Contacts of the helix formed by residues 274 - 294 (chain B) in PDB entry 1YAA
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 274 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273B GLN* 1.3 74.6 + - - +
275B GLN* 1.3 65.2 + - + +
276B ASN* 3.2 5.3 + - - +
277B LYS* 4.3 7.6 + - - +
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Residues in contact with GLN 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A ASN* 5.0 8.5 - - + +
273B GLN* 3.3 2.0 - - - +
274B ALA* 1.3 83.5 + - - +
276B ASN* 1.3 57.4 + - - -
277B LYS* 3.0 18.7 + - - +
278B THR* 2.9 49.3 + - + +
279B ILE* 3.3 20.8 + - + +
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Residues in contact with ASN 276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B ASP 6.2 0.2 - - - -
99B ARG* 3.8 20.4 - - + +
270B LEU* 3.8 18.9 - - - +
271B THR* 2.9 27.0 + - - +
272B LYS* 4.6 0.2 - - - -
273B GLN* 3.4 19.3 + - - +
274B ALA 3.2 2.4 - - - +
275B GLN* 1.3 77.1 - - - +
277B LYS* 1.3 61.6 + - - +
278B THR 3.2 0.2 - - - -
279B ILE* 3.6 32.2 - - - +
280B LYS* 3.0 27.9 + - - +
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Residues in contact with LYS 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274B ALA 4.3 6.8 + - - +
275B GLN* 3.0 15.1 + - - +
276B ASN* 1.3 77.9 - - - +
278B THR* 1.3 64.1 + - + +
280B LYS* 4.3 1.2 - - - +
281B PRO* 3.0 22.3 - - - +
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Residues in contact with THR 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A LEU* 5.7 0.7 - - - +
275B GLN* 2.9 37.8 + - - +
277B LYS* 1.3 87.3 - - + +
279B ILE* 1.3 65.0 + - - +
280B LYS 3.3 0.4 - - - -
281B PRO* 3.2 8.6 - - - +
282B ALA* 3.1 24.9 + - - +
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Residues in contact with ILE 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A PHE* 3.8 35.0 - - + +
7A ASN* 3.6 41.1 - - - +
270B LEU* 4.1 9.6 - - + -
273B GLN* 4.3 6.3 - - + -
275B GLN* 3.3 23.5 + - + +
276B ASN* 3.5 27.6 + - - +
278B THR* 1.3 77.5 + - - +
280B LYS* 1.3 66.2 + - - +
282B ALA* 3.1 6.9 + - - +
283B VAL* 2.9 28.3 + - + +
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Residues in contact with LYS 280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B ASP* 3.2 47.2 + - - +
100B VAL 3.5 25.9 + - - -
101B ILE* 3.6 27.8 - - + +
270B LEU* 3.7 20.2 - - + +
276B ASN 3.0 17.9 + - - +
277B LYS* 4.3 1.1 - - - +
279B ILE* 1.3 80.8 - - - +
281B PRO* 1.4 71.0 - - + +
284B THR* 2.8 28.9 + - - +
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Residues in contact with PRO 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A LEU* 3.4 17.4 - - + +
277B LYS 3.0 28.3 - - - +
278B THR* 3.2 15.9 - - - +
280B LYS* 1.4 87.1 - - + +
282B ALA* 1.3 58.1 + - - +
284B THR* 4.0 8.5 - - - -
285B SER* 3.2 23.6 + - - -
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Residues in contact with ALA 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 5.7 0.9 - - - +
9A ILE* 3.5 25.1 - - + +
10A GLU 3.4 8.3 - - - +
11A LEU* 4.0 12.1 - - + -
278B THR* 3.1 21.0 + - - +
279B ILE* 3.1 9.2 + - - +
281B PRO* 1.3 75.6 - - - +
283B VAL* 1.3 64.4 - - + +
285B SER* 2.4 24.1 + - - -
286B GLN* 3.4 11.4 - - - +
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Residues in contact with VAL 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A PHE* 3.9 34.3 - - + +
9A ILE* 4.5 12.6 - - + -
101B ILE* 3.8 18.8 - - + -
118B PHE* 3.9 24.7 - - + -
269B LEU* 4.2 14.8 - - - +
270B LEU* 4.7 1.8 - - + -
279B ILE* 2.9 23.9 + - + +
282B ALA* 1.3 72.9 - - + +
284B THR* 1.3 68.3 + - - +
286B GLN* 2.9 19.3 + - - +
287B LEU* 3.0 16.2 + - + +
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Residues in contact with THR 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B THR* 4.9 16.3 - - + +
101B ILE* 3.4 24.2 - - + +
103B VAL* 5.3 3.1 - - + -
280B LYS* 2.8 27.8 + - - +
281B PRO* 4.0 8.7 - - - +
283B VAL* 1.3 76.1 - - - +
285B SER* 1.3 58.2 + - - +
287B LEU* 3.2 14.7 + - - +
288B ALA* 3.0 27.5 + - + +
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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
----------------------------------------------------------
10A GLU 4.0 0.9 + - - -
11A LEU* 4.1 2.0 - - - -
12A LEU* 3.1 48.6 + - - +
281B PRO 3.2 12.9 + - - -
282B ALA* 2.4 26.5 + - - -
284B THR* 1.3 80.5 - - - +
286B GLN* 1.3 62.0 + - - +
288B ALA* 3.5 8.7 + - - +
289B LYS* 3.2 21.8 + - - +
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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
----------------------------------------------------------
9A ILE* 3.5 18.1 - - + +
10A GLU* 2.7 38.2 + - - +
12A LEU* 3.1 32.0 - - - +
118B PHE* 4.3 16.2 - - + -
121B LYS* 4.5 6.8 + - - -
122B PHE* 3.5 21.7 - - + -
282B ALA 3.4 11.8 + - - +
283B VAL* 2.9 9.3 + - - +
285B SER* 1.3 76.6 + - - +
287B LEU* 1.3 63.0 + - - +
289B LYS* 3.3 8.2 + - - +
290B ILE* 3.2 27.1 + - + +
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Residues in contact with LEU 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B ILE* 3.4 32.3 - - + -
103B VAL* 4.1 19.5 - - + -
114B ILE* 4.0 23.7 - - + +
118B PHE* 3.9 29.4 - - + -
269B PHE* 4.0 24.0 - - - +
283B VAL* 3.0 20.4 + - + +
284B THR* 3.4 6.5 - - - +
286B GLN* 1.3 73.0 - - - +
288B ALA* 1.3 66.2 + - - +
290B ILE* 3.1 11.1 + - + +
291B ILE* 3.1 28.2 + - - +
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Residues in contact with ALA 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B ILE* 3.3 30.7 - - + +
74B THR* 4.3 17.8 - - + +
284B THR* 3.0 15.8 + - + +
285B SER* 3.7 9.2 - - - +
287B LEU* 1.3 75.9 - - - +
289B LYS* 1.3 55.7 + - - +
291B ILE* 3.5 2.4 + - - -
292B ARG* 2.9 26.6 + - - +
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Residues in contact with LYS 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A LEU* 4.1 23.6 - - + -
142A ASN* 5.3 1.6 + - - -
145A ALA* 3.4 33.0 - - - +
149A ASN* 5.7 3.8 - - - +
121B LYS* 6.6 0.2 - - - -
285B SER 3.2 11.2 + - - +
286B GLN* 3.3 11.0 - - - +
287B LEU 3.1 0.4 - - - -
288B ALA* 1.3 77.7 - - - +
290B ILE* 1.3 65.2 + - + +
292B ARG* 3.3 8.6 + - + +
293B SER* 2.8 35.2 + - - +
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Residues in contact with ILE 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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149A ASN* 4.9 7.9 - - - +
114B ILE* 4.5 23.6 - - + +
117B LYS* 3.9 35.7 - - + -
118B PHE* 4.3 33.0 - - + +
121B LYS* 4.6 16.4 - - + +
122B PHE* 5.8 0.9 - - + -
286B GLN* 3.2 14.8 + - + +
287B LEU* 3.1 11.7 + - - +
289B LYS* 1.3 78.3 - - + +
291B ILE* 1.3 65.2 + - + +
293B SER* 3.9 3.7 - - - -
294B GLU* 3.2 39.9 + - - +
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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
----------------------------------------------------------
73B ILE* 3.4 29.2 - - + +
74B THR* 4.7 3.1 - - - -
103B VAL* 4.3 17.9 - - + -
104B GLN 4.1 18.2 - - - +
114B ILE* 4.1 25.4 - - + -
287B LEU* 3.1 17.8 + - + +
288B ALA* 3.8 8.5 - - - +
290B ILE* 1.3 77.1 - - + +
292B ARG* 1.3 53.6 + - - +
294B GLU* 5.3 1.1 - - - -
295B VAL* 2.9 21.3 + - + +
296B SER 2.7 37.8 + - - +
297B ASN* 4.5 4.7 - - - +
298B PRO* 4.7 4.7 - - + -
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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 39.9 + - - +
17A LEU* 4.1 8.5 - - - +
18A PHE* 3.5 11.5 - - - -
109A THR* 3.8 2.1 - - - +
140A TRP* 3.8 3.0 - - - +
142A ASN* 3.1 56.8 + - - +
901A MAE 2.7 42.6 + - - -
73B ILE* 4.0 19.5 - - + +
288B ALA 2.9 19.5 + - - +
289B LYS* 3.8 11.2 - - + +
291B ILE* 1.3 76.4 - - - +
293B SER* 1.3 60.4 + - - +
294B GLU 3.4 0.5 + - - -
296B SER* 2.8 47.4 + - - +
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Residues in contact with SER 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A THR* 4.4 1.2 - - - +
113A HIS* 4.4 1.7 + - - +
142A ASN* 4.4 6.2 + - - -
145A ALA* 3.7 34.1 + - - +
146A ILE* 3.4 34.5 - - - +
149A ASN* 3.9 19.6 + - - +
289B LYS* 2.8 31.3 + - - +
290B ILE 3.9 3.8 - - - -
292B ARG* 1.3 77.6 - - - +
294B GLU* 1.3 59.5 + - - +
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Residues in contact with GLU 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* 3.8 4.9 - - - +
110A GLY* 3.6 12.3 - - - -
113A HIS* 3.5 52.5 + - + +
149A ASN* 3.2 20.6 - - - +
150A GLN* 4.3 0.7 + - - -
294A GLU* 5.3 0.2 - - - +
113B HIS* 2.8 38.2 + - - -
117B LYS* 3.8 17.8 - - - +
290B ILE* 3.2 24.8 + - - +
291B ILE* 5.1 1.0 - - - -
293B SER* 1.3 82.6 - - - +
295B VAL* 1.3 70.4 + - + +
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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
------------------------------------------------------------
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