Contacts of the helix formed by residues 277 - 295 (chain A) in PDB entry 1AY8
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 ALA 277 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98A GLU* 3.7 44.2 + - + +
99A THR* 3.7 4.4 - - - +
276A ASP* 1.3 69.4 - - - +
278A ALA* 1.3 65.4 + - - +
280A ARG* 3.0 1.6 + - - +
281A GLU* 3.0 35.9 + - + +
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Residues in contact with ALA 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 ASP* 3.2 11.5 + - - +
277A ALA* 1.3 77.6 - - - +
279A THR* 1.3 61.6 + - - +
281A GLU* 3.3 8.8 + - - +
282A LEU* 3.2 25.4 + - - +
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Residues in contact with THR 279 (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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249A GLU* 4.6 4.7 - - - +
274A CYS* 4.0 14.4 - - + -
275A ALA* 4.9 3.2 + - + +
276A ASP* 2.6 36.4 + - - -
278A ALA* 1.3 74.0 - - - +
280A ARG* 1.3 60.6 + - - +
282A LEU* 3.1 11.7 + - - +
283A ALA* 2.8 27.4 + - - +
6B LEU* 3.7 41.1 - - + +
7B GLY* 3.7 11.2 - - - +
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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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97A SER 3.8 6.1 + - - -
98A GLU* 3.2 28.3 - - - +
99A THR* 3.4 23.1 - - - +
100A THR 3.3 29.0 + - - +
101A ALA* 3.8 3.8 - - + +
102A THR 5.1 0.2 - - - +
274A CYS* 3.8 10.2 - - - +
276A ASP 2.9 10.5 + - - +
277A ALA 3.0 8.9 + - - +
279A THR* 1.3 77.6 - - - +
281A GLU* 1.3 94.5 + - - +
283A ALA* 3.2 1.7 + - - +
284A GLN* 2.8 72.2 + - - +
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Residues in contact with GLU 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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98A GLU 4.6 0.7 - - - +
277A ALA* 3.0 25.3 + - + +
278A ALA* 3.7 8.7 - - - +
279A THR 3.3 0.2 - - - -
280A ARG* 1.3 118.1 + - - +
282A LEU* 1.3 58.9 + - + +
284A GLN* 4.0 1.1 - - - +
285A GLY* 3.0 25.8 + - - -
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Residues in contact with LEU 282 (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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278A ALA 3.2 13.9 + - - +
279A THR* 3.1 15.2 + - - +
281A GLU* 1.3 81.2 - - + +
283A ALA* 1.3 61.6 + - - +
285A GLY* 4.0 0.7 - - - -
286A ALA* 3.2 23.6 + - - +
6B LEU 4.3 7.0 - - - +
7B GLY* 3.9 19.7 - - - +
9B LEU* 3.1 37.2 - - + +
10B LYS 5.1 3.3 - - - +
11B PRO* 4.8 22.5 - - + +
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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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101A ALA* 4.2 7.6 - - + -
118A LEU* 4.5 2.9 - - + +
272A ALA* 4.4 9.0 - - + -
274A CYS* 3.9 19.5 - - - -
279A THR 2.8 15.2 + - - +
280A ARG 3.6 3.1 - - - +
282A LEU* 1.3 75.2 - - - +
284A GLN* 1.3 60.3 + - - +
286A ALA* 3.2 2.6 + - - +
287A MET* 2.9 36.8 + - - +
6B LEU* 4.6 7.0 - - + -
9B LEU* 3.6 18.8 - - + -
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Residues in contact with GLN 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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74A SER* 3.8 21.9 + - - +
80A GLN* 4.3 5.3 + - - -
101A ALA* 3.7 11.5 - - + +
102A THR 3.1 43.4 + - - +
280A ARG* 2.8 49.4 + - - +
281A GLU 4.0 3.1 - - - +
283A ALA* 1.3 71.6 - - - +
285A GLY* 1.3 62.5 + - - +
287A MET* 3.4 7.6 + - - +
288A ALA* 3.0 22.5 + - + +
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Residues in contact with GLY 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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281A GLU 3.0 17.6 + - - -
282A LEU 4.0 1.3 - - - -
284A GLN* 1.3 78.0 - - - +
286A ALA* 1.3 55.4 + - - +
288A ALA* 3.3 7.1 + - - +
289A PHE* 3.0 28.7 + - - +
292A ARG* 5.5 0.7 + - - -
12B GLN* 4.5 8.8 - - - +
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Residues in contact with ALA 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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118A LEU* 3.8 22.4 - - + -
121A MET* 4.5 8.7 - - - +
282A LEU 3.2 17.9 + - - +
283A ALA 3.8 0.7 - - - +
285A GLY* 1.3 73.6 - - - +
287A MET* 1.3 60.5 + - - +
289A PHE* 3.5 3.3 - - - +
290A LEU* 3.0 31.9 + - - +
9B LEU* 4.2 15.7 - - + -
10B LYS 5.1 1.3 - - - +
12B GLN* 4.1 20.3 - - + +
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Residues in contact with MET 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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101A ALA* 3.7 31.2 - - - +
102A THR 4.7 0.7 - - - -
103A LEU* 3.4 40.7 - - + +
118A LEU* 3.9 19.1 - - + -
270A LEU* 3.2 53.4 - - + +
272A ALA* 3.9 13.9 - - + -
283A ALA 2.9 20.7 + - - +
284A GLN* 3.7 6.5 - - - +
286A ALA* 1.3 73.1 - - - +
288A ALA* 1.3 65.9 + - - +
290A LEU* 3.1 13.9 + - + +
291A ASN 3.1 17.3 + - - -
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Residues in contact with ALA 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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73A LEU* 3.6 23.9 - - + +
74A SER* 4.6 12.3 - - - +
103A LEU* 4.0 9.3 - - - +
284A GLN* 3.0 18.8 + - + +
285A GLY* 3.6 6.5 - - - +
287A MET* 1.3 75.8 - - - +
289A PHE* 1.3 62.2 + - - +
291A ASN* 3.2 3.8 + - - +
292A ARG* 3.0 29.5 + - - +
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Residues in contact with PHE 289 (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* 4.5 4.9 - - + -
285A GLY 3.0 17.2 + - - +
286A ALA 3.5 7.2 - - - +
288A ALA* 1.3 78.0 - - - +
290A LEU* 1.3 68.9 + - + +
292A ARG* 3.2 33.7 + - - +
293A GLN* 3.0 57.4 + - + +
12B GLN* 3.8 48.2 - - + -
13B ALA* 4.6 3.6 - - + -
145B SER* 5.8 1.1 - - - -
149B PHE* 3.7 34.3 - + + -
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Residues in contact with LEU 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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103A LEU* 5.3 0.9 - - + -
114A GLN* 3.6 39.1 - - + +
117A GLU* 3.8 24.5 - - + -
118A LEU* 3.8 20.4 - - + +
121A MET* 3.5 28.5 - - + -
270A LEU* 6.4 0.2 - - + -
286A ALA 3.0 16.3 + - - +
287A MET* 3.1 13.9 + - + +
289A PHE* 1.3 75.8 - - + +
291A ASN* 1.3 62.8 + - - +
293A GLN* 3.7 2.7 + - - +
294A THR* 2.8 31.2 + - - +
149B PHE* 4.1 20.0 - - + -
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Residues in contact with ASN 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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73A LEU* 3.3 22.8 + - + +
74A SER* 4.4 0.2 - - - +
103A LEU* 3.6 22.4 - - + +
104A ALA 3.2 22.9 + - - +
114A GLN* 3.1 12.7 - - - +
287A MET 3.1 7.6 + - - +
288A ALA* 3.2 7.4 + - - +
290A LEU* 1.3 76.2 - - - +
292A ARG* 1.3 58.6 + - - +
294A THR* 3.1 1.7 + - - -
295A TYR* 2.8 56.1 + - + -
296A SER 3.0 15.9 + - - +
298A PRO* 3.8 11.5 - - - +
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Residues in contact with ARG 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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73A LEU* 3.5 33.1 - - + +
285A GLY 5.5 0.8 + - - -
288A ALA* 3.0 19.1 + - - +
289A PHE* 3.2 28.9 + - - +
291A ASN* 1.3 76.7 - - - +
293A GLN* 1.3 84.8 + - - +
295A TYR 3.8 0.3 + - - -
296A SER* 3.2 27.1 + - - +
12B GLN* 5.5 1.6 - - - +
13B ALA 2.8 28.4 + - - -
14B PRO* 3.9 15.4 + - - +
15B ASP* 3.9 33.2 + - - +
18B LEU* 5.2 0.2 - - - -
109B THR* 4.0 9.9 - - - +
142B ASN* 5.6 6.1 + - - +
145B SER* 5.7 2.4 - - - -
146B ILE* 4.6 2.4 - - - +
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Residues in contact with GLN 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 PHE* 3.0 55.7 + - + +
290A LEU 3.7 3.3 + - - +
291A ASN 3.4 0.2 - - - -
292A ARG* 1.3 100.1 - - - +
294A THR* 1.3 52.3 + - - +
113B ARG* 2.7 32.3 + - - +
145B SER* 3.4 20.7 + - - -
146B ILE* 3.3 42.0 + - + +
149B PHE* 3.9 25.6 - - + -
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Residues in contact with THR 294 (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* 4.2 14.5 + - - +
290A LEU* 2.8 23.0 + - - +
291A ASN 3.1 3.0 + - - -
292A ARG 4.4 0.4 - - - -
293A GLN* 1.3 81.3 - - - +
295A TYR* 1.3 86.4 + - + +
109B THR* 4.8 1.8 - - - -
110B GLY* 3.6 14.6 - - - -
113B ARG* 3.3 36.1 + - + +
149B PHE* 5.4 1.4 - - - -
294B THR* 4.0 23.6 - - + -
295B TYR* 5.4 1.1 - - + -
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Residues in contact with TYR 295 (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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105A THR* 4.1 6.8 - - - -
106A VAL* 3.7 31.7 + - + +
110A GLY* 5.7 2.3 - - - -
114A GLN* 3.9 9.3 + - - +
291A ASN* 2.8 47.3 + - - -
292A ARG 3.8 0.4 + - - -
294A THR* 1.3 100.4 - - + +
296A SER* 1.3 66.0 + - - +
297A PHE 2.8 32.9 + - - +
298A PRO* 4.0 8.1 - - + -
106B VAL* 3.5 37.7 - - + +
109B THR* 3.9 11.0 - - - -
110B GLY* 4.0 5.2 - - - +
266B ARG* 2.9 17.5 + - - -
294B THR* 5.6 0.7 - - + -
295B TYR* 4.5 11.7 - + + -
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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