Contacts of the helix formed by residues 370 - 386 (chain N) in PDB entry 5A31
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 GLN 370 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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334N ARG* 3.9 13.2 - - + +
337N ALA* 3.2 25.9 - - + +
338N SER* 3.5 16.7 + - - +
341N ILE* 3.3 23.8 - - + +
365N LEU* 4.7 17.9 + - + +
368N THR* 3.7 5.5 + - - +
369N ASP* 1.3 78.2 - - - +
371N ARG* 1.3 64.4 + - - +
372N GLN 3.3 2.6 + - - -
373N GLN* 2.9 46.1 + - + +
374N LEU* 3.1 20.0 + - - +
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Residues in contact with ARG 371 (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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365N LEU* 4.1 32.2 + - + +
366N GLU* 3.6 29.7 + - - +
368N THR* 4.2 13.0 + - - -
369N ASP* 3.7 4.0 + - - -
370N GLN* 1.3 75.9 - - - +
372N GLN* 1.3 63.3 + - + +
374N LEU* 3.1 23.2 - - + +
375N LEU* 3.3 16.7 + - + +
411N ASP* 4.3 18.6 + - - +
416N ILE* 5.5 1.1 - - + +
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Residues in contact with GLN 372 (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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369N ASP 5.1 1.2 + - - +
370N GLN 3.4 0.6 - - - -
371N ARG* 1.3 76.2 - - + +
373N GLN* 1.3 65.7 + - - +
375N LEU* 3.3 23.1 + - - +
376N VAL* 3.1 29.3 + - + +
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Residues in contact with GLN 373 (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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338N SER* 5.7 1.7 - - - -
341N ILE* 5.0 2.6 - - - +
342N GLU* 5.2 3.1 - - - +
370N GLN* 2.9 45.5 + - + +
372N GLN* 1.3 74.9 - - - +
374N LEU* 1.3 65.0 + - - +
376N VAL* 3.3 13.1 + - + +
377N SER* 3.0 33.3 + - - -
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Residues in contact with LEU 374 (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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341N ILE* 3.7 31.8 - - + +
344N LEU* 3.3 35.9 - - + -
361N LEU* 4.7 9.4 - - + -
365N LEU* 3.9 28.9 - - + -
370N GLN 3.1 11.3 + - - +
371N ARG* 3.1 14.6 + - - +
373N GLN* 1.3 76.6 - - - +
375N LEU* 1.3 57.4 + - - +
377N SER* 3.7 1.2 - - - -
378N LEU* 2.9 32.6 + - + +
407N LEU* 6.2 0.4 - - + -
410N ILE* 5.2 2.9 - - + -
411N ASP* 4.7 1.8 - - - +
416N ILE* 3.6 25.6 - - + -
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Residues in contact with LEU 375 (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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371N ARG* 3.3 16.4 + - + +
372N GLN* 3.3 26.9 + - - +
374N LEU* 1.3 77.2 - - - +
376N VAL* 1.3 67.8 + - - +
378N LEU* 4.0 4.6 - - + +
379N LYS* 3.1 24.6 + - - +
416N ILE* 3.7 42.6 - - + +
419N VAL* 4.1 26.9 - - + -
420N ALA* 4.2 11.9 - - + +
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Residues in contact with VAL 376 (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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372N GLN* 3.1 22.4 + - + +
373N GLN* 3.5 12.8 - - + +
375N LEU* 1.3 76.4 - - - +
377N SER* 1.3 62.1 + - - +
379N LYS* 3.4 6.3 + - - +
380N ALA* 3.0 30.5 + - + +
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Residues in contact with SER 377 (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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341N ILE* 3.4 30.4 + - - +
342N GLU* 3.6 15.7 + - - -
344N LEU* 6.0 0.3 - - - +
373N GLN* 3.0 22.2 + - - -
374N LEU 3.8 0.9 - - - -
376N VAL* 1.3 77.2 - - - +
378N LEU* 1.3 59.8 + - - +
380N ALA* 3.8 4.8 - - - +
381N ALA* 2.8 32.6 + - - +
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Residues in contact with LEU 378 (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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344N LEU* 3.6 31.3 - - + +
345N PHE* 5.5 5.4 - - + +
374N LEU* 2.9 22.8 + - + +
375N LEU* 4.0 5.4 - - + +
377N SER* 1.3 74.2 - - - +
379N LYS* 1.3 59.0 + - - +
381N ALA* 3.2 5.5 + - - +
382N LEU* 2.8 63.8 + - + +
407N LEU* 4.1 23.3 - - + -
416N ILE* 5.1 4.7 - - + -
420N ALA* 3.8 29.2 - - + -
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Residues in contact with LYS 379 (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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375N LEU 3.1 17.8 + - - +
376N VAL* 3.8 4.7 - - - +
378N LEU* 1.3 77.1 - - - +
380N ALA* 1.3 65.6 + - + +
382N LEU* 3.5 6.3 + - - +
383N GLU* 3.1 50.5 + - - +
420N ALA* 5.7 6.8 - - - +
422N GLU* 5.7 3.4 + - - -
423N PRO* 4.1 32.3 - - + +
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Residues in contact with ALA 380 (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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376N VAL* 3.0 22.2 + - + +
377N SER* 3.9 5.2 - - - +
379N LYS* 1.3 78.7 - - + +
381N ALA* 1.3 59.2 + - - +
383N GLU* 3.5 6.5 + - - +
384N THR* 2.9 38.5 + - + +
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Residues in contact with ALA 381 (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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345N PHE* 4.1 26.5 - - + -
377N SER* 2.8 26.1 + - - +
378N LEU* 3.6 6.1 - - - +
380N ALA* 1.3 72.5 - - - +
382N LEU* 1.3 54.5 + - - +
384N THR* 2.7 20.8 + - - -
385N ARG* 2.8 31.3 + - - +
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Residues in contact with LEU 382 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345N PHE* 3.4 31.6 - - + -
378N LEU* 2.8 46.6 + - + +
379N LYS* 3.8 7.2 - - - +
381N ALA* 1.3 72.9 - - - +
383N GLU* 1.3 57.8 + - - +
386N LEU* 2.7 33.1 + - + -
387N LEU* 3.0 24.3 + - + -
399N LEU* 4.5 9.6 - - + -
420N ALA 4.5 12.3 - - - +
421N CYS* 6.1 0.2 - - - -
423N PRO* 5.2 1.1 - - + -
424N ILE* 3.4 38.8 - - + -
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Residues in contact with GLU 383 (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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166I LYS* 5.0 10.7 + - - -
379N LYS* 3.1 49.0 + - - +
380N ALA* 3.9 5.1 - - - +
382N LEU* 1.3 76.0 - - - +
384N THR* 1.3 64.0 + - + +
387N LEU* 4.3 23.5 - - + +
388N HIS* 3.9 18.2 + - - +
423N PRO* 4.8 5.1 - - + +
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Residues in contact with THR 384 (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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380N ALA* 2.9 22.2 + - + +
381N ALA* 2.7 25.8 + - - -
383N GLU* 1.3 78.0 - - + +
385N ARG* 1.3 64.6 + - - +
388N HIS* 3.6 19.2 + - - -
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Residues in contact with ARG 385 (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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342N GLU 4.7 4.2 + - - -
345N PHE* 2.9 59.5 - - + +
346N SER* 3.8 22.4 + - - +
349N ARG* 5.2 3.8 - - - +
381N ALA* 2.8 25.0 + - - +
384N THR* 1.3 84.0 - - - +
386N LEU* 1.3 61.3 + - - +
388N HIS* 4.3 9.9 - - - -
391N VAL* 4.7 5.2 - - - +
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Residues in contact with LEU 386 (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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345N PHE* 3.8 14.6 - - + -
382N LEU* 2.7 27.0 + - + +
385N ARG* 1.3 75.5 - - - +
387N LEU* 1.3 92.9 + - + +
388N HIS* 2.3 35.9 + - - +
391N VAL* 3.9 17.1 - - + +
395N ASP 5.6 0.2 - - - +
396N ILE* 3.8 29.1 - - + +
399N LEU* 3.7 45.8 - - + -
424N ILE* 4.8 1.8 - - + -
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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