Contacts of the helix formed by residues 357 - 366 (chain A) in PDB entry 2N97
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 ASP 357 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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355A ALA* 3.3 25.1 - - - +
356A GLY* 1.3 75.5 - - - +
358A THR* 1.3 69.6 + - - +
359A TRP* 3.3 3.1 - - - +
360A ARG* 3.0 34.3 + - - +
361A HIS* 3.7 12.2 + - + +
410A ARG* 2.8 32.1 + - - -
374B ASP* 4.9 13.9 - - - +
377B THR* 3.5 26.1 + - - +
378B HIS* 5.0 6.1 + - - +
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Residues in contact with THR 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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351A LEU* 3.6 19.1 - - - +
355A ALA* 4.3 5.5 + - + +
356A GLY 3.6 0.8 - - - -
357A ASP* 1.3 89.8 - - - +
359A TRP* 1.3 58.1 + - - +
361A HIS* 3.3 10.6 + - - +
362A LEU* 2.9 36.1 + - - +
405A LEU* 6.0 0.4 - - - -
408A ILE* 4.0 7.3 - - - +
410A ARG* 3.5 29.6 - - - +
413A LEU* 3.7 31.7 - - + +
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Residues in contact with TRP 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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351A LEU* 3.9 20.5 - - + +
356A GLY 3.1 28.6 + - - -
357A ASP 4.2 0.4 - - - -
358A THR* 1.3 79.7 + - - +
360A ARG* 1.3 80.5 + - + +
362A LEU* 3.5 13.7 + - + +
363A ALA* 2.9 34.5 + - + +
373A ILE* 3.7 33.4 - - + -
376A PHE* 4.1 19.5 - + + -
377A THR* 3.4 33.7 - - + -
382A PRO* 3.3 30.0 - - + +
383A VAL* 4.7 10.3 - - + -
386A LEU* 3.9 28.6 - - + +
360B ARG* 5.1 0.2 - - - -
377B THR* 5.7 2.1 - - + +
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Residues in contact with ARG 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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357A ASP* 3.0 17.2 + - - +
359A TRP* 1.3 109.9 - - + +
361A HIS* 1.3 65.5 + - + +
363A ALA* 3.3 5.0 + - - +
364A GLY* 3.1 24.9 + - - -
373A ILE* 5.0 13.4 - - + +
360B ARG* 3.8 29.0 - - - +
373B ILE* 3.9 25.5 - - - +
374B ASP* 5.0 6.5 + - - -
377B THR* 4.3 26.1 + - - +
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Residues in contact with HIS 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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357A ASP* 3.7 22.2 + - + +
358A THR* 3.3 7.3 + - - +
360A ARG* 1.3 77.8 - - + +
362A LEU* 1.3 65.0 + - - +
364A GLY* 3.4 3.4 + - - -
365A GLU* 3.2 18.7 + - - +
408A ILE* 3.5 36.4 - - + +
410A ARG* 3.8 30.6 + - - -
374B ASP* 4.6 14.7 + - - -
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Residues in contact with LEU 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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351A LEU* 6.5 0.2 - - + -
358A THR* 2.9 22.9 + - - +
359A TRP* 3.6 16.4 - - + +
361A HIS* 1.3 74.7 - - - +
363A ALA* 1.3 56.6 + - - +
365A GLU* 3.1 3.8 + - - +
366A LEU* 2.8 43.7 + - + +
386A LEU* 5.3 5.4 - - + -
401A LEU* 4.3 20.0 - - + +
404A ALA* 3.5 30.5 - - + -
405A LEU* 3.8 24.9 - - + +
408A ILE* 4.0 12.3 - - + -
413A LEU* 6.5 0.2 - - + -
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Residues in contact with ALA 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 TRP* 2.9 29.4 + - + +
360A ARG* 3.3 8.0 + - - +
362A LEU* 1.3 71.2 - - - +
364A GLY* 1.3 59.4 + - - +
366A LEU* 3.6 8.1 + - - +
367A GLY 3.2 3.5 + - - -
368A TYR* 3.1 44.7 + - + +
373A ILE* 4.2 24.7 - - + -
376A PHE* 5.5 2.5 - - + -
386A LEU* 4.8 7.4 - - + +
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Residues in contact with GLY 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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360A ARG 3.1 13.4 + - - -
361A HIS 3.4 4.2 + - - -
362A LEU 3.2 0.2 - - - -
363A ALA* 1.3 76.1 - - - +
365A GLU* 1.3 59.6 + - - +
367A GLY* 3.1 19.1 + - - -
368A TYR 5.6 2.0 - - - -
373A ILE* 5.1 5.5 - - - +
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Residues in contact with GLU 365 (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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361A HIS 3.2 6.9 + - - +
362A LEU 3.1 4.4 + - - +
364A GLY* 1.3 72.1 - - - +
366A LEU* 1.3 59.9 + - - +
367A GLY* 3.2 6.6 + - - -
404A ALA* 4.6 14.4 - - + -
407A ARG* 3.8 33.7 + - + +
408A ILE* 3.5 29.4 - - + -
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Residues in contact with LEU 366 (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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362A LEU* 2.8 36.3 + - + +
363A ALA* 3.8 7.0 - - - +
365A GLU* 1.3 69.9 - - - +
367A GLY* 1.3 59.9 + - - +
368A TYR* 3.4 21.4 + - + -
386A LEU* 4.9 8.3 - - + -
390A TRP* 3.5 43.5 - - + +
400A ALA* 5.1 2.9 - - + +
401A LEU* 5.8 0.9 - - - -
404A ALA* 3.5 29.4 - - + -
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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