + +
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Residues in contact with VAL 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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75A GLN* 3.3 33.4 - - + +
79A THR* 4.5 6.7 - - + +
102A GLY* 4.6 5.4 - - - -
105A LEU* 5.9 1.6 - - + -
106A CYS* 3.9 22.7 - - - -
109A SER* 6.1 0.2 - - - +
117A LEU* 2.8 36.1 + - + +
118A VAL* 3.6 7.0 - - - +
120A GLN* 1.3 76.6 - - + +
122A GLN* 1.3 57.8 + - - +
124A TRP* 3.2 12.7 + - + +
125A MET* 2.9 46.7 + - + +
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Residues in contact with GLN 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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10A ARG* 5.8 8.3 - - + -
13A VAL* 5.0 18.9 - - + +
17A VAL* 6.0 0.3 - - - +
102A GLY 5.1 1.4 + - - -
103A ALA* 6.1 0.2 - - - +
106A CYS* 3.0 33.7 - - - +
118A VAL* 2.9 29.8 + - + +
119A GLY* 4.0 6.1 - - - +
121A VAL* 1.3 74.7 - - - +
123A GLU* 1.3 58.0 + - - +
125A MET* 3.2 29.0 + - + +
126A VAL* 2.9 40.5 + - + +
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Residues in contact with GLU 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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119A GLY 3.0 20.9 + - - +
120A GLN* 3.5 9.5 - - - +
122A GLN* 1.3 77.2 - - - +
124A TRP* 1.3 69.0 + - + +
126A VAL* 3.5 5.0 + - - +
127A ALA* 3.0 31.2 + - + +
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Residues in contact with TRP 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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75A GLN* 6.2 1.6 - - - -
76A GLN* 3.8 42.4 - - + -
80A GLN* 4.8 11.9 - - - -
120A GLN* 2.9 30.7 + - + +
121A VAL* 3.6 9.9 - - + +
123A GLU* 1.3 85.9 + - - +
125A MET* 1.3 60.1 + - + +
127A ALA* 3.3 8.1 + - + +
128A TYR* 2.8 32.8 + - - +
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Residues in contact with MET 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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79A THR* 4.8 6.1 - - + -
98A PHE* 4.0 46.2 - - + +
99A PHE* 4.5 19.3 - - + +
102A GLY* 4.3 13.5 - - - -
103A ALA 5.6 0.2 - - - +
121A VAL* 2.9 29.9 + - + +
122A GLN* 3.4 31.0 - - + +
124A TRP* 1.3 77.4 - - + +
126A VAL* 1.3 59.9 + - + +
128A TYR* 3.7 4.8 - - - +
129A LEU* 2.9 45.7 + - + +
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Residues in contact with VAL 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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10A ARG* 4.4 30.7 - - + +
122A GLN* 2.9 25.9 + - + +
123A GLU* 3.9 5.4 - - - +
125A MET* 1.3 75.6 - - + +
127A ALA* 1.3 62.9 + - - +
129A LEU* 3.3 9.5 + - + +
130A GLU* 3.0 39.1 + - + +
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Residues in contact with ALA 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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123A GLU* 3.0 19.5 + - + +
124A TRP* 3.6 11.4 - - + +
126A VAL* 1.3 78.8 - - - +
128A TYR* 1.3 55.1 - - - +
130A GLU* 3.2 5.1 + - - -
131A THR* 2.6 39.9 + - - +
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Residues in contact with TYR 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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80A GLN* 5.2 5.2 - - - -
83A ASP* 2.6 49.1 + - + +
86A PHE* 4.6 4.3 - - + +
87A GLN* 4.1 3.1 + - - +
98A PHE* 4.1 17.7 - + + -
124A TRP 2.8 21.9 + - - +
125A MET* 3.7 5.6 - - - +
127A ALA* 1.3 72.6 - - - +
129A LEU* 1.3 60.9 - - - +
131A THR* 4.5 3.8 - - - -
132A ARG* 3.0 59.8 + - + +
133A LEU* 3.1 44.8 + - + +
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Residues in contact with LEU 129 (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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95A LEU* 5.3 6.7 - - + -
98A PHE* 5.2 10.1 - - + -
125A MET* 2.9 36.1 + - + +
126A VAL* 3.7 8.7 - - + +
127A ALA 3.3 0.2 - - - -
128A TYR* 1.3 76.5 - - - +
130A GLU* 1.3 62.6 + - + +
131A THR 3.4 0.4 - - - -
133A LEU* 3.3 34.4 - - + +
134A ALA* 3.1 23.0 + - - -
137A ILE* 4.1 25.2 - - + +
143A TRP* 5.9 7.9 - - + -
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Residues in contact with GLU 130 (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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126A VAL* 3.0 31.6 + - + +
127A ALA* 3.2 4.2 + - - +
129A LEU* 1.3 81.2 - - + +
131A THR* 1.3 61.0 + - - +
134A ALA* 3.7 15.7 - - - +
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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