Contacts of the helix formed by residues 391 - 402 (chain N) in PDB entry 3L73
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 391 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8N LEU 5.9 0.9 - - - -
11N ILE* 6.5 2.0 - - - -
389N ARG* 4.0 13.8 + - - +
390N ILE* 1.3 77.3 - - - +
392N LEU* 1.3 61.9 + - - +
393N GLU* 3.5 14.9 + - - +
394N GLU* 2.8 34.9 + - - +
395N TRP* 2.9 13.1 + - - +
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Residues in contact with LEU 392 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8N LEU* 3.5 23.1 - - + -
11N ILE* 4.3 16.9 - - + +
365N MET* 3.7 37.5 - - + +
366N VAL* 3.9 23.8 - - + -
369N LEU* 3.4 37.9 - - + -
389N ARG* 5.3 2.3 - - - +
390N ILE 4.0 0.4 + - - +
391N SER* 1.3 72.6 - - - +
393N GLU* 1.3 65.9 + - - +
395N TRP* 3.7 11.6 - - + +
396N ASP* 2.8 27.5 + - - +
43O PRO* 4.4 6.3 - - + -
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Residues in contact with GLU 393 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5N ALA 5.1 0.7 - - - +
8N LEU* 3.9 32.5 + - + +
9N GLN* 3.1 42.6 + - - +
11N ILE* 5.9 0.2 - - - +
391N SER* 3.5 12.0 + - - +
392N LEU* 1.3 80.1 - - - +
394N GLU* 1.3 60.2 + - - +
396N ASP* 3.8 2.9 - - - +
397N SER* 3.3 18.2 + - - -
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Residues in contact with GLU 394 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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388N ARG* 3.2 39.6 + - - -
389N ARG 4.7 0.2 - - - +
390N ILE* 3.3 20.2 - - + +
391N SER* 2.8 19.1 + - - +
393N GLU* 1.3 77.1 - - - +
395N TRP* 1.3 68.0 + - - +
396N ASP 2.9 1.3 - - - -
397N SER* 2.6 22.2 + - - +
398N ARG* 3.1 38.6 + - + +
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Residues in contact with TRP 395 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268N VAL* 4.0 22.0 - - + -
365N MET* 3.6 26.7 - - + -
382N HIS* 3.9 18.1 + + - -
386N TYR* 3.7 32.8 - + - -
390N ILE* 3.8 36.1 - - + -
391N SER 2.9 14.1 + - - -
392N LEU* 3.7 21.1 - - + +
394N GLU* 1.3 76.3 - - - +
396N ASP* 1.3 56.9 + - - +
398N ARG* 3.2 28.2 + - - +
399N ILE* 2.8 38.2 + - + +
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Residues in contact with ASP 396 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4N TYR* 2.5 42.2 + - - +
8N LEU* 4.0 11.2 - - + -
362N ARG* 3.1 16.6 + - - -
365N MET* 4.4 4.7 - - + -
392N LEU 2.8 17.5 + - - +
393N GLU 3.8 5.4 - - - +
394N GLU 2.9 0.4 + - - -
395N TRP* 1.3 75.1 - - - +
397N SER* 1.3 63.7 + - - +
399N ILE* 3.9 7.5 - - - +
400N SER* 2.7 42.1 + - - -
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Residues in contact with SER 397 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393N GLU 3.3 11.3 + - - -
394N GLU* 2.6 20.1 + - - -
396N ASP* 1.3 77.8 - - - +
398N ARG* 1.3 61.8 + - - +
400N SER* 3.6 5.0 + - - -
401N ALA* 3.5 18.7 + - - +
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Residues in contact with ARG 398 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265N PRO* 4.3 26.1 - - - +
268N VAL* 4.3 18.7 - - + +
388N ARG* 4.7 6.3 - - - +
390N ILE* 5.7 1.4 - - - +
394N GLU* 3.1 37.2 + - + +
395N TRP* 3.5 34.4 - - - +
397N SER* 1.3 76.8 - - - +
399N ILE* 1.3 65.4 + - - +
401N ALA* 3.1 19.8 + - - +
402N VAL* 3.5 11.6 - - - +
406N MET* 5.1 0.3 - - - +
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Residues in contact with ILE 399 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268N VAL* 3.9 16.2 - - + -
272N VAL* 4.8 1.3 - - + -
358N LYS* 3.2 42.7 - - + +
361N LEU* 3.4 40.6 - - + -
362N ARG* 4.4 16.4 - - + +
365N MET* 4.1 24.0 - - + -
395N TRP* 2.8 24.7 + - + +
396N ASP* 3.9 5.6 - - - +
398N ARG* 1.3 75.8 - - - +
400N SER* 1.3 61.6 + - - +
401N ALA 3.4 0.7 + - - -
402N VAL* 3.4 13.7 + - - +
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Residues in contact with SER 400 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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358N LYS* 3.3 23.4 + - - +
362N ARG* 3.3 18.9 + - - +
396N ASP* 2.7 31.7 + - - -
397N SER* 3.9 5.8 - - - -
398N ARG 3.2 0.2 - - - -
399N ILE* 1.3 76.9 - - - +
401N ALA* 1.3 61.0 + - - +
402N VAL 3.2 0.7 - - - +
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Residues in contact with ALA 401 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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397N SER 3.5 10.8 + - - +
398N ARG* 3.1 14.4 + - - +
400N SER* 1.3 78.6 - - - +
402N VAL* 1.3 63.1 + - - +
403N ASP* 3.7 7.8 + - - +
406N MET* 4.1 13.3 - - + +
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Residues in contact with VAL 402 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268N VAL* 4.3 6.7 - - + -
269N VAL* 4.1 13.0 - - + -
272N VAL* 4.1 26.5 - - + -
354N VAL* 5.0 0.8 - - + +
358N LYS* 3.1 30.8 + - + +
398N ARG 3.5 15.0 - - - +
399N ILE* 3.5 15.3 - - - +
400N SER 3.2 1.1 - - - +
401N ALA* 1.3 79.1 - - - +
403N ASP* 1.3 65.2 + - - +
406N MET* 3.1 28.5 - - + -
407N VAL* 3.7 26.0 - - + -
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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