Contacts of the helix formed by residues 414 - 429 (chain A) in PDB entry 1YI1
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 414 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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281A PRO* 5.1 0.2 - - - +
282A LYS 5.4 0.6 + - - -
284A PRO* 4.8 3.6 - - - +
396A ILE* 3.4 11.9 - - + +
413A GLY* 1.3 69.2 - - - -
415A VAL* 1.3 65.5 + - - +
416A LYS* 2.9 31.4 + - - +
417A LEU* 3.0 40.5 + - + +
418A ALA* 3.0 11.8 + - - +
701A FAD 3.2 23.3 + - - -
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Residues in contact with VAL 415 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309A GLY 3.2 30.3 - - - +
310A CYS* 4.3 6.7 - - - -
313A SER* 3.5 13.5 - - - +
370A PHE* 3.7 35.9 - - + -
371A GLY 5.0 0.7 - - - +
394A ILE* 4.0 18.6 - - + +
413A GLY 3.2 2.0 + - - -
414A ASP* 1.3 71.4 - - - +
416A LYS* 1.3 60.5 + - - +
418A ALA* 3.6 4.0 - - + +
419A LEU* 2.9 38.8 + - + +
701A FAD 2.8 26.6 + - + +
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Residues in contact with LYS 416 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312A ASN* 3.1 34.4 + - + +
313A SER* 3.1 20.2 - - - +
316A GLU* 3.2 30.5 + - - +
414A ASP* 2.9 20.3 + - - +
415A VAL* 1.3 81.3 - - - +
417A LEU* 1.3 60.7 + - + +
419A LEU* 3.5 0.8 + - - -
420A GLN* 3.0 41.4 + - - +
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Residues in contact with LEU 417 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283A PRO* 4.2 17.0 - - + -
284A PRO* 3.6 29.2 - - + +
414A ASP* 3.0 32.3 + - + +
416A LYS* 1.3 77.7 - - + +
418A ALA* 1.3 66.5 + - - +
420A GLN* 3.5 25.2 - - - +
421A GLY* 2.9 21.5 + - - -
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Residues in contact with ALA 418 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284A PRO* 3.8 15.4 - - + +
289A LEU* 3.7 11.9 - - + +
394A ILE* 3.5 35.2 - - + -
411A VAL* 5.0 2.5 - - + -
414A ASP 3.0 12.1 + - - +
415A VAL* 3.6 10.8 - - + +
417A LEU* 1.3 77.7 - - - +
419A LEU* 1.3 57.0 + - - +
421A GLY 3.4 0.2 + - - -
422A MET* 2.9 37.3 + - + +
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Residues in contact with LEU 419 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310A CYS* 5.6 2.2 - - - -
313A SER* 3.7 15.7 - - - -
316A GLU* 3.6 17.0 - - + -
317A LEU* 3.5 33.0 - - + +
320A PHE* 3.7 35.4 - - + -
370A PHE* 4.1 14.4 - - + -
415A VAL* 2.9 30.9 + - + +
416A LYS 3.7 0.4 - - - +
418A ALA* 1.3 74.7 - - - +
420A GLN* 1.3 60.8 + - - +
422A MET* 3.2 14.6 + - + +
423A ASN* 2.8 40.2 + - - +
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Residues in contact with GLN 420 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316A GLU* 3.2 30.8 + - + +
416A LYS* 3.0 37.8 + - - +
417A LEU* 3.2 25.1 + - - +
419A LEU* 1.3 77.2 - - - +
421A GLY* 1.3 61.7 + - - +
423A ASN* 3.5 9.4 + - - +
424A LYS* 3.4 33.8 + - - +
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Residues in contact with GLY 421 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284A PRO* 5.9 0.2 - - - -
286A ASP* 5.9 1.8 - - - -
289A LEU* 3.6 22.0 - - - -
417A LEU 2.9 12.7 + - - -
420A GLN* 1.3 74.9 - - - +
422A MET* 1.3 63.6 + - - +
424A LYS* 3.1 22.9 + - - +
425A VAL* 3.2 16.7 + - - +
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Residues in contact with MET 422 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289A LEU* 3.5 23.1 - - + +
292A ILE* 3.6 40.8 - - - -
293A VAL* 4.2 11.4 - - + +
320A PHE* 3.7 29.2 - - + -
370A PHE* 3.9 25.6 - - + -
394A ILE* 4.3 7.6 - - + -
418A ALA* 2.9 29.9 + - + +
419A LEU* 3.9 9.2 - - + +
421A GLY* 1.3 75.5 - - - +
423A ASN* 1.3 57.8 + - - +
425A VAL* 3.5 5.4 + - - +
426A LEU* 2.9 35.7 + - - +
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Residues in contact with ASN 423 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316A GLU* 3.3 25.1 + - - +
319A ARG* 3.8 17.7 - - + +
320A PHE* 2.9 34.4 + - - +
323A LEU* 3.6 14.0 - - + +
419A LEU* 2.8 32.7 + - - +
420A GLN* 3.7 8.0 - - - +
422A MET* 1.3 73.5 - - - +
424A LYS* 1.3 61.2 + - - +
426A LEU* 3.2 2.5 + - - +
427A GLU* 2.8 40.0 + - - +
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Residues in contact with LYS 424 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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420A GLN* 3.4 22.6 + - - +
421A GLY* 3.1 14.4 + - - +
423A ASN* 1.3 78.2 - - - +
425A VAL* 1.3 65.8 + - + +
427A GLU* 2.9 21.9 + - - +
428A ASN* 3.1 25.6 + - - +
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Residues in contact with VAL 425 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286A ASP* 5.8 5.4 - - + +
289A LEU* 5.2 9.2 - - + +
290A GLU* 3.4 25.1 - - - +
293A VAL* 3.9 26.7 - - + -
421A GLY 3.2 16.6 + - - +
422A MET* 3.8 7.4 - - - +
424A LYS* 1.3 76.6 - - + +
426A LEU* 1.3 62.7 + - - +
428A ASN* 4.3 2.0 - - - +
429A ARG* 3.1 57.3 + - - +
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Residues in contact with LEU 426 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293A VAL* 3.6 29.2 - - + +
296A ILE* 5.2 2.5 - - + -
320A PHE* 3.7 24.7 - - + -
323A LEU* 4.0 24.6 - - + +
324A THR* 3.3 26.2 - - + -
422A MET* 2.9 24.9 + - + +
423A ASN* 3.5 6.1 - - - +
424A LYS 3.1 0.2 - - - -
425A VAL* 1.3 77.7 - - - +
427A GLU* 1.3 60.5 + - - +
429A ARG 4.0 0.7 - - - -
430A ALA* 3.4 21.0 + - - +
433A LEU* 3.9 8.9 - - + +
435A LEU* 3.8 27.1 - - + -
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Residues in contact with GLU 427 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319A ARG* 3.1 44.0 + - - +
323A LEU* 3.9 10.3 - - + +
423A ASN* 2.8 29.6 + - - +
424A LYS* 2.9 10.5 + - - +
426A LEU* 1.3 76.5 - - - +
428A ASN* 1.3 69.0 + - - +
430A ALA* 3.4 14.6 - - - +
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Residues in contact with ASN 428 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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424A LYS* 3.1 27.6 + - - +
425A VAL* 4.0 5.8 - - - +
427A GLU* 1.3 80.4 - - - +
429A ARG* 1.3 67.0 + - + +
430A ALA* 2.7 17.4 + - - +
431A GLU 4.6 1.2 + - - -
432A GLU* 4.5 2.2 - - - +
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Residues in contact with ARG 429 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290A GLU* 2.9 33.0 + - - -
293A VAL* 5.5 2.0 - - - -
425A VAL* 3.1 43.8 + - - +
426A LEU 4.0 3.8 - - - -
428A ASN* 1.3 85.4 - - + +
430A ALA* 1.3 66.3 + - - +
431A GLU 3.7 0.2 - - - -
432A GLU* 3.1 38.7 + - + +
433A LEU* 3.0 33.8 + - + +
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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