Contacts of the helix formed by residues 365 - 379 (chain L) in PDB entry 1QDU
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 365 (chain L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363L GLY 3.7 3.0 + - - -
364L ASP* 1.3 71.8 - - - +
366L ILE* 1.3 73.0 + - - +
367L LEU* 3.1 16.3 + - - +
368L THR* 2.7 47.0 + - - +
369L ILE* 3.0 14.0 + - - +
394L LEU* 5.9 0.3 - - - +
397L LYS* 2.8 55.6 + - + +
398L LEU 3.7 18.9 + - - +
399L VAL* 4.7 4.5 - - + +
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Residues in contact with ILE 366 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279K VAL* 6.1 0.4 - - + -
281K PHE* 4.9 13.5 - - + -
328L LEU* 3.4 30.3 - - + -
353L LEU* 5.4 1.1 - - + -
357L LEU* 4.8 8.1 - - + -
364L ASP 3.7 0.8 + - - -
365L ASP* 1.3 70.1 - - - +
367L LEU* 1.3 73.8 + - + +
369L ILE* 3.0 22.9 + - + +
370L LEU* 2.7 47.6 + - + +
394L LEU* 4.4 5.4 - - + -
398L LEU* 3.0 33.1 + - + +
400L PHE* 4.2 24.7 - - + -
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Residues in contact with LEU 367 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367J LEU* 4.2 19.3 - - + -
371J THR* 3.9 15.0 - - - +
392J PHE* 4.2 26.3 - - + -
328L LEU* 4.4 15.0 - - + -
365L ASP* 3.1 16.8 + - - +
366L ILE* 1.3 93.8 - - + +
368L THR* 1.3 53.0 + - - +
370L LEU* 3.2 5.6 + - + +
371L THR* 2.7 39.0 + - - -
392L PHE* 3.9 37.0 - - + -
394L LEU* 4.8 8.3 - - + -
396L LYS 6.1 0.9 - - - +
397L LYS* 4.5 5.2 - - - +
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Residues in contact with THR 368 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150I ASP* 3.7 17.9 - - - +
367J LEU* 6.1 0.7 - - - -
397J LYS* 2.9 32.2 + - + +
360L ARG* 4.1 20.2 - - - +
364L ASP* 4.4 8.6 + - - +
365L ASP* 2.7 35.3 + - - +
367L LEU* 1.3 76.5 - - - +
369L ILE* 1.3 66.5 + - - +
371L THR* 3.1 9.8 + - + -
372L GLU* 3.1 17.3 + - - +
397L LYS* 4.5 1.9 + - - -
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Residues in contact with ILE 369 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353L LEU* 4.7 2.0 - - + +
356L SER* 3.6 32.1 - - - +
357L LEU* 4.1 11.0 - - + +
360L ARG* 3.5 30.1 - - + -
361L CYS* 4.3 17.7 - - - -
364L ASP* 3.1 19.7 - - + +
365L ASP 3.0 25.5 + - - +
366L ILE* 3.0 21.9 + - + +
368L THR* 1.3 76.6 - - - +
370L LEU* 1.3 57.4 + - - +
372L GLU* 2.6 30.5 + - - +
373L VAL* 2.8 17.0 + - + -
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Residues in contact with LEU 370 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392J PHE* 4.4 7.6 - - + -
281K PHE* 4.4 9.4 - - + -
328L LEU* 4.0 28.7 - - + -
330L GLY* 4.8 2.5 - - - -
349L TYR* 3.8 23.8 - - + +
353L LEU* 4.2 20.9 - - + -
366L ILE* 2.7 29.3 + - + +
367L LEU* 3.6 10.1 - - + +
369L ILE* 1.3 73.5 - - - +
371L THR* 1.3 61.4 + - - +
373L VAL* 3.3 12.0 + - + +
374L ASN* 3.1 26.1 + - - +
389L PRO* 3.5 30.4 - - + +
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Residues in contact with THR 371 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367J LEU* 3.6 23.4 - - - +
392J PHE* 3.7 12.7 - - - -
394J LEU* 4.4 3.3 + - - +
395J ARG* 3.8 6.4 - - - +
396J LYS* 3.8 35.7 - - - +
397J LYS* 4.4 8.1 - - + +
367L LEU 2.7 15.0 + - - -
368L THR* 3.3 13.5 - - + +
369L ILE 3.0 0.2 - - - -
370L LEU* 1.3 77.2 - - - +
372L GLU* 1.3 62.8 + - - +
374L ASN* 3.0 22.9 - - - +
375L TYR* 3.0 6.9 + - - +
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Residues in contact with GLU 372 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150I ASP* 5.5 0.3 - - - +
395J ARG 5.3 0.2 - - - -
356L SER* 2.7 23.9 + - - +
359L GLU* 4.1 9.7 - - - +
360L ARG* 2.4 50.9 + - - +
368L THR 3.1 10.0 + - - +
369L ILE* 2.6 18.8 + - - +
371L THR* 1.3 71.1 - - - +
373L VAL* 1.3 56.5 + - - +
375L TYR* 2.8 27.2 + - + +
376L GLU* 2.9 34.2 + - + +
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Residues in contact with VAL 373 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349L TYR* 3.8 33.7 - - + -
352L SER* 3.9 17.7 - - - +
353L LEU* 3.8 28.7 - - + +
356L SER* 4.0 15.0 - - - -
369L ILE* 2.8 21.7 + - + +
370L LEU* 3.5 16.2 - - + +
372L GLU* 1.3 78.0 - - - +
374L ASN* 1.3 61.8 + - - +
376L GLU* 4.6 6.3 - - - +
377L VAL* 3.0 34.7 + - + +
387L PRO* 4.9 1.3 - - + -
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Residues in contact with ASN 374 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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392J PHE* 3.6 24.0 + - - -
393J THR* 3.8 10.3 - - - +
394J LEU 3.0 26.1 + - - +
395J ARG* 4.2 1.6 - - - -
370L LEU 3.1 11.2 + - - +
371L THR 3.0 13.2 + - - +
373L VAL* 1.3 76.1 - - - +
375L TYR* 1.3 56.6 + - - +
377L VAL* 4.1 0.9 - - - +
378L SER* 2.6 33.0 + - - -
386L MET* 3.8 13.8 - - + +
387L PRO* 3.1 33.5 - - - +
389L PRO* 3.8 11.7 - - - +
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Residues in contact with TYR 375 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151I LYS* 5.0 10.0 - - + +
319J ARG* 4.5 7.8 + - - -
395J ARG* 3.3 53.4 - - + +
396J LYS* 4.7 9.4 - - + -
299K ASP* 3.3 30.1 + - + +
371L THR 3.0 4.9 + - - -
372L GLU* 2.8 16.3 + - + +
374L ASN* 1.3 76.0 - - - +
376L GLU* 1.3 86.0 + - - +
378L SER* 2.7 21.9 + - - -
379L ASN* 3.0 30.2 + - - +
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Residues in contact with GLU 376 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352L SER* 4.4 17.7 - - - +
355L GLN* 6.1 1.6 - - - +
356L SER* 4.8 4.9 - - - +
372L GLU* 2.9 43.1 + - + +
373L VAL* 4.0 5.4 - - - +
375L TYR* 1.3 92.9 - - - +
377L VAL* 1.3 62.5 + - - +
379L ASN* 3.2 17.3 + - - +
381L LYS* 3.6 15.5 - - - +
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Residues in contact with VAL 377 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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348L TRP* 4.2 21.5 - - + +
349L TYR* 4.3 4.3 - - - -
352L SER* 3.5 24.0 - - - +
373L VAL* 3.0 23.9 + - + +
374L ASN 4.3 0.2 - - - +
375L TYR 3.0 0.2 + - - -
376L GLU* 1.3 74.0 - - - +
378L SER* 1.3 62.5 + - - +
379L ASN 3.2 0.5 + - - -
381L LYS* 3.2 23.9 + - - +
385L GLN* 3.6 42.7 + - + +
387L PRO* 3.7 21.3 - - + -
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Residues in contact with SER 378 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320J TYR 3.7 2.1 - - - +
321J ILE* 4.7 1.1 - - - -
322J PRO* 3.5 32.9 - - - +
395J ARG* 3.2 27.5 - - - +
374L ASN 2.6 19.6 + - - -
375L TYR 2.7 18.9 + - - -
377L VAL* 1.3 72.1 - - - +
379L ASN* 1.3 62.3 + - - -
384L LYS* 3.1 28.1 + - - +
385L GLN 4.4 1.6 - - - +
386L MET* 3.9 5.2 - - - +
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Residues in contact with ASN 379 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319J ARG* 5.7 7.8 - - - +
320J TYR 4.4 3.5 - - - +
321J ILE* 4.3 7.8 - - - +
395J ARG* 4.3 8.8 + - - -
299K ASP* 5.4 2.2 + - - +
375L TYR* 3.0 41.7 + - - +
376L GLU* 3.2 9.5 + - - +
377L VAL 3.1 1.0 - - - -
378L SER* 1.3 88.0 - - - +
381L LYS* 1.3 74.1 + - - +
384L LYS* 4.3 2.7 - - - +
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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
------------------------------------------------------------
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