Contacts of the helix formed by residues 276 - 293 (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 GLN 276 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273A TYR* 2.7 43.6 + - - +
274A ARG 3.6 5.4 + - - +
275A TRP* 1.3 78.1 + - - +
277A GLY* 1.3 67.7 + - - +
278A ASP 3.6 1.2 + - - -
279A ALA* 3.7 13.0 + - - +
280A ARG* 3.5 27.0 + - - +
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Residues in contact with GLY 277 (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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276A GLN* 1.3 79.2 + - - +
278A ASP* 1.3 63.9 - - - -
280A ARG* 3.5 3.5 + - - +
281A GLN* 3.3 20.9 + - - +
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Residues in contact with ASP 278 (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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276A GLN 3.6 0.4 + - - -
277A GLY* 1.3 71.1 - - - -
279A ALA* 1.3 65.3 + - - +
281A GLN* 3.3 6.5 + - - +
282A LYS* 2.9 26.9 + - - +
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Residues in contact with ALA 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A TYR* 5.3 0.5 + - - -
131A PHE* 3.5 15.8 - - + -
275A TRP* 4.4 22.7 - - + -
276A GLN 3.7 8.9 + - - +
277A GLY 3.3 1.0 - - - -
278A ASP* 1.3 78.3 - - - +
280A ARG* 1.3 57.6 + - - +
282A LYS* 3.6 5.7 + - - +
283A ALA* 3.1 22.3 + - - +
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Residues in contact with ARG 280 (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 LEU* 5.5 1.6 - - - +
103A GLU* 3.1 44.3 + - - +
127A LEU* 4.0 26.4 - - + +
131A PHE* 4.1 10.7 - - + -
275A TRP* 3.4 27.6 - - + +
276A GLN* 3.5 24.8 + - - +
277A GLY 3.5 9.4 + - - +
278A ASP 3.2 0.2 - - - -
279A ALA* 1.3 77.5 - - - +
281A GLN* 1.3 64.4 + - - +
283A ALA* 3.4 1.9 + - - +
284A LEU* 3.0 41.4 + - + +
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Residues in contact with GLN 281 (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 LEU* 3.7 25.7 - - - +
107A THR 6.1 0.4 - - - +
108A GLU* 5.7 0.4 + - - -
277A GLY 3.3 14.4 + - - +
278A ASP* 3.9 6.7 - - - +
280A ARG* 1.3 79.7 + - - +
282A LYS* 1.3 61.9 + - - +
284A LEU* 3.5 13.7 + - - +
285A LYS* 3.0 58.0 + - - +
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Residues in contact with LYS 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A TYR* 4.2 7.8 + - - +
278A ASP 2.9 17.0 + - - +
279A ALA* 3.7 6.3 - - - +
281A GLN* 1.3 73.6 - - - +
283A ALA* 1.3 63.0 + - - +
285A LYS* 3.4 8.9 + - + +
286A ASP* 3.0 44.4 + - - +
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Residues in contact with ALA 283 (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* 3.4 25.1 - - + -
130A TYR* 3.4 38.0 + - + -
131A PHE* 3.6 16.8 - - + -
279A ALA 3.1 7.0 + - - +
280A ARG 3.6 2.9 - - - +
281A GLN 3.3 0.2 - - - -
282A LYS* 1.3 75.3 - - - +
284A LEU* 1.3 61.7 + - - +
286A ASP* 3.2 4.7 + - - +
287A LEU* 3.1 25.8 + - - +
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Residues in contact with LEU 284 (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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103A GLU* 4.4 8.3 - - - +
106A LEU* 3.8 20.4 - - + +
122A VAL* 3.7 42.9 - - + +
123A GLY* 4.3 1.8 - - - +
127A LEU* 3.9 21.7 - - + +
280A ARG* 3.0 42.6 + - - +
281A GLN* 3.6 23.3 - - - +
282A LYS 3.4 0.2 - - - -
283A ALA* 1.3 75.8 - - - +
285A LYS* 1.3 58.6 + - - +
287A LEU* 3.5 4.4 + - + +
288A LEU* 3.0 28.2 + - - +
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Residues in contact with LYS 285 (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 LEU* 4.2 6.1 - - + -
108A GLU* 3.3 37.5 - - + +
281A GLN* 3.0 48.0 + - + +
282A LYS* 3.8 8.1 - - + +
283A ALA 3.2 0.2 - - - -
284A LEU* 1.3 75.9 - - - +
286A ASP* 1.3 59.2 + - - +
288A LEU* 3.6 6.4 + - - +
289A LYS* 2.9 33.5 + - + +
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Residues in contact with ASP 286 (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* 2.7 37.6 + - + -
282A LYS* 3.0 27.0 + - - +
283A ALA 3.2 8.3 + - - +
285A LYS* 1.3 75.8 - - - +
287A LEU* 1.3 59.7 + - - +
289A LYS* 3.5 15.4 - - - +
290A TRP* 2.9 55.3 + - + -
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Residues in contact with LEU 287 (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 THR* 3.5 27.8 - - + +
122A VAL* 4.3 11.7 - - + -
126A GLY 3.6 29.2 - - - +
127A LEU* 3.8 19.3 - - + +
130A TYR* 4.3 8.3 - - + -
157A VAL* 4.1 8.1 - - + -
161A ILE* 4.2 9.9 - - + -
283A ALA 3.1 17.0 + - - +
284A LEU* 3.8 8.7 - - + +
285A LYS 3.4 0.2 - - - -
286A ASP* 1.3 78.5 - - - +
288A LEU* 1.3 57.5 + - - +
290A TRP* 3.9 4.7 - - + +
291A VAL* 3.0 35.8 + - - +
296A ILE* 4.0 22.3 - - + +
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Residues in contact with LEU 288 (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 LEU* 3.6 24.7 - - + -
108A GLU* 3.8 25.1 - - + +
109A TRP* 4.2 11.7 - - + -
110A PRO* 3.9 19.7 - - + -
113A ILE* 3.5 31.9 - - + -
122A VAL* 4.0 10.8 - - + +
284A LEU 3.0 18.8 + - - +
285A LYS* 3.7 5.4 - - - +
287A LEU* 1.3 73.2 - - - +
289A LYS* 1.3 68.3 + - - +
290A TRP 3.2 0.2 + - - -
291A VAL* 3.2 4.0 + - + +
292A LEU* 3.1 40.7 + - + +
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Residues in contact with LYS 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285A LYS* 2.9 20.2 + - + +
286A ASP* 3.5 21.5 - - - +
288A LEU* 1.3 73.6 - - - +
290A TRP* 1.3 67.9 + - + +
292A LEU* 3.2 6.6 + - - +
293A GLU* 2.9 46.6 + - - +
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Residues in contact with TRP 290 (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* 3.8 38.4 - + - -
134A LEU* 4.6 0.9 - - + -
161A ILE* 4.0 17.3 - - + -
164A LEU* 3.5 34.9 - - + +
165A LYS* 3.7 25.6 - - - -
286A ASP* 2.9 40.0 + - + +
287A LEU* 4.0 3.1 - - + +
288A LEU 3.2 0.2 - - - -
289A LYS* 1.3 79.1 - - + +
291A VAL* 1.3 61.4 + - - +
293A GLU* 3.9 17.0 - - - -
294A GLY 3.3 1.4 + - - -
295A LYS* 2.8 41.1 + - + +
296A ILE* 2.9 38.3 + - + -
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Residues in contact with VAL 291 (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 ILE* 4.2 20.6 - - + -
117A LEU* 4.3 5.8 - - + -
121A THR* 3.6 30.1 - - + -
122A VAL* 4.0 8.7 - - + -
287A LEU 3.0 22.3 + - - +
288A LEU* 3.2 6.7 + - + +
290A TRP* 1.3 75.3 - - - +
292A LEU* 1.3 59.1 + - + +
294A GLY* 2.9 20.6 + - - -
296A ILE* 3.5 18.6 - - + +
298A TYR* 4.0 30.2 - - + -
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Residues in contact with LEU 292 (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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108A GLU 5.6 1.3 - - - +
110A PRO* 3.8 25.4 - - + -
112A THR* 4.5 6.5 - - - +
113A ILE* 3.7 30.3 - - + -
288A LEU* 3.1 31.8 + - + +
289A LYS* 3.7 5.2 - - - +
291A VAL* 1.3 76.4 - - + +
293A GLU* 1.3 61.9 + - + +
294A GLY 3.5 0.2 + - - -
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Residues in contact with GLU 293 (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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289A LYS* 2.9 34.6 + - - +
290A TRP* 3.9 14.7 - - - +
291A VAL 3.3 0.2 - - - -
292A LEU* 1.3 77.5 - - + +
294A GLY* 1.3 57.0 + - - +
295A LYS* 3.2 44.0 + - + +
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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