Contacts of the helix formed by residues 321 - 332 (chain A) in PDB entry 1NYX
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 GLY 321 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296A ILE* 5.7 0.2 - - - -
317A LEU 3.0 16.3 + - - -
319A LYS 3.2 0.8 - - - -
320A TYR* 1.3 80.1 - - - +
322A VAL* 1.3 68.7 + - - +
323A HIS 3.2 2.8 + - - -
324A GLU* 3.4 5.6 + - - +
325A ILE* 3.2 30.1 + - - +
391A ILE* 4.6 4.7 - - - -
392A ILE* 5.2 6.3 - - - -
397A ARG* 3.7 11.4 - - - -
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Residues in contact with VAL 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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293A VAL* 3.1 49.8 - - + -
296A ILE* 3.4 24.5 - - + +
318A LEU* 3.2 16.8 + - + +
319A LYS 4.1 0.4 - - - +
321A GLY* 1.3 76.4 - - - +
323A HIS* 1.3 96.0 + - + +
325A ILE* 3.4 0.4 + - - -
326A ILE* 2.8 33.8 + - + +
472A ILE* 3.6 21.8 - - + -
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Residues in contact with HIS 323 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A DRF 2.6 31.8 + - + -
319A LYS 5.4 0.2 + - - -
320A TYR 5.5 0.4 - - - -
321A GLY 3.3 0.6 - - - +
322A VAL* 1.3 97.9 - - + +
324A GLU* 1.3 67.7 + - + +
325A ILE 2.6 6.6 + - - -
326A ILE* 2.8 22.5 + - + +
327A TYR* 3.0 44.7 + + + -
446A VAL* 4.1 12.5 - - + +
469A LEU* 3.9 5.1 - - + +
472A ILE* 3.3 33.3 - - + +
473A TYR* 2.8 34.0 + + - -
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Residues in contact with GLU 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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320A TYR 3.9 13.0 - - - +
321A GLY 3.4 5.1 + - - +
323A HIS* 1.3 75.9 - - - +
325A ILE* 1.3 58.0 + - - +
328A THR* 2.9 19.2 + - - -
391A ILE* 3.9 15.4 - - + +
397A ARG* 3.3 33.5 + - - -
439A MET* 5.0 11.1 - - - +
442A LEU* 3.2 41.5 - - + +
443A ARG* 3.4 34.1 + - - +
446A VAL* 4.2 16.5 - - + +
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Residues in contact with ILE 325 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A ILE* 3.3 31.6 - - + -
321A GLY 3.2 11.1 + - - +
322A VAL 3.6 2.5 - - - +
323A HIS 2.6 4.8 + - - -
324A GLU* 1.3 73.7 - - - +
326A ILE* 1.3 60.4 + - - +
327A TYR 3.0 2.0 - - - -
328A THR* 2.8 22.2 + - - -
329A MET* 2.9 23.3 + - + +
388A ILE* 2.9 58.3 - - + +
391A ILE* 3.4 21.5 - - + -
392A ILE* 3.5 25.8 - - + -
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Residues in contact with ILE 326 (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 DRF 3.6 31.4 - - + -
289A SER* 3.8 23.3 - - - +
292A ALA* 3.5 27.4 - - + -
293A VAL* 4.4 1.8 - - + -
296A ILE* 3.6 13.5 - - + -
322A VAL* 2.8 34.4 + - + +
323A HIS* 2.8 19.6 + - + +
325A ILE* 1.3 72.5 - - - +
327A TYR* 1.3 67.5 + - + +
329A MET* 3.7 9.7 + - + +
330A LEU* 2.9 26.1 + - + +
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Residues in contact with TYR 327 (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 DRF 3.9 12.2 - + - +
323A HIS* 3.0 51.4 + + + -
326A ILE* 1.3 91.3 - - + +
328A THR* 1.3 66.0 + - - +
330A LEU* 3.7 13.1 - - + +
331A ALA* 3.5 11.6 + - - +
367A LYS* 3.9 32.3 - - + -
370A PHE* 3.6 20.6 - - + -
442A LEU* 3.6 17.5 - - + -
445A ILE* 3.7 27.8 - - + -
446A VAL* 4.0 17.7 - - + -
449A HIS* 3.4 28.3 + - - -
473A TYR* 4.0 0.7 + - - -
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Residues in contact with THR 328 (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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324A GLU 2.9 19.5 + - - -
325A ILE* 2.8 9.5 + - - -
327A TYR* 1.3 75.5 - - - +
329A MET* 1.3 72.5 + - + +
330A LEU 3.0 1.1 - - - -
331A ALA* 3.0 20.6 + - - +
332A SER* 3.7 4.9 + - - -
370A PHE* 4.6 6.7 - - - -
374A PHE* 3.9 28.3 - - + -
384A LEU* 4.3 11.5 - - + +
387A PHE* 4.1 12.1 - - + -
388A ILE* 3.9 21.3 - - + -
391A ILE* 4.3 0.7 - - - +
442A LEU* 3.7 13.7 - - - +
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Residues in contact with MET 329 (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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222A TYR* 4.1 19.1 - - + +
226A PHE* 4.2 33.9 - - + -
296A ILE* 5.1 3.6 - - + -
325A ILE* 2.9 32.4 + - + +
326A ILE* 3.9 8.1 - - + +
328A THR* 1.3 82.2 - - + +
330A LEU* 1.3 59.5 + - - +
332A SER* 2.6 24.4 + - - +
333A LEU* 3.8 11.7 + - - +
384A LEU* 4.4 7.9 - - + -
388A ILE* 3.3 33.0 - - + -
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Residues in contact with LEU 330 (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 DRF 3.0 45.8 - - + +
326A ILE* 2.9 18.0 + - + +
327A TYR* 3.7 22.7 - - + +
328A THR 3.0 0.4 - - - -
329A MET* 1.3 79.3 - - - +
331A ALA* 1.3 60.9 + - - +
333A LEU* 3.0 18.7 + - + +
334A MET* 3.0 36.4 + - + +
339A VAL* 4.7 7.4 - - + -
364A MET* 3.7 29.8 - - + -
367A LYS* 4.2 8.5 - - + -
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Residues in contact with ALA 331 (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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234A ARG* 4.1 0.3 + - - -
327A TYR 3.5 8.7 + - - +
328A THR 3.0 12.3 + - - +
330A LEU* 1.3 78.7 - - - +
332A SER* 1.3 56.7 + - - +
333A LEU 3.0 0.4 - - - -
334A MET* 3.2 12.6 + - - +
370A PHE* 4.9 0.9 - - + -
371A ALA* 3.6 32.5 - - - +
374A PHE* 3.9 16.4 - - + -
375A ASN* 2.7 38.4 + - - +
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Residues in contact with SER 332 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222A TYR* 5.5 1.0 + - - -
229A THR 5.5 0.5 - - - -
230A LYS* 3.3 43.1 + - - +
233A ALA* 2.9 28.2 - - - +
234A ARG* 3.3 12.5 + - - +
328A THR 3.7 1.7 + - - -
329A MET* 2.6 29.5 + - - +
330A LEU 3.2 0.2 - - - -
331A ALA* 1.3 75.5 - - - +
333A LEU* 1.3 59.4 + - - +
334A MET 3.4 0.7 - - - -
375A ASN* 4.3 3.8 - - - -
384A LEU* 4.4 10.2 - - - +
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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