Contacts of the helix formed by residues 363 - 375 (chain D) in PDB entry 5YD6
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 363 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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542B ASN* 3.3 39.8 + - - +
361D PRO 3.8 3.6 + - - -
362D VAL* 1.3 80.6 - - - +
364D LEU* 1.3 64.8 + - - +
365D ILE* 3.8 4.2 + - - +
366D SER* 3.2 25.7 + - - -
367D ALA* 3.1 18.9 + - - +
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Residues in contact with LEU 364 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362D VAL 4.0 0.2 + - - -
363D SER* 1.3 73.4 - - - +
365D ILE* 1.3 58.8 + - - +
367D ALA* 3.2 5.8 + - - +
368D LEU* 3.0 43.5 + - + +
425D PRO* 3.8 31.2 - - + -
527D LEU* 4.7 9.9 - - + -
530D LYS* 3.7 47.3 - - + +
531D ILE* 4.1 10.8 - - + +
534D CYS* 4.0 13.0 - - + -
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Residues in contact with ILE 365 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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538B HIS* 6.0 1.3 - - - +
542B ASN* 3.8 21.5 - - - +
363D SER* 3.8 3.1 + - - +
364D LEU* 1.3 74.9 - - - +
366D SER* 1.3 63.6 + - - +
368D LEU* 3.1 7.2 + - + +
369D VAL* 2.8 32.0 + - + +
501D SER* 3.7 28.9 - - - +
502D ALA* 5.5 0.2 - - - -
505D CYS* 3.6 30.7 - - - -
534D CYS* 3.8 34.5 - - + +
538D HIS* 3.8 20.4 - - + -
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Residues in contact with SER 366 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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499B ASP* 3.0 30.1 + - - +
500B ILE* 5.5 1.2 + - - +
538B HIS* 4.7 0.7 - - - -
542B ASN* 2.8 31.0 + - - -
362D VAL* 4.0 10.8 - - - -
363D SER* 3.5 13.6 + - - -
365D ILE* 1.3 79.5 - - - +
367D ALA* 1.3 57.3 + - - +
369D VAL* 3.3 8.6 + - - +
370D ARG* 2.9 30.1 + - - +
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Residues in contact with ALA 367 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362D VAL* 3.9 12.7 - - + +
363D SER 3.1 11.0 + - - +
364D LEU 3.2 9.8 + - - +
366D SER* 1.3 79.2 - - - +
368D LEU* 1.3 58.4 + - - +
370D ARG* 3.4 9.0 + - - +
371D ALA* 3.0 29.5 + - - +
423D LYS* 4.2 7.2 - - - +
425D PRO* 3.6 29.6 - - + -
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Residues in contact with LEU 368 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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364D LEU* 3.0 31.4 + - + +
365D ILE* 3.6 9.2 - - + +
367D ALA* 1.3 75.2 - - - +
369D VAL* 1.3 64.8 - - - +
371D ALA* 3.4 4.4 + - - +
372D HIS* 3.0 24.4 + - - +
420D TRP* 4.8 2.6 + - - +
424D ILE* 3.8 34.3 - - + -
425D PRO* 4.2 4.9 - - + -
504D SER* 3.5 17.9 + - - +
505D CYS* 3.9 20.4 - - - +
508D ALA* 3.9 14.8 - - + -
531D ILE* 3.8 33.2 - - + -
534D CYS* 5.1 0.9 - - - -
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Residues in contact with VAL 369 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369B VAL* 5.3 2.9 - - + -
500B ILE* 4.2 26.7 - - + -
501B SER* 5.5 6.3 - - - +
365D ILE* 2.8 24.8 + - + +
366D SER* 3.6 7.9 - - - +
368D LEU* 1.3 72.3 - - - +
370D ARG* 1.3 56.3 + - - +
372D HIS* 3.4 3.5 + - - +
373D VAL* 2.9 31.0 + - + +
500D ILE* 3.9 15.0 - - + -
501D SER* 3.5 42.4 - - - +
504D SER* 3.4 11.0 - - - +
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Residues in contact with ARG 370 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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379B MET* 5.9 1.6 - - - +
453B TYR* 3.1 44.9 + - - -
498B ILE 4.6 1.6 + - - -
499B ASP* 5.7 0.2 - - - +
500B ILE* 3.7 28.6 - - + +
366D SER 2.9 17.9 + - - +
367D ALA* 3.7 8.7 - - - +
368D LEU 3.3 0.2 - - - -
369D VAL* 1.3 72.9 - - - +
371D ALA* 1.3 61.1 + - - +
373D VAL* 3.3 0.7 + - - +
374D ASP* 2.8 72.3 + - - +
423D LYS* 5.1 7.9 - - + +
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Residues in contact with ALA 371 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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367D ALA 3.0 16.9 + - - +
368D LEU* 3.7 7.2 - - - +
369D VAL 3.4 0.2 - - - -
370D ARG* 1.3 75.8 - - - +
372D HIS* 1.3 61.3 + - - +
374D ASP* 3.9 1.6 - - - +
375D SER* 2.9 28.4 + - - -
420D TRP* 3.5 26.1 - - + +
423D LYS* 3.6 38.8 - - + +
424D ILE* 4.8 2.9 - - + +
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Residues in contact with HIS 372 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368D LEU 3.0 8.0 + - - +
369D VAL 3.5 7.6 - - - +
371D ALA* 1.3 75.6 - - - +
373D VAL* 1.3 66.8 + - - +
375D SER* 3.1 10.5 + - - -
376D ASN* 2.7 54.0 + - + -
420D TRP* 3.6 11.0 - - - +
450D ARG* 4.3 8.6 - - + +
453D TYR* 4.1 23.4 - + - -
500D ILE* 4.2 20.3 - - + +
503D PHE* 3.4 34.0 - + - -
504D SER* 3.5 21.3 - - - +
507D ALA* 5.6 1.6 - - + -
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Residues in contact with VAL 373 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369B VAL* 5.5 0.2 - - + -
372B HIS* 6.0 2.9 - - + +
373B VAL* 3.9 41.5 - - + -
378B ALA* 5.9 0.7 - - - -
379B MET 5.6 1.4 + - - -
500B ILE* 3.8 25.1 - - + -
369D VAL* 2.9 31.1 + - + +
370D ARG* 3.3 1.1 + - - +
372D HIS* 1.3 77.0 - - - +
374D ASP* 1.3 65.9 + - - +
375D SER 3.2 4.3 + - - -
376D ASN* 3.3 19.0 + - - +
500D ILE* 4.6 12.8 - - + -
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Residues in contact with ASP 374 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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379B MET* 3.7 38.0 - - + +
380B THR* 3.4 16.8 + - - +
370D ARG* 2.8 60.3 + - - +
371D ALA 3.9 2.9 - - - +
373D VAL* 1.3 79.0 - - - +
375D SER* 1.3 58.2 + - - +
376D ASN 3.6 1.1 - - - -
423D LYS* 3.3 28.4 + - + +
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Residues in contact with SER 375 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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380B THR* 3.8 11.0 - - - -
371D ALA 2.9 20.5 + - - -
372D HIS 3.1 3.4 + - - -
374D ASP* 1.3 79.6 - - - +
376D ASN* 1.3 55.0 + - - +
377D PRO* 4.7 1.0 - - - +
416D ILE* 3.3 33.2 - - - +
419D GLY 5.4 0.7 - - - -
420D TRP* 3.6 12.9 - - - +
423D LYS* 6.4 0.9 - - - -
450D ARG* 2.7 48.7 + - - -
465D CYS* 5.1 1.0 - - - +
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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