Contacts of the helix formed by residues 352 - 364 (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 LEU 352 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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306D VAL* 3.8 13.0 - - + +
307D LYS* 5.1 2.9 - - - -
310D CYS* 3.6 36.6 - - + -
322D ILE* 4.0 17.0 - - + -
327D LEU* 5.8 0.7 - - + -
330D ILE* 3.4 33.7 - - + -
348D VAL 5.1 1.3 - - - +
349D ILE* 3.4 20.6 - - + +
350D MSE 2.6 4.9 + - - -
351D GLY* 1.3 75.2 - - - +
353D SER* 1.3 62.9 + - - +
354D PRO 3.7 0.2 - - - -
355D ILE* 3.4 12.7 + - + +
356D LEU* 3.2 28.6 + - + +
365D LEU* 3.6 22.2 - - + -
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Residues in contact with SER 353 (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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350D MSE 2.7 22.2 + - - +
352D LEU* 1.3 73.2 - - - +
354D PRO* 1.3 68.9 - - - +
355D ILE 2.8 11.1 + - - -
356D LEU 3.3 1.2 + - - -
357D GLY* 3.0 21.1 + - - -
361D THR* 3.3 33.2 + - - +
365D LEU* 3.8 3.0 - - - +
369D PHE* 3.5 16.6 - - - -
390D CYS* 5.6 0.4 - - - -
391D VAL* 5.5 0.8 - - - +
394D VAL* 3.8 17.6 - - - +
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Residues in contact with PRO 354 (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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350D MSE 3.8 5.2 - - - +
351D GLY* 3.8 15.3 - - - +
353D SER* 1.3 93.8 - - - +
355D ILE* 1.3 62.1 + - + +
357D GLY* 4.2 5.4 + - - +
390D CYS* 4.9 12.6 - - - -
394D VAL* 4.1 16.4 - - + -
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Residues in contact with ILE 355 (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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307D LYS 5.3 0.2 - - - +
310D CYS* 4.1 9.6 - - + -
311D GLU* 4.5 16.4 - - + +
318D ARG* 3.2 39.5 - - + +
319D GLU* 3.5 19.0 - - + +
322D ILE* 3.7 28.0 - - + -
351D GLY 3.5 23.1 - - - +
352D LEU* 3.6 17.9 - - + +
353D SER 2.8 3.2 + - - -
354D PRO* 1.3 81.4 - - + +
356D LEU* 1.3 66.9 + - + +
357D GLY* 3.2 2.2 + - - -
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Residues in contact with LEU 356 (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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319D GLU* 3.9 19.5 - - + +
322D ILE* 3.6 36.1 - - + -
323D MSE 3.8 27.6 - - + -
327D LEU* 5.4 3.6 - - + -
352D LEU* 3.2 10.7 + - + +
353D SER 3.3 2.3 + - - +
355D ILE* 1.3 80.7 - - + +
357D GLY* 1.3 64.8 + - - +
359D ASP* 4.9 0.7 + - - +
360D ASN* 3.3 38.9 + - + +
361D THR* 4.5 2.7 - - - +
364D HIS* 5.6 0.4 - - + -
365D LEU* 3.3 39.5 - - + -
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Residues in contact with GLY 357 (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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353D SER 3.0 11.1 + - - -
354D PRO* 4.8 4.7 - - - -
355D ILE 3.2 4.5 - - - +
356D LEU* 1.3 80.5 - - - +
358D LYS* 1.3 64.5 + - - -
359D ASP 3.2 1.5 + - - -
361D THR* 2.7 31.9 + - - -
394D VAL* 3.7 3.8 - - - -
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Residues in contact with LYS 358 (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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357D GLY* 1.3 71.7 - - - +
359D ASP* 1.3 76.7 + - - +
361D THR* 3.5 0.9 + - - -
362D ILE* 2.9 37.4 + - + +
394D VAL* 3.1 33.6 - - - +
395D ILE* 4.3 0.2 - - - -
396D GLY* 3.8 27.8 - - - +
398D ARG* 5.9 4.2 - - - +
399D GLN* 5.9 1.8 - - - -
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Residues in contact with ASP 359 (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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356D LEU 5.5 0.7 - - - +
357D GLY 3.2 1.2 + - - -
358D LYS* 1.3 91.4 + - - +
360D ASN* 1.3 60.3 + - - +
362D ILE* 2.8 24.4 + - - +
363D GLU* 3.2 10.9 + - - +
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Residues in contact with ASN 360 (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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319D GLU* 4.9 7.1 + - - -
323D MSE 3.1 36.2 - - + +
356D LEU* 3.3 29.5 + - + +
357D GLY 3.6 1.4 + - - -
359D ASP* 1.3 83.0 - - - +
361D THR* 1.3 56.8 + - - +
362D ILE 3.1 0.2 - - - -
363D GLU* 3.8 10.2 - - - +
364D HIS* 2.9 51.7 + - + +
365D LEU* 3.7 1.0 + - - +
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Residues in contact with THR 361 (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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353D SER* 3.3 44.7 + - - +
356D LEU* 4.5 1.5 - - - +
357D GLY 2.7 24.3 + - - -
358D LYS 3.9 4.5 - - - -
359D ASP 2.9 2.6 + - - -
360D ASN* 1.3 74.3 - - - +
362D ILE* 1.3 54.4 + - - +
365D LEU* 3.1 15.2 + - + +
366D LEU* 2.6 34.4 + - - +
369D PHE* 4.0 14.1 - - + -
391D VAL* 6.0 0.2 - - + -
394D VAL* 3.3 8.4 - - + +
395D ILE* 3.9 18.8 - - + -
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Residues in contact with ILE 362 (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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358D LYS* 2.9 34.8 - - + +
359D ASP* 2.8 7.4 + - - +
361D THR* 1.3 77.4 - - - +
363D GLU* 1.3 64.4 + - - +
366D LEU* 3.4 25.5 - - + +
367D PRO* 3.6 15.2 - - - +
395D ILE* 3.9 23.8 - - + -
399D GLN* 3.7 36.1 - - + +
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Residues in contact with GLU 363 (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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359D ASP 3.2 9.6 + - - +
360D ASN* 4.2 12.6 - - - +
362D ILE* 1.3 79.6 - - - +
364D HIS* 1.3 89.3 + - + +
367D PRO* 4.0 10.4 - - - +
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Residues in contact with HIS 364 (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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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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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