Contacts of the helix formed by residues 352 - 364 (chain A) 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 LEU 352 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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306A VAL* 4.2 14.1 - - + +
307A LYS* 5.1 3.4 - - - -
310A CYS* 3.9 29.2 - - + -
322A ILE* 4.0 17.3 - - + -
330A ILE* 3.3 33.2 - - + -
348A VAL 4.4 1.1 + - - +
349A ILE* 3.2 23.3 - - + +
350A MSE 2.5 6.1 + - - -
351A GLY* 1.3 76.9 - - - +
353A SER* 1.3 64.9 + - - +
354A PRO 3.4 0.2 - - - -
355A ILE* 2.8 30.6 + - + +
356A LEU* 3.2 12.9 + - + +
365A LEU* 3.5 26.2 - - + -
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Residues in contact with SER 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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350A MSE 2.8 18.6 + - - +
352A LEU* 1.3 71.4 - - - +
354A PRO* 1.3 65.7 - - - +
355A ILE 2.9 6.4 + - - -
356A LEU 3.2 0.2 + - - -
357A GLY 3.0 21.1 + - - -
361A THR* 3.1 36.9 + - - +
365A LEU* 3.7 5.1 - - - +
369A PHE* 3.6 17.7 - - - -
390A CYS* 5.4 2.2 - - - -
391A VAL* 4.2 9.3 - - - +
394A VAL* 3.6 17.7 - - - +
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Residues in contact with PRO 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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311A GLU* 5.9 0.4 - - - +
350A MSE 3.7 4.7 - - - +
351A GLY* 3.4 21.3 - - - +
353A SER* 1.3 94.5 - - - +
355A ILE* 1.3 60.6 + - + +
357A GLY* 4.4 3.3 + - - +
390A CYS* 4.9 11.7 - - - -
394A VAL* 4.2 18.4 - - + -
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Residues in contact with ILE 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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307A LYS* 4.9 1.3 - - - +
310A CYS* 4.0 10.3 - - + -
311A GLU* 4.1 22.4 - - + +
318A ARG* 3.1 36.6 - - + +
319A GLU* 3.6 17.4 - - + +
322A ILE* 3.2 22.7 - - + -
351A GLY 3.6 20.9 - - - +
352A LEU* 2.8 30.5 + - + +
354A PRO* 1.3 84.1 - - + +
356A LEU* 1.3 66.9 + - + +
357A GLY 3.3 1.0 + - - -
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Residues in contact with LEU 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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319A GLU* 3.7 20.0 - - + +
322A ILE* 3.4 43.5 - - + -
323A MSE 3.7 26.5 - - + -
327A LEU* 4.9 3.6 - - + -
352A LEU* 3.2 12.9 + - + +
353A SER 4.3 1.8 - - - +
355A ILE* 1.3 79.8 - - - +
357A GLY* 1.3 63.3 + - - +
359A ASP* 5.3 0.5 - - - +
360A ASN* 3.0 40.8 + - + -
361A THR* 4.4 4.7 - - - +
364A HIS* 5.8 0.2 - - + -
365A LEU* 3.5 37.9 - - + -
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Residues in contact with GLY 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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319A GLU* 5.3 0.4 - - - -
353A SER 3.0 10.7 + - - -
354A PRO* 4.4 2.4 - - - -
355A ILE 3.3 4.4 + - - +
356A LEU* 1.3 81.5 - - - +
358A LYS* 1.3 68.9 + - - -
359A ASP 2.8 4.6 + - - -
361A THR* 2.9 24.1 + - - -
394A VAL* 3.6 3.8 - - - -
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Residues in contact with LYS 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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357A GLY* 1.3 70.0 - - - +
359A ASP* 1.3 68.3 + - - +
361A THR* 3.8 1.7 - - - -
362A ILE* 2.8 43.2 + - + +
394A VAL* 3.4 36.4 + - - +
396A GLY* 3.7 30.0 - - - +
398A ARG* 5.9 3.2 - - - +
399A GLN* 5.7 2.5 - - - -
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Residues in contact with ASP 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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356A LEU 5.3 0.4 - - - +
357A GLY 2.8 4.8 + - - +
358A LYS* 1.3 77.4 - - - +
360A ASN* 1.3 60.6 + - - +
361A THR 3.0 0.2 - - - -
362A ILE* 2.6 34.3 + - - +
363A GLU* 3.2 11.6 + - - +
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Residues in contact with ASN 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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319A GLU* 4.3 11.9 + - - -
323A MSE 3.0 36.3 - - + +
356A LEU* 3.0 30.0 + - + +
357A GLY 3.4 1.2 + - - -
359A ASP* 1.3 81.6 - - - +
361A THR* 1.3 54.5 + - - +
363A GLU* 4.4 8.6 + - - +
364A HIS* 2.7 57.5 + - + +
365A LEU* 4.8 1.1 - - - -
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Residues in contact with THR 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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353A SER* 3.1 47.7 + - - +
356A LEU* 4.3 2.3 - - - +
357A GLY 2.9 19.0 + - - -
358A LYS 3.8 4.9 - - - -
359A ASP 2.8 4.0 + - - -
360A ASN* 1.3 75.6 - - - +
362A ILE* 1.3 53.1 + - - -
365A LEU* 3.3 13.1 + - + +
366A LEU* 2.5 36.8 + - + +
369A PHE* 4.3 10.8 - - + -
394A VAL* 3.7 4.3 - - + +
395A ILE* 3.7 23.8 - - + -
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Residues in contact with ILE 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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358A LYS* 2.8 34.3 - - + +
359A ASP* 2.6 12.8 + - - +
361A THR* 1.3 72.5 - - - +
363A GLU* 1.3 63.1 + - - +
364A HIS 3.3 0.4 - - - -
366A LEU* 3.3 26.2 - - + +
367A PRO* 3.6 16.5 - - - +
395A ILE* 4.0 24.9 - - + -
396A GLY 4.7 0.4 - - - +
399A GLN* 3.7 36.8 - - + +
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Residues in contact with GLU 363 (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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359A ASP* 3.2 9.5 + - - +
360A ASN* 3.2 13.1 + - - +
362A ILE* 1.3 78.4 - - - +
364A HIS* 1.3 87.3 + - + +
367A PRO* 4.0 8.9 - - - +
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Residues in contact with HIS 364 (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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323A MSE 4.0 14.2 - - - +
327A LEU* 3.9 24.5 - - + +
331A LYS* 3.8 25.8 + - - +
356A LEU* 5.8 0.7 - - + -
360A ASN* 2.7 53.1 + - + +
363A GLU* 1.3 101.8 + - + +
365A LEU* 1.3 63.9 + - + +
367A PRO* 2.8 26.1 - - - +
368A LEU* 3.7 11.3 - - - +
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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