Contacts of the helix formed by residues 123 - 136 (chain A) in PDB entry 1ZSV
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 GLY 123 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86A LEU* 6.0 0.9 - - - -
118A ALA 3.3 19.1 - - - -
120A GLY 2.8 9.6 + - - -
122A VAL* 1.3 79.2 - - - +
124A MET* 1.3 64.3 + - - -
126A GLY* 3.4 1.6 + - - -
127A LEU* 3.1 31.0 + - - +
284A LEU* 4.5 5.6 - - - -
287A LEU* 4.6 0.2 - - - +
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Residues in contact with MET 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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47A ASP* 4.0 18.2 - - + +
49A TYR* 3.7 34.5 - - + -
66A GLN* 4.5 15.2 + - - +
118A ALA 4.4 2.2 + - - -
119A LEU 4.7 1.9 - - - +
123A GLY* 1.3 71.1 - - - -
125A PRO* 1.3 71.3 - - + +
127A LEU* 3.4 9.7 + - - -
128A THR* 2.5 46.1 + - - -
154A VAL* 6.1 0.9 - - - -
272A VAL* 3.5 23.5 - - + +
273A TYR* 4.0 22.4 - - + +
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Residues in contact with PRO 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A ASP* 4.5 6.1 - - - +
119A LEU 3.5 18.8 - - - +
120A GLY* 3.4 17.0 - - - +
124A MET* 1.3 103.5 - - + +
126A GLY* 1.3 58.4 + - - +
128A THR* 3.4 7.5 + - - +
129A ALA* 3.1 26.5 + - - +
153A ALA* 3.9 33.9 - - + +
154A VAL* 3.8 18.5 - - + +
324A LYS* 4.3 7.0 - - - -
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Residues in contact with GLY 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 GLY 3.4 9.7 + - - -
121A THR* 3.5 23.5 - - - +
123A GLY 3.4 1.1 + - - -
125A PRO* 1.3 75.8 - - - +
127A LEU* 1.3 59.6 + - - +
129A ALA* 3.5 1.7 + - - +
130A TYR* 2.8 31.2 + - - +
157A VAL* 4.1 16.8 - - - +
287A LEU* 3.6 11.3 - - - +
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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 GLY* 3.1 22.1 + - - +
124A MET* 3.5 11.7 - - - +
126A GLY* 1.3 74.3 - - - +
128A THR* 1.3 59.6 + - - +
130A TYR* 4.2 2.0 - - - -
131A PHE* 2.9 46.9 + - + +
272A VAL* 3.6 14.3 - - + +
280A ARG* 4.0 36.1 - - + +
283A ALA* 3.4 31.6 - - + -
284A LEU* 3.9 26.7 - - + +
287A LEU* 3.8 8.0 - - + +
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Residues in contact with THR 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A MET* 2.5 26.8 + - - -
125A PRO* 3.5 11.5 - - - +
127A LEU* 1.3 76.1 - - - +
129A ALA* 1.3 57.6 + - - +
132A GLY* 2.9 30.5 + - - -
154A VAL* 3.9 10.4 - - + +
215A PHE* 3.8 1.0 - - - -
239A CYS* 3.4 33.0 - - - -
270A PHE* 3.5 16.0 - - + -
272A VAL* 3.2 25.9 - - + +
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Residues in contact with ALA 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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125A PRO 3.1 8.7 + - - +
126A GLY 3.6 7.6 - - - +
128A THR* 1.3 75.3 - - - +
130A TYR* 1.3 66.8 + - - +
133A LEU* 2.9 29.7 + - - +
154A VAL* 3.5 11.7 - - - +
157A VAL* 3.7 9.9 - - + -
158A VAL* 3.3 44.4 - - + +
161A ILE* 4.4 2.0 - - + -
215A PHE* 3.9 1.8 - - - -
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Residues in contact with TYR 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 GLY 2.8 21.0 + - - +
127A LEU* 3.8 6.3 - - - +
128A THR 3.4 0.2 - - - -
129A ALA* 1.3 73.7 - - - +
131A PHE* 1.3 80.2 + + - +
134A LEU* 2.8 54.4 + - + +
135A GLU* 5.5 3.1 - - - -
161A ILE* 3.7 15.9 - - + +
279A ALA 5.3 0.6 + - - -
282A LYS* 4.2 11.4 - - - +
283A ALA* 3.4 38.4 + - + -
286A ASP* 2.7 40.3 + - + -
287A LEU* 4.3 5.8 - - + -
290A TRP* 3.8 26.7 - + - -
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Residues in contact with PHE 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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127A LEU* 2.9 37.8 + - + +
128A THR* 4.6 0.9 - - - +
130A TYR* 1.3 89.6 - + - +
132A GLY* 1.3 62.2 + - - +
135A GLU* 2.9 52.6 + - + +
136A ILE* 3.2 7.8 + - - +
270A PHE* 5.3 0.7 - - + -
272A VAL* 5.0 2.9 - - + -
275A TRP* 3.6 69.8 - + + -
279A ALA* 3.5 30.7 - - + -
280A ARG* 4.3 5.2 - - + -
283A ALA* 3.6 20.0 - - + -
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Residues in contact with GLY 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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128A THR 2.9 11.8 + - - -
131A PHE* 1.3 79.2 - - - +
133A LEU* 1.3 56.9 + - - +
136A ILE* 3.2 7.3 + - - +
137A CYS* 2.8 28.8 + - - +
215A PHE* 3.6 9.6 - - - -
237A ALA* 3.9 1.3 - - - +
270A PHE* 3.3 35.1 - - - -
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Residues in contact with LEU 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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129A ALA 2.9 18.4 + - - +
130A TYR* 4.0 1.1 - - - +
132A GLY* 1.3 76.9 - - - +
134A LEU* 1.3 60.6 + - + +
137A CYS* 3.4 15.5 - - - +
138A GLY 3.0 21.5 + - - -
139A VAL* 3.4 33.0 + - + -
145A VAL* 4.1 19.1 - - + -
158A VAL* 3.1 46.0 - - + +
161A ILE* 3.7 18.6 - - + -
162A ALA* 3.6 18.2 - - + +
215A PHE* 3.6 3.6 - - + -
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Residues in contact with LEU 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A TYR* 2.8 57.7 + - + +
133A LEU* 1.3 76.2 - - + +
135A GLU* 1.3 65.8 + - + +
138A GLY* 3.3 17.1 - - - -
139A VAL* 3.9 29.4 - - + +
140A LYS* 5.6 2.8 + - - -
161A ILE* 3.8 27.4 - - + -
165A LYS* 4.0 30.1 - - + +
290A TRP* 4.6 1.3 - - + -
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Residues in contact with GLU 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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130A TYR* 5.5 2.8 - - - -
131A PHE* 2.9 45.5 + - + +
134A LEU* 1.3 85.9 - - + +
136A ILE* 1.3 65.0 + - + +
137A CYS 3.9 0.2 - - - -
138A GLY* 4.0 4.8 + - - -
275A TRP* 3.9 24.5 + - + +
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Residues in contact with ILE 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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131A PHE 3.2 8.0 + - - +
132A GLY* 3.4 10.8 - - - +
135A GLU* 1.3 79.5 - - + +
137A CYS* 1.3 66.0 + - - +
138A GLY 3.2 0.2 - - - -
235A ARG* 4.7 8.3 - - - +
236A ILE 4.5 2.4 - - - +
237A ALA* 3.5 24.2 - - + -
266A ARG* 6.0 2.3 - - - +
268A GLU* 3.7 49.0 - - + +
270A PHE* 4.1 18.2 - - + -
274A ARG* 4.3 8.7 - - - +
275A TRP* 3.3 40.6 - - + -
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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