Contacts of the helix formed by residues 374 - 392 (chain B) in PDB entry 4D2Y
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 374 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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371B ARG* 2.5 43.3 + - - +
372B PHE 3.1 2.0 + - - -
373B GLY* 1.3 83.4 - - - +
375B LYS* 1.3 59.1 + - - +
376B ALA* 3.5 8.1 + - - +
377B HIS* 3.0 16.3 + - - +
378B MET* 2.9 27.5 + - - +
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Residues in contact with LYS 375 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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374B SER* 1.3 72.7 - - - +
376B ALA* 1.3 57.7 + - - +
378B MET* 4.4 5.6 - - + +
379B ASP* 2.5 75.5 + - - +
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Residues in contact with ALA 376 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366B TYR* 3.5 16.1 + - + +
371B ARG* 5.7 3.8 - - + -
374B SER* 3.1 9.7 + - - +
375B LYS* 1.3 80.4 - - - +
377B HIS* 1.3 61.8 + - - +
379B ASP* 3.6 4.9 + - - +
380B ARG* 3.1 24.4 + - - +
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Residues in contact with HIS 377 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362B LEU 3.7 9.8 + - - -
363B ASP* 3.0 29.8 + - - -
366B TYR* 3.5 33.3 - + + -
371B ARG 3.5 7.0 - - - +
372B PHE* 3.6 26.4 - + - -
373B GLY 2.9 19.4 + - - +
374B SER* 3.0 24.6 + - - +
376B ALA* 1.3 75.5 - - - +
378B MET* 1.3 78.1 + - + +
380B ARG* 3.2 3.6 + - - +
381B LEU* 3.0 33.4 + - + +
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Residues in contact with MET 378 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372B PHE* 5.9 1.8 - - + -
373B GLY* 3.8 18.8 - - - +
374B SER 2.9 20.9 + - - +
375B LYS* 4.0 6.3 - - + +
377B HIS* 1.3 113.2 - - + +
379B ASP* 1.3 65.9 + - - +
381B LEU* 3.4 21.1 + - + +
382B GLU* 3.0 25.6 + - - +
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Residues in contact with ASP 379 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375B LYS* 2.5 64.4 + - - +
376B ALA* 4.0 5.4 - - - +
378B MET* 1.3 74.4 - - - +
380B ARG* 1.3 57.6 + - - +
382B GLU* 3.3 8.8 - - - +
383B GLU* 2.8 29.5 + - - +
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Residues in contact with ARG 380 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362B LEU* 3.8 16.3 - - + +
366B TYR* 3.4 24.7 - - + +
376B ALA 3.1 11.2 + - - +
377B HIS 3.2 4.5 + - - +
379B ASP* 1.3 73.9 - - - +
381B LEU* 1.3 60.1 + - - +
383B GLU* 2.9 37.0 + - - +
384B VAL* 2.9 56.2 + - - +
387B GLU* 4.7 5.1 + - - -
394B TYR* 4.4 3.2 - - - -
395B GLN 2.9 27.5 + - - -
396B LEU* 3.8 0.8 - - - +
397B LYS* 3.6 23.8 - - - +
400B GLU* 2.7 43.8 + - - +
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Residues in contact with LEU 381 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355B PHE* 3.6 15.5 - - + -
359B LYS* 4.2 36.1 - - + +
362B LEU* 3.7 36.8 - - + -
363B ASP* 4.2 6.3 - - - +
377B HIS* 3.0 25.7 + - + +
378B MET* 3.6 38.6 - - + +
380B ARG* 1.3 74.6 - - - +
382B GLU* 1.3 59.0 + - - +
384B VAL* 3.3 0.9 + - - +
385B ASN* 2.9 30.2 + - - +
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Residues in contact with GLU 382 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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378B MET 3.0 11.5 + - - +
379B ASP* 3.3 13.2 - - - +
381B LEU* 1.3 79.6 - - - +
383B GLU* 1.3 61.5 + - - +
385B ASN* 3.3 14.2 + - - +
386B LYS* 3.1 51.6 + - + +
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Residues in contact with GLU 383 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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379B ASP 2.8 18.9 + - - +
380B ARG* 2.9 40.4 + - - +
382B GLU* 1.3 73.9 - - - +
384B VAL* 1.3 58.0 + - - +
386B LYS* 3.5 7.6 + - - +
387B GLU* 2.9 35.6 + - + +
397B LYS* 4.3 16.5 + - - -
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Residues in contact with VAL 384 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355B PHE* 4.2 4.7 - - + -
358B ALA* 3.8 19.7 - - + -
362B LEU* 3.6 20.6 - - + -
380B ARG* 2.9 48.2 + - - +
381B LEU 3.6 4.0 - - - +
383B GLU* 1.3 72.9 - - - +
385B ASN* 1.3 60.8 + - - +
387B GLU* 3.3 7.8 + - - +
388B ILE* 2.8 48.8 + - + +
394B TYR* 3.9 18.8 - - + -
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Residues in contact with ASN 385 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355B PHE* 3.3 44.8 - - + +
381B LEU 2.9 12.5 + - - +
382B GLU* 3.6 17.3 + - - +
384B VAL* 1.3 76.0 - - - +
386B LYS* 1.3 63.5 + - - +
388B ILE* 3.3 4.4 + - - +
389B GLU* 3.0 36.8 + - - +
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Residues in contact with LYS 386 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382B GLU* 3.1 40.2 + - - +
383B GLU* 3.9 6.1 - - - +
385B ASN* 1.3 80.7 - - + +
387B GLU* 1.3 61.7 + - - +
389B GLU* 3.8 15.6 - - - +
390B SER* 3.0 27.3 + - - -
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Residues in contact with GLU 387 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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380B ARG* 4.7 7.4 + - - -
383B GLU* 2.9 23.8 + - + +
384B VAL* 3.7 6.8 - - - +
386B LYS* 1.3 74.7 - - - +
388B ILE* 1.3 60.5 + - - +
390B SER* 4.5 3.8 - - - -
391B THR* 2.8 48.8 + - + +
393B THR* 3.4 8.2 - - - +
394B TYR* 3.5 18.2 - - + +
395B GLN* 3.1 37.0 + - - +
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Residues in contact with ILE 388 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351B LYS* 3.3 33.5 + - + +
354B LEU* 4.1 9.6 - - + -
355B PHE* 3.8 34.5 - - + +
358B ALA* 4.2 1.8 - - + -
384B VAL* 2.8 40.0 + - + +
385B ASN* 3.6 7.2 - - - +
387B GLU* 1.3 72.0 - - - +
389B GLU* 1.3 61.1 + - + +
392B SER* 2.4 38.8 + - - -
393B THR 3.3 17.5 - - - +
394B TYR* 3.9 18.4 - - + -
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Residues in contact with GLU 389 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351B LYS* 3.5 25.1 + - + +
385B ASN* 3.0 32.3 + - - +
386B LYS* 3.8 17.6 - - - +
388B ILE* 1.3 78.4 - - + +
390B SER* 1.3 62.3 + - - +
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Residues in contact with SER 390 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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386B LYS 3.0 20.7 + - - -
387B GLU* 3.9 3.6 - - - -
389B GLU* 1.3 80.1 - - - +
391B THR* 1.3 68.7 + - - +
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Residues in contact with THR 391 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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387B GLU* 2.8 34.6 + - + +
390B SER* 1.3 89.1 - - - +
392B SER* 1.3 65.2 + - - +
393B THR* 2.9 33.0 + - - +
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Residues in contact with SER 392 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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349B ARG 4.9 8.3 + - - +
350B THR* 5.8 0.2 - - - -
351B LYS* 3.3 35.6 + - - +
354B LEU* 3.7 14.9 - - - +
388B ILE* 2.4 32.3 + - - +
390B SER 3.7 0.8 - - - -
391B THR* 1.3 69.8 - - - +
393B THR* 1.3 58.5 + - - +
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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