Contacts of the helix formed by residues 277 - 294 (chain B) in PDB entry 1AIA
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 SER 277 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97B ASP 4.2 7.4 + - - -
98B LYS* 3.4 37.5 + - - -
276B ASP* 1.3 74.9 - - - +
278B GLU* 1.3 60.2 + - - +
280B VAL* 3.1 3.4 + - - +
281B ASP* 2.9 40.0 + - - +
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Residues in contact with GLU 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276B ASP* 3.4 14.5 + - - +
277B SER* 1.3 81.5 + - - +
279B THR* 1.3 67.4 + - - +
281B ASP* 3.5 7.3 + - - +
282B ARG* 2.8 66.5 + - - +
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Residues in contact with THR 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A PHE* 3.8 30.9 - - + +
7A GLU* 4.1 10.0 - - + +
249B GLU* 5.0 2.0 - - - +
274B ALA* 3.9 17.0 - - + -
275B ALA* 4.8 4.8 - - + +
276B ASP* 2.7 30.4 + - - -
278B GLU* 1.3 90.2 + - - +
280B VAL* 1.3 58.4 + - - +
282B ARG* 3.3 12.8 + - - +
283B ALA* 3.0 26.3 + - - +
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Residues in contact with VAL 280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98B LYS 3.6 20.9 - - - +
99B ARG 3.5 15.3 - - - +
101B ARG* 3.6 19.0 - - + +
272B LEU* 3.5 37.5 - - + +
273B VAL 4.4 0.2 - - - -
274B ALA* 3.7 17.7 - - + +
276B ASP 3.2 2.9 + - - +
277B SER* 3.1 21.5 + - - +
279B THR* 1.3 76.5 - - - +
281B ASP* 1.3 66.0 + - - +
283B ALA* 4.5 3.4 - - - -
284B PHE* 3.0 30.7 + - - +
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Residues in contact with ASP 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98B LYS 5.0 0.2 - - - +
101B ARG* 2.7 33.3 + - - +
277B SER* 2.9 30.2 + - - +
278B GLU* 3.7 8.7 - - - +
279B THR 3.2 0.4 - - - -
280B VAL* 1.3 84.9 - - - +
282B ARG* 1.3 60.7 + - - +
284B PHE* 3.8 1.8 - - - +
285B SER* 3.3 21.7 + - - -
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Residues in contact with ARG 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A PHE 5.0 1.6 + - - -
7A GLU 3.0 26.0 + - - -
9A ILE* 2.9 28.5 + - - +
10A THR* 3.9 8.3 - - - +
11A ALA* 3.6 27.4 - - + +
278B GLU* 2.8 54.8 + - - +
279B THR* 3.3 17.1 + - - +
281B ASP* 1.3 77.2 - - - +
283B ALA* 1.3 57.2 + - - +
285B SER* 2.6 24.3 + - - -
286B GLN* 3.8 2.6 + - - +
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Residues in contact with ALA 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A PHE* 4.3 14.8 - - + +
9A ILE* 3.9 31.4 - - + +
118B PHE* 3.4 14.2 - - + -
272B LEU* 3.8 17.3 - - + -
279B THR 3.0 17.1 + - - +
280B VAL* 4.2 2.9 - - - +
282B ARG* 1.3 74.1 - - - +
284B PHE* 1.3 65.1 + - - +
286B GLN* 3.2 2.4 + - - +
287B MET* 3.1 16.6 + - - +
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Residues in contact with PHE 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74B ASP* 3.9 25.1 - - + -
101B ARG* 3.6 50.0 - - + -
102B THR 3.5 23.6 - - - -
103B ALA* 3.8 19.7 - - + -
270B CYS 4.8 0.2 - - - -
272B LEU* 3.6 9.1 - - + +
280B VAL 3.0 21.6 + - - +
281B ASP* 3.8 5.4 - - - +
282B ARG 3.4 0.2 - - - -
283B ALA* 1.3 76.3 - - - +
285B SER* 1.3 56.2 + - - +
287B MET* 3.1 29.7 + - + +
288B LYS* 3.0 44.4 + - + +
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Residues in contact with SER 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A ALA* 2.5 31.1 + - - -
12A ALA* 3.7 8.6 - - - +
281B ASP 3.3 12.7 + - - -
282B ARG* 2.6 22.3 + - - -
284B PHE* 1.3 75.1 - - - +
286B GLN* 1.4 57.3 + - - +
288B LYS* 3.5 15.8 + - - +
289B ALA* 3.0 25.1 + - - +
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Residues in contact with GLN 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A ILE* 3.8 10.2 - - + +
10A THR* 2.9 39.1 + - - +
12A ALA* 3.5 25.1 - - - +
118B PHE* 4.2 5.3 - - + -
122B ASN* 3.0 41.6 + - - +
282B ARG 4.0 2.5 - - - +
283B ALA 3.2 8.2 + - - +
284B PHE 3.2 0.4 - - - -
285B SER* 1.4 76.0 + - - +
287B MET* 1.3 66.0 + - - +
289B ALA* 3.7 11.1 + - - +
290B ALA* 3.3 19.2 + - - +
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Residues in contact with MET 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103B ALA* 4.9 2.5 - - - -
114B VAL* 4.5 8.1 - - + +
115B ALA* 4.4 7.6 - - + -
118B PHE* 3.9 40.6 - - + -
251B ILE* 5.4 2.5 - - + -
270B CYS* 3.8 36.6 - - - +
272B LEU* 4.1 18.2 - - + -
283B ALA 3.1 12.0 + - - +
284B PHE* 3.1 38.5 + - + +
286B GLN* 1.3 78.2 - - - +
288B LYS* 1.3 63.3 + - - +
290B ALA* 3.2 5.7 + - - +
291B ILE* 3.2 29.6 + - + +
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Residues in contact with LYS 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73B ILE* 3.5 25.4 - - + +
74B ASP* 4.1 27.6 + - + +
101B ARG* 5.5 3.0 - - - +
284B PHE* 3.0 45.3 + - + +
285B SER* 3.7 13.5 - - - +
287B MET* 1.3 74.6 - - - +
289B ALA* 1.3 65.4 + - - +
291B ILE* 3.1 12.4 + - + +
292B ARG* 3.0 24.8 + - - +
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Residues in contact with ALA 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A ALA* 4.5 7.6 - - + -
285B SER 3.0 17.9 + - - +
286B GLN* 3.7 18.6 - - - +
288B LYS* 1.3 75.9 - - - +
290B ALA* 1.4 59.0 + - - +
292B ARG* 3.6 8.3 + - - +
293B ALA* 3.4 22.0 + - - +
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Residues in contact with ALA 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A ARG* 4.5 3.1 + - - -
114B VAL* 4.7 8.9 - - + +
117B ASP* 4.3 26.8 - - + +
118B PHE* 4.5 10.3 - - - +
121B LYS* 5.0 12.1 - - + +
122B ASN* 5.9 0.2 - - - +
286B GLN 3.3 10.2 + - - +
287B MET* 3.2 12.8 + - - +
289B ALA* 1.4 75.4 - - - +
291B ILE* 1.3 65.4 + - + +
293B ALA* 3.5 6.7 + - - +
294B ASN* 3.3 21.0 + - - +
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Residues in contact with ILE 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73B ILE* 3.4 30.1 - - + +
103B ALA* 3.8 29.2 - - + -
104B GLN 5.2 0.2 - - - +
105B THR* 5.2 0.2 - - - +
114B VAL* 4.0 19.1 - - + -
287B MET* 3.2 21.0 + - + +
288B LYS* 3.1 16.7 + - + +
290B ALA* 1.3 73.7 - - - +
292B ARG* 1.3 53.4 + - - +
294B ASN* 2.8 24.0 + - - -
295B TYR* 2.8 57.8 + - + +
296B SER 3.2 7.9 + - - +
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Residues in contact with ARG 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A ASP* 2.9 47.0 + - - +
17A ILE* 5.0 6.7 - - - +
18A LEU* 3.6 23.1 - - - +
109A THR* 3.8 6.8 - - - +
140A TRP* 4.1 22.0 - - - +
141A PRO* 6.2 1.2 - - - +
142A ASN* 3.0 48.8 + - - +
145A SER* 6.1 0.2 - - - -
73B ILE* 3.7 21.5 - - + +
288B LYS 3.0 15.5 + - - +
289B ALA* 3.7 9.2 - - - +
291B ILE* 1.3 75.0 - - - +
293B ALA* 1.3 58.5 + - - +
294B ASN 3.6 0.2 + - - -
296B SER* 3.4 39.4 + - - +
297B ASN* 5.6 1.6 - - - +
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Residues in contact with ALA 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A ARG* 3.0 21.4 + - - +
142A ASN* 4.1 5.8 - - - -
145A SER* 3.6 20.6 - - - +
146A VAL* 3.5 18.4 - - - +
149A SER* 3.5 24.0 - - - +
289B ALA 3.4 13.7 + - - +
290B ALA* 4.0 6.1 - - - +
291B ILE 3.2 0.8 - - - -
292B ARG* 1.3 78.7 - - + +
294B ASN* 1.3 59.8 + - - +
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Residues in contact with ASN 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A THR* 3.4 22.7 - - - +
110A GLY* 3.6 3.9 + - - -
113A ARG* 3.4 27.5 + - - +
294A ASN* 2.8 44.6 + - - +
295A TYR* 5.2 2.6 - - - -
113B ARG* 4.4 3.8 - - - +
114B VAL* 4.7 6.5 - - + +
117B ASP* 4.4 10.7 - - - +
290B ALA 3.3 12.2 + - - +
291B ILE* 2.8 10.6 + - - +
293B ALA* 1.3 79.1 - - - +
295B TYR* 1.3 78.8 + - + +
296B SER 3.6 0.4 - - - -
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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