Contacts of the helix formed by residues 364 - 374 (chain D) in PDB entry 2NYM
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 HIS 364 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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323D MSE 3.8 22.7 - - - +
327D LEU* 3.6 22.9 - - + +
331D LYS* 4.0 26.2 + - - +
356D LEU* 5.6 0.4 - - + -
360D ASN* 2.9 35.6 + - - +
363D GLU* 1.3 111.7 + - + +
365D LEU* 1.3 66.4 + - + +
366D LEU 3.5 1.8 - - - -
367D PRO* 3.2 13.5 - - - +
368D LEU* 3.8 14.4 - - - +
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Residues in contact with LEU 365 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327D LEU* 3.7 27.4 - - + -
330D ILE* 5.3 0.9 - - + -
349D ILE* 4.7 10.1 - - + +
352D LEU* 3.6 44.4 - - + +
353D SER* 3.8 11.9 - - - +
356D LEU* 3.3 31.2 - - + -
360D ASN 3.7 0.2 + - - -
361D THR* 3.1 15.3 + - + +
364D HIS* 1.3 75.6 - - + +
366D LEU* 1.3 68.4 + - - +
368D LEU* 3.0 25.0 + - + +
369D PHE* 3.1 25.9 + - + -
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Residues in contact with LEU 366 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361D THR* 2.6 21.2 + - + +
362D ILE* 3.4 34.5 - - + +
365D LEU* 1.3 70.6 - - - +
367D PRO* 1.3 61.8 - - + +
369D PHE* 2.6 53.1 + - + +
370D LEU* 3.0 13.5 - - + +
395D ILE* 4.5 13.9 - - + -
399D GLN* 3.7 4.3 - - - +
403D SER* 3.6 23.8 - - - +
404D LEU* 3.8 30.5 - - + -
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Residues in contact with PRO 367 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362D ILE 3.6 11.2 - - - +
363D GLU 4.0 10.8 - - - +
364D HIS 3.2 17.3 - - - +
366D LEU* 1.3 95.1 - - + +
368D LEU* 1.3 63.3 + - + +
370D LEU* 2.8 30.2 + - + +
371D ALA* 2.9 12.5 + - - +
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Residues in contact with LEU 368 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327D LEU* 4.8 0.9 - - + -
330D ILE* 3.9 13.2 - - + -
331D LYS* 4.3 26.2 - - + +
334D VAL* 3.6 36.1 - - + -
349D ILE* 3.8 24.5 - - + -
364D HIS 3.8 15.0 - - - +
365D LEU* 3.0 18.8 + - + +
367D PRO* 1.3 79.8 - - + +
369D PHE* 1.3 64.3 + - - +
371D ALA* 2.9 9.3 + - + +
372D GLN* 2.9 28.6 + - - +
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Residues in contact with PHE 369 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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349D ILE* 3.6 36.1 - - + -
350D MSE 3.2 41.7 - - + -
353D SER* 3.5 20.0 - - - -
361D THR* 4.0 11.0 - - + -
365D LEU* 3.1 22.2 + - + -
366D LEU* 2.6 48.0 + - + +
368D LEU* 1.3 72.0 - - - +
370D LEU* 1.3 55.1 + - + +
372D GLN* 3.6 7.8 + - - +
373D LEU* 2.8 34.7 + - + +
384D ILE* 4.1 13.7 - - + +
388D LEU* 5.6 0.9 - - + -
391D VAL* 4.4 4.5 - - + -
404D LEU* 4.5 7.6 - - + -
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Residues in contact with LEU 370 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366D LEU* 3.0 39.0 - - + +
367D PRO* 2.8 11.4 + - + +
369D PHE* 1.3 73.0 - - - +
371D ALA* 1.3 67.5 + - - +
372D GLN 2.9 2.0 - - - -
373D LEU* 2.7 17.6 + - + +
374D LYS* 2.8 34.5 + - + +
403D SER* 3.7 15.5 - - - +
404D LEU* 3.7 30.7 - - + -
407D ALA* 4.4 21.1 - - + -
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Residues in contact with ALA 371 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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334D VAL* 3.8 21.3 - - + -
367D PRO 2.9 11.3 + - - +
368D LEU* 3.4 12.3 - - + +
370D LEU* 1.3 76.9 - - - +
372D GLN* 1.3 56.0 + - - +
374D LYS* 3.4 6.7 + - - +
375D ASP* 3.2 24.0 + - - +
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Residues in contact with GLN 372 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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334D VAL* 4.2 15.2 - - + +
345D LEU* 3.1 34.2 - - - +
346D ALA* 3.3 19.2 - - - +
349D ILE* 3.6 18.0 - - - +
368D LEU 2.9 20.9 + - - +
369D PHE* 3.7 6.5 - - - +
371D ALA* 1.3 73.2 - - - +
373D LEU* 1.3 64.8 + - - +
374D LYS 2.8 6.5 + - - -
375D ASP* 3.0 14.8 + - - +
380D VAL* 4.0 24.1 - - + +
381D ARG* 3.5 13.9 - - - +
384D ILE* 3.3 27.0 - - + +
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Residues in contact with LEU 373 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369D PHE* 2.8 29.7 + - + +
370D LEU* 2.7 15.9 + - + +
372D GLN* 1.3 71.5 - - - +
374D LYS* 1.3 58.8 + - + +
381D ARG* 3.3 20.8 - - - +
384D ILE* 3.7 17.7 - - + -
385D ILE* 3.3 35.0 - - + -
388D LEU* 4.3 18.6 - - + -
404D LEU* 4.2 21.1 - - + -
407D ALA* 4.2 13.5 - - + -
408D ILE* 5.3 4.5 - - + +
411D LEU* 3.5 28.8 - - + +
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Residues in contact with LYS 374 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370D LEU* 2.8 34.2 + - + +
371D ALA* 3.6 5.6 - - - +
372D GLN 2.8 0.6 + - - -
373D LEU* 1.3 82.5 - - + +
375D ASP* 1.3 65.3 + - - +
376D GLU* 5.0 2.9 - - - +
381D ARG* 4.7 1.3 - - - +
407D ALA* 4.4 21.9 - - + +
410D GLU* 5.8 4.5 - - - -
411D LEU* 5.9 0.9 - - + -
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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