Contacts of the helix formed by residues 351 - 362 (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 SER 351 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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350A VAL* 1.3 80.6 - - - +
352A PRO* 1.3 66.2 - - - +
353A GLU* 3.6 10.6 + - - +
354A GLU* 3.0 33.3 + - - +
355A ARG* 2.7 31.0 + - - +
487A TRP* 4.2 19.6 - - - +
490A ALA* 5.5 1.1 - - - -
491A TYR* 3.5 4.7 - - - -
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Residues in contact with PRO 352 (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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351A SER* 1.3 88.1 - - - +
353A GLU* 1.3 69.8 + - + +
355A ARG* 3.3 6.5 + - + +
356A GLU* 2.9 32.2 + - - +
490A ALA* 3.8 27.1 - - + +
491A TYR* 3.2 30.9 - - + +
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Residues in contact with GLU 353 (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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283A LEU* 3.7 23.0 - - + +
351A SER* 3.6 9.4 + - - +
352A PRO* 1.3 89.5 - - + +
354A GLU* 1.3 66.1 - - - +
356A GLU* 3.2 20.3 + - - +
357A TRP* 3.2 19.6 + - - +
490A ALA* 5.6 0.7 - - - +
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Residues in contact with GLU 354 (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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279A TYR 4.1 2.3 - - - +
282A PRO* 5.5 1.2 - - - +
283A LEU* 4.2 23.9 + - + -
286A ARG* 2.8 32.3 + - - +
349A GLY* 3.0 43.9 + - - +
350A VAL 3.3 0.2 + - - -
351A SER* 3.0 28.6 + - - +
353A GLU* 1.3 76.7 - - + +
355A ARG* 1.3 58.3 + - - +
357A TRP* 3.1 5.4 + - - +
358A LEU* 3.0 32.5 + - + +
487A TRP* 5.3 2.4 - - - +
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Residues in contact with ARG 355 (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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350A VAL* 3.4 31.0 + - - +
351A SER 2.7 17.2 + - - +
352A PRO* 3.6 6.5 - - + +
353A GLU 3.2 0.2 - - - -
354A GLU* 1.3 78.1 - - - +
356A GLU* 1.3 56.6 + - - +
358A LEU* 3.5 8.3 + - + +
359A GLU 3.1 19.9 + - - -
365A TRP* 3.7 15.9 - - + -
366A ASN* 2.6 49.4 + - - +
370A GLY* 3.2 24.2 + - - -
373A TRP* 4.2 8.1 + - - +
374A ASP* 2.7 38.0 + - - +
377A THR* 4.9 4.8 + - - -
491A TYR* 3.6 16.9 + - - -
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Residues in contact with GLU 356 (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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352A PRO* 2.9 20.8 + - - +
353A GLU* 3.3 23.5 - - - +
355A ARG* 1.3 72.5 - - - +
357A TRP* 1.3 64.6 + - - +
359A GLU* 3.3 8.8 + - + +
360A GLU* 3.0 24.6 + - - +
366A ASN* 5.1 0.7 - - - +
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Residues in contact with TRP 357 (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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277A MET 4.6 1.3 - - - -
278A ASP* 3.4 38.6 - - + -
283A LEU* 3.7 30.4 - - + +
286A ARG* 3.2 59.1 + - + +
288A GLN* 4.3 1.1 - - - -
289A SER* 4.0 15.0 - - - -
353A GLU 3.2 8.1 + - - +
354A GLU 3.1 8.4 + - - +
356A GLU* 1.3 76.3 - - - +
358A LEU* 1.3 83.2 + - + +
360A GLU* 2.9 19.1 + - - +
361A LYS* 2.8 66.3 + - + +
362A TYR* 4.7 1.3 - + - -
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Residues in contact with LEU 358 (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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278A ASP* 3.9 15.0 - - + +
279A TYR* 3.8 24.9 - - + +
286A ARG* 5.1 0.7 - - - +
329A HIS* 4.6 0.2 - - + -
349A GLY 4.0 12.6 - - - +
354A GLU 3.0 20.2 + - - +
355A ARG* 3.6 9.2 - - + +
357A TRP* 1.3 101.0 - - + +
359A GLU* 1.3 53.0 + - - +
361A LYS 4.5 0.2 - - - +
362A TYR* 2.7 51.0 + - + +
365A TRP* 3.4 50.3 - - + +
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Residues in contact with GLU 359 (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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355A ARG 3.1 17.6 + - - +
356A GLU* 3.6 9.6 - - - +
357A TRP 3.2 0.2 - - - -
358A LEU* 1.3 75.4 - - - +
360A GLU* 1.3 61.3 + - - +
362A TYR 3.8 2.7 - - - -
363A PRO* 3.4 24.8 - - - +
364A GLY* 2.8 29.4 + - - -
365A TRP* 3.5 1.0 + - - +
366A ASN* 2.7 50.2 + - - +
367A ASP 5.5 0.2 - - - -
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Residues in contact with GLU 360 (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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356A GLU 3.0 13.9 + - - +
357A TRP* 2.9 20.5 + - - +
359A GLU* 1.3 79.7 - - - +
361A LYS* 1.3 79.8 + - + +
363A PRO* 4.2 8.5 - - - +
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Residues in contact with LYS 361 (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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286A ARG 6.1 0.2 - - - -
287A ASN 5.2 1.8 + - - -
288A GLN* 4.5 4.3 - - - +
289A SER* 3.9 9.3 + - - +
291A LYS* 4.8 9.7 + - - +
292A GLU* 2.9 42.1 + - - +
357A TRP* 2.8 62.1 + - + +
358A LEU* 4.6 0.4 - - - -
360A GLU* 1.3 92.9 + - + +
362A TYR* 1.3 91.0 + - + +
363A PRO* 3.8 5.3 - - - +
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Residues in contact with TYR 362 (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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278A ASP* 2.4 34.0 + - - -
289A SER* 3.4 6.1 - - - -
290A PHE 3.3 3.6 + - - -
291A LYS* 3.2 43.8 + - + -
324A LEU 3.7 9.6 - - - -
325A ASP* 3.9 24.2 - - + +
328A HIS* 3.5 5.9 + + - -
329A HIS* 3.5 31.0 - + - +
357A TRP* 4.7 0.4 - + - -
358A LEU* 2.7 26.9 + - + +
359A GLU* 3.5 4.5 - - - +
361A LYS* 1.3 94.1 - - + +
363A PRO* 1.3 67.0 - - - +
364A GLY 3.2 0.2 + - - -
365A TRP* 3.1 27.7 + + + +
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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