Contacts of the helix formed by residues 316 - 324 (chain A) in PDB entry 3N1Y
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 TYR 316 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259A ASP* 2.6 40.1 + - + -
262A ILE* 3.3 16.2 - - + +
263A TRP* 3.2 53.4 + + + -
314A PRO* 3.4 23.1 - - + +
315A TRP* 1.3 117.8 - + + +
317A TRP* 1.3 79.6 - + - +
318A ASP 3.4 2.2 - - - -
319A GLN* 3.1 14.5 + - + +
320A PHE* 2.9 25.6 + + + -
432A ALA* 4.3 5.4 - - + -
435A TRP* 5.0 2.5 - + - -
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Residues in contact with TRP 317 (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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262A ILE* 4.2 14.8 - - + -
299A VAL* 3.7 29.4 - - + -
302A PHE* 3.8 28.3 - + + -
303A GLU* 3.2 25.8 + - + -
306A LEU* 5.1 1.8 - - + -
313A LYS* 3.5 31.4 - - + +
314A PRO* 3.1 47.9 + - + +
315A TRP 3.3 1.6 - - - -
316A TYR* 1.3 82.0 - + - +
318A ASP* 1.3 67.2 + - - +
320A PHE* 3.3 34.9 + + - +
321A MET* 3.0 42.9 + - + +
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Residues in contact with ASP 318 (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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315A TRP 4.9 2.7 + - - +
316A TYR 3.4 1.0 - - - -
317A TRP* 1.3 81.2 - - - +
319A GLN* 1.3 63.8 + - - +
321A MET* 3.1 13.6 + - - +
322A GLN* 3.0 32.4 + - + +
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Residues in contact with GLN 319 (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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263A TRP* 5.1 6.1 - - + -
316A TYR* 3.1 17.7 + - + +
318A ASP* 1.3 76.5 - - - +
320A PHE* 1.3 57.5 + - - +
322A GLN* 3.0 30.3 + - - +
323A ASP* 2.7 67.3 + - - +
406A HIS* 5.4 3.0 + - - -
417A TYR* 6.1 1.3 - - - -
431A GLU* 6.0 6.1 - - + -
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Residues in contact with PHE 320 (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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200A PHE* 4.7 5.4 - + - -
262A ILE* 4.8 7.9 - - + -
263A TRP* 4.0 17.9 - + + -
266A TRP* 3.4 50.9 - + + -
294A MET* 3.8 22.4 - - + -
298A ILE* 5.5 0.4 - - + -
299A VAL* 4.3 15.3 - - + -
302A PHE* 5.5 2.2 - + - -
316A TYR* 2.9 17.8 + + + +
317A TRP* 3.3 51.6 - + - +
319A GLN* 1.3 76.9 - - - +
321A MET* 1.3 65.4 + - - +
323A ASP* 3.3 12.7 + - - +
324A LEU* 3.4 21.1 + - + +
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Residues in contact with MET 321 (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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291A LYS* 5.5 2.1 - - - -
295A LEU* 4.4 17.5 - - + -
299A VAL* 3.7 36.3 - - + -
303A GLU* 3.8 11.2 - - - +
317A TRP* 3.0 32.4 + - + +
318A ASP* 3.1 14.3 + - - +
320A PHE* 1.3 78.6 - - - +
322A GLN* 1.3 63.9 + - + +
324A LEU* 3.2 27.1 + - + +
325A ASP* 4.5 2.9 + - - +
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Residues in contact with GLN 322 (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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318A ASP* 3.0 21.4 + - - +
319A GLN* 3.0 32.7 + - - +
321A MET* 1.3 78.3 - - + +
323A ASP* 1.3 63.8 + - - +
324A LEU 3.0 1.4 + - - -
325A ASP* 3.0 27.5 + - - +
326A GLU* 4.1 4.4 + - - +
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Residues in contact with ASP 323 (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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263A TRP* 3.7 23.4 - - - -
266A TRP* 4.2 11.8 + - + +
319A GLN* 2.7 48.9 + - - +
320A PHE* 3.3 8.4 + - - +
322A GLN* 1.3 68.3 - - - +
324A LEU* 1.3 56.3 + - - +
325A ASP 2.9 6.1 - - - -
326A GLU* 2.8 22.7 + - - +
327A THR* 3.1 33.4 + - - +
328A HIS 4.8 0.7 + - - -
406A HIS* 3.8 17.5 + - - -
430A SER* 5.6 2.3 - - - -
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Residues in contact with LEU 324 (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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266A TRP* 3.8 20.9 - - + -
290A PHE* 5.1 1.6 - - + -
291A LYS* 3.8 22.4 - - + +
294A MET* 4.0 23.8 - - + -
295A LEU* 3.7 35.7 - - + -
299A VAL* 4.6 6.5 - - + -
320A PHE* 3.4 33.5 + - + +
321A MET* 3.3 24.0 - - - +
322A GLN 3.0 1.0 + - - -
323A ASP* 1.3 75.6 - - - +
325A ASP* 1.3 58.2 + - - +
326A GLU 3.4 0.2 - - - -
328A HIS* 3.6 22.3 - - - -
362A TYR* 3.7 7.6 - - - -
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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