Contacts of the helix formed by residues 286 - 297 (chain B) in PDB entry 3NAY
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 ASN 286 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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241A SEP 5.0 2.9 - - - +
243A VAL* 3.8 26.1 - - + +
253A LEU 3.7 9.3 + - - -
254A LEU* 3.1 20.9 + - - -
257A LYS* 3.3 26.4 - - + +
284B ALA 3.4 1.2 - - - -
285B GLY* 1.3 76.3 - - - +
287B GLU* 1.4 57.6 + - - +
288B TYR* 2.9 32.9 + - - +
289B LEU* 3.0 16.9 + - - +
290B ILE* 3.0 36.7 + - - +
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Residues in contact with GLU 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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243A VAL* 5.4 2.1 - - + +
287A GLU* 3.9 16.8 - - - +
291A PHE* 4.9 5.4 - - + -
246B ALA* 3.7 24.7 + - + +
286B ASN* 1.4 71.8 - - - +
288B TYR* 1.4 59.9 + - - +
290B ILE* 3.4 9.8 + - + +
291B PHE* 2.9 53.6 + - + -
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Residues in contact with TYR 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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254A LEU* 3.3 36.1 - - + -
255A THR* 3.9 21.2 - - + +
288A TYR* 5.4 1.8 - + - -
291A PHE* 3.7 44.2 - + + -
292A GLN* 3.6 23.1 + - - -
295A ILE* 3.9 27.9 - - + +
286B ASN* 2.9 8.7 + - - +
287B GLU* 1.4 75.5 - - - +
289B LEU* 1.3 74.6 + - + +
291B PHE* 3.3 8.7 + + - +
292B GLN* 3.0 54.9 + - + +
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Residues in contact with LEU 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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254A LEU 3.8 5.6 - - - +
255A THR* 4.0 13.7 - - - +
257A LYS* 3.7 34.3 - - + +
284B ALA* 3.6 17.2 - - + +
285B GLY 4.4 4.7 - - - +
286B ASN* 3.0 31.8 + - - +
288B TYR* 1.3 92.8 - - + +
290B ILE* 1.4 63.2 + - - +
292B GLN* 3.5 9.5 + - + +
293B LYS* 3.4 26.2 + - - +
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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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246B ALA* 3.6 36.8 - - + +
247B GLN* 4.3 20.0 - - + +
282B PHE* 4.2 14.2 - - + +
283B ARG* 4.1 5.2 - - - -
284B ALA* 3.4 34.8 - - - +
286B ASN* 3.0 28.2 + - - +
287B GLU* 3.7 10.3 - - + +
288B TYR 3.3 0.2 - - - -
289B LEU* 1.4 73.7 - - - +
291B PHE* 1.3 63.6 + - - +
293B LYS* 3.3 7.6 + - - +
294B ILE* 3.2 27.9 + - + +
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Residues in contact with PHE 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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287A GLU* 4.6 7.2 - - + -
288A TYR* 3.5 48.5 - + + -
291A PHE* 4.0 20.0 - + - -
243B VAL* 5.0 11.0 - - + -
246B ALA* 3.7 33.4 - - + -
249B VAL* 5.3 0.7 - - + -
254B LEU* 3.7 31.0 - - + +
287B GLU* 2.9 42.3 + - + -
288B TYR* 3.3 12.1 + - - +
290B ILE* 1.3 77.5 - - - +
292B GLN* 1.3 60.0 + - - +
294B ILE* 3.4 4.2 + - - +
295B ILE* 3.1 28.9 + - - +
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Residues in contact with GLN 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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288A TYR* 3.4 27.9 + - - -
292A GLN* 3.3 24.6 + - - +
288B TYR* 3.0 48.4 + - + +
289B LEU* 3.6 14.4 - - + +
290B ILE 3.3 0.2 - - - -
291B PHE* 1.3 75.1 - - - +
293B LYS* 1.3 61.1 + - + +
295B ILE* 3.3 13.5 - - - +
296B LYS* 3.0 49.4 + - - +
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Residues in contact with LYS 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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282B PHE* 4.0 9.5 - - + -
283B ARG 3.1 31.9 + - - +
284B ALA* 4.4 8.6 - - + +
289B LEU 3.4 12.0 + - - +
290B ILE* 3.3 9.5 + - - +
292B GLN* 1.3 75.6 - - + +
294B ILE* 1.3 51.7 + - - +
296B LYS* 3.4 3.5 + - - +
297B LEU* 2.8 14.6 + - - -
298B GLU* 2.8 83.3 + - - +
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Residues in contact with ILE 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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246B ALA 3.3 26.7 - - - +
247B GLN 4.8 2.7 - - - +
249B VAL 3.4 25.6 - - - +
251B PRO* 3.8 19.0 - - + +
254B LEU* 4.0 15.7 - - + -
266B TRP* 3.8 9.6 - - + -
282B PHE* 3.5 33.7 - - + -
290B ILE* 3.2 27.8 + - + +
291B PHE* 3.6 10.1 - - + +
292B GLN 3.3 0.2 - - - -
293B LYS* 1.3 74.6 - - - +
295B ILE* 1.4 62.9 + - - +
297B LEU* 3.1 12.8 + - - -
319B LEU* 3.6 12.8 - - - +
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Residues in contact with ILE 295 (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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288A TYR* 3.5 23.8 - - + +
251B PRO* 4.0 21.1 - - + -
254B LEU* 4.2 12.8 - - + -
255B THR* 3.9 27.6 - - + -
291B PHE 3.1 13.9 + - - +
292B GLN* 3.3 26.9 - - - +
294B ILE* 1.4 73.3 - - - +
296B LYS* 1.4 69.2 + - + +
319B LEU* 3.7 18.9 - - - +
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Residues in contact with LYS 296 (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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292B GLN* 3.0 47.7 + - - +
293B LYS* 3.8 5.8 - - - +
295B ILE* 1.4 83.7 - - + +
297B LEU* 1.4 67.0 + - - +
298B GLU* 3.2 30.0 + - + +
319B LEU* 4.9 2.8 - - - +
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Residues in contact with LEU 297 (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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266B TRP* 3.7 27.1 - - + -
282B PHE* 4.1 6.1 - - + -
293B LYS 2.8 6.1 + - - -
294B ILE 3.1 6.5 + - - -
295B ILE 3.4 0.6 - - - -
296B LYS* 1.4 78.3 - - - +
298B GLU* 1.3 57.5 + - - +
299B TYR* 3.5 31.1 + - + +
317B LEU 3.6 25.6 - - - +
318B VAL* 4.9 1.3 - - + -
319B LEU* 3.9 30.3 - - + +
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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