Contacts of the helix formed by residues 122 - 144 (chain A) in PDB entry 1ZYB
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 TYR 122 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24A SER 5.1 0.7 + - - -
25A ILE* 3.6 45.3 - - + +
28A LYS* 4.4 17.7 - - + +
118A ASP* 3.3 30.6 + - + -
119A LEU* 3.1 26.3 + - + +
121A ARG* 1.3 86.0 - - + +
123A ASP* 1.3 69.2 + - - +
124A ILE* 3.3 2.5 - - + +
125A PHE* 3.1 8.1 + - + +
126A ARG* 3.1 22.9 + - - +
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Residues in contact with ASP 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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121A ARG 3.9 2.2 + - - -
122A TYR* 1.3 73.8 - - - +
124A ILE* 1.3 73.4 + - - +
126A ARG* 3.4 28.8 + - - +
127A LEU* 2.9 31.5 + - - +
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Residues in contact with ILE 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A GLN 3.4 25.6 - - - +
16A GLY* 3.4 24.2 - - - +
17A LEU* 4.4 20.9 - - + -
21A ASP* 6.0 1.8 - - - +
122A TYR* 3.3 2.3 - - + +
123A ASP* 1.3 96.6 + - - +
125A PHE* 1.3 62.7 + - - +
127A LEU* 3.8 9.2 - - + +
128A ASN* 2.9 36.2 + - - +
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Residues in contact with PHE 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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13A LEU* 3.6 42.0 - - + +
14A PHE* 3.9 21.1 - + - -
17A LEU* 5.8 5.7 - - + +
25A ILE* 5.4 7.4 - - + -
52A LEU* 4.6 1.3 - - + -
115A VAL* 3.9 6.5 - - + -
119A LEU* 3.2 67.5 - - + +
120A PHE* 3.8 15.5 - + - -
122A TYR* 3.1 10.3 + - + +
124A ILE* 1.3 79.6 - - - +
126A ARG* 1.3 60.0 + - - +
128A ASN* 3.2 9.4 + - - +
129A TYR* 3.0 47.5 + + - +
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Residues in contact with ARG 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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120A PHE* 2.9 55.1 + - + +
121A ARG* 3.3 23.4 + - - +
122A TYR 3.1 9.3 + - - +
123A ASP* 3.5 33.1 - - - +
125A PHE* 1.3 80.0 - - - +
127A LEU* 1.3 67.5 + - + +
129A TYR* 3.4 2.1 + - - +
130A MSE 2.9 28.4 + - + +
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Residues in contact with LEU 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 ASP 2.9 18.9 + - - +
124A ILE* 3.8 10.3 - - + +
126A ARG* 1.3 79.5 - - - +
128A ASN* 1.3 63.2 + - - +
130A MSE 3.3 6.1 + - + +
131A ASN* 2.9 58.8 + - - +
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Residues in contact with ASN 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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12A PRO 3.7 7.4 - - - +
13A LEU 3.0 29.5 + - - +
14A PHE 3.9 0.6 - - - -
15A GLN* 2.8 52.9 + - - +
17A LEU* 5.4 0.8 - - - +
124A ILE* 2.9 32.3 + - - +
125A PHE* 3.5 2.8 - - - +
127A LEU* 1.3 83.1 - - - +
129A TYR* 1.3 62.4 + - - +
131A ASN* 3.3 10.1 + - - +
132A ILE* 3.1 28.4 + - - +
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Residues in contact with TYR 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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13A LEU* 3.7 24.0 - - + +
52A LEU* 3.4 25.8 - - + +
85A PRO* 2.7 42.4 + - + -
88A LEU* 3.3 25.1 - - + +
89A PHE* 3.9 14.1 - + - -
115A VAL* 4.3 2.0 - - + -
120A PHE* 3.6 34.3 - + + -
125A PHE* 3.0 21.4 + + - +
126A ARG* 3.8 4.3 - - - +
128A ASN* 1.3 78.6 - - - +
130A MSE 1.3 60.9 + - - +
132A ILE* 3.2 5.7 + - + +
133A VAL* 3.1 35.7 + - + +
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Residues in contact with MSE 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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120A PHE* 5.5 9.0 - - + -
126A ARG* 2.9 19.8 + - + +
127A LEU* 3.7 8.7 - - + +
129A TYR* 1.3 75.8 - - - +
131A ASN* 1.3 64.5 + - - +
133A VAL* 3.6 5.5 + - - +
134A SER* 2.7 40.9 + - - -
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Residues in contact with ASN 131 (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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15A GLN* 5.7 6.1 - - - +
127A LEU* 2.9 48.4 + - - +
128A ASN* 3.6 11.6 + - - +
129A TYR 3.2 0.2 - - - -
130A MSE 1.3 79.2 - - - +
132A ILE* 1.3 56.6 + - + +
134A SER* 4.0 3.4 - - - -
135A ASN* 3.0 43.5 + - - +
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Residues in contact with ILE 132 (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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12A PRO* 4.2 17.5 - - + -
13A LEU* 3.8 40.8 - - + +
15A GLN* 5.5 1.6 - - - +
82A LEU* 5.2 7.0 - - + -
85A PRO* 3.8 31.2 - - + -
86A GLN* 5.7 0.4 - - - +
128A ASN 3.1 19.8 + - - +
129A TYR* 3.2 8.7 + - + +
131A ASN* 1.3 77.3 - - + +
133A VAL* 1.3 64.4 + - + +
135A ASN* 3.4 7.8 + - - +
136A ARG* 3.2 21.3 + - + +
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Residues in contact with VAL 133 (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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86A GLN* 4.2 31.6 - - + +
89A PHE* 5.8 2.7 - - + -
129A TYR* 3.1 38.3 + - + +
130A MSE 4.4 6.7 - - - +
132A ILE* 1.3 84.4 - - + +
134A SER* 1.3 60.9 + - - +
136A ARG* 3.2 8.2 + - + +
137A ALA* 3.0 22.1 + - + +
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Residues in contact with SER 134 (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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130A MSE 2.7 35.5 + - - +
131A ASN* 4.0 4.7 - - - -
133A VAL* 1.3 73.8 - - - +
135A ASN* 1.3 60.6 + - - +
137A ALA* 3.2 6.9 + - - +
138A GLN* 2.8 50.8 + - - +
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Residues in contact with ASN 135 (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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131A ASN* 3.0 35.4 + - - +
132A ILE* 3.6 8.3 - - - +
134A SER* 1.3 75.5 - - - +
136A ARG* 1.3 58.5 + - - +
138A GLN* 3.4 16.8 + - - +
139A ASN* 2.9 46.7 + - - +
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Residues in contact with ARG 136 (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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86A GLN* 3.3 53.0 + - - +
132A ILE* 3.2 12.3 + - + +
133A VAL* 3.5 10.8 - - + +
134A SER 3.2 0.2 - - - -
135A ASN* 1.3 79.1 - - - +
137A ALA* 1.3 62.4 + - - +
139A ASN* 3.9 6.5 - - - +
140A LEU* 3.1 42.5 + - + +
165A GLU* 2.9 40.6 + - - -
227A GOL 3.6 25.3 + - - +
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Residues in contact with ALA 137 (chain A).
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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133A VAL* 3.0 14.5 + - + +
134A SER* 3.2 9.8 + - - +
136A ARG* 1.3 76.4 - - - +
138A GLN* 1.3 63.6 + - + +
140A LEU* 4.0 6.8 - - - +
141A TYR* 3.0 26.0 + - - +
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Residues in contact with GLN 138 (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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134A SER* 2.8 39.6 + - - +
135A ASN* 3.7 16.1 + - - +
137A ALA* 1.3 74.0 - - + +
139A ASN* 1.3 60.7 + - - +
141A TYR* 3.4 6.1 + - - +
142A SER* 2.9 30.5 + - - -
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Residues in contact with ASN 139 (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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135A ASN* 2.9 40.5 + - - +
136A ARG* 3.4 5.2 + - - +
138A GLN* 1.3 75.8 - - - +
140A LEU* 1.3 63.3 + - - +
142A SER* 3.4 7.5 + - - -
143A ARG* 3.3 30.4 + - - +
227A GOL 4.4 14.0 + - - +
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Residues in contact with LEU 140 (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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136A ARG* 3.1 44.9 + - + +
137A ALA* 4.0 6.1 - - - +
139A ASN* 1.3 77.3 - - - +
141A TYR* 1.3 64.0 + - - +
143A ARG* 3.5 33.8 + - - +
144A LEU* 3.7 10.4 + - - +
227A GOL 3.6 27.6 - - - -
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Residues in contact with TYR 141 (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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137A ALA 3.0 19.5 + - - +
138A GLN* 3.8 6.1 - - - +
140A LEU* 1.3 73.4 - - - +
142A SER* 1.3 69.4 + - - +
144A LEU* 2.9 31.0 + - + +
145A TRP* 3.0 58.3 - + - -
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Residues in contact with SER 142 (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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138A GLN 2.9 18.5 + - - -
139A ASN* 3.6 8.5 - - - -
140A LEU 3.4 0.2 - - - -
141A TYR* 1.3 81.2 - - - +
143A ARG* 1.3 61.7 + - - +
145A TRP* 3.1 21.0 + - - +
146A ASP* 3.6 13.7 + - - +
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Residues in contact with ARG 143 (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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139A ASN* 3.3 17.1 + - - +
140A LEU* 3.7 23.2 - - - +
141A TYR 3.2 0.6 - - - -
142A SER* 1.3 72.9 - - - +
144A LEU* 1.3 64.6 + - + +
145A TRP 3.1 3.2 + - - -
146A ASP* 3.6 29.2 + - - +
158A ARG* 5.6 1.0 + - - -
161A LEU 3.8 7.1 + - - -
162A SER* 3.0 46.2 + - - +
164A CYS 4.0 1.0 + - - -
227A GOL 3.1 41.3 + - - -
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Residues in contact with LEU 144 (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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140A LEU 3.7 8.5 + - - +
141A TYR* 2.9 38.2 + - + +
143A ARG* 1.3 77.0 - - + +
145A TRP* 1.3 74.7 - - + +
146A ASP 3.5 2.5 + - - +
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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
------------------------------------------------------------
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