Contacts of the helix formed by residues 418 - 429 (chain A) in PDB entry 1DIY
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 GLY 418 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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262A TYR* 4.1 11.4 - - - -
414A LEU* 2.8 23.5 + - - -
415A VAL 4.9 1.3 - - - -
416A ASP 3.6 0.8 - - - -
417A TYR* 1.3 74.2 - - - +
419A VAL* 1.3 67.9 + - - -
420A GLU* 3.4 4.5 - - - -
421A ALA 3.1 4.2 + - - -
422A LEU* 2.7 24.4 + - - +
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Residues in contact with VAL 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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262A TYR* 4.5 5.1 + - + +
300A LEU* 3.5 27.6 - - + -
303A THR* 4.2 16.8 - - + -
304A ILE* 4.2 14.1 - - + -
307A ARG* 3.1 28.3 - - - +
414A LEU* 4.4 8.8 + - + +
418A GLY* 1.3 69.6 - - - +
420A GLU* 1.3 77.0 + - - +
422A LEU 2.9 0.3 + - - -
423A VAL* 2.8 37.4 + - + +
568A VAL* 4.6 0.9 - - + -
572A THR* 3.7 22.2 - - + -
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Residues in contact with GLU 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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260A GLU* 3.8 13.7 - - - +
307A ARG* 4.7 2.6 + - - -
418A GLY* 4.5 2.2 - - - -
419A VAL* 1.3 89.1 + - - +
421A ALA* 1.3 63.1 + - - +
423A VAL* 3.4 0.6 + - - +
424A ASP* 3.2 17.0 + - - +
572A THR* 3.4 17.4 - - - +
573A LYS* 2.9 32.3 + - - +
574A THR* 3.2 39.0 + - - +
576A PRO* 3.5 25.5 - - + +
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Residues in contact with ALA 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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397A VAL* 4.9 1.9 - - + +
417A TYR* 3.5 32.1 - - + +
418A GLY 3.1 2.2 + - - -
420A GLU* 1.3 79.4 - - + +
422A LEU* 1.3 58.7 + - - +
424A ASP* 3.6 7.8 + - - +
425A ALA* 3.1 26.2 + - - +
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Residues in contact with LEU 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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296A PRO* 4.4 13.9 - - + -
300A LEU* 4.1 14.8 - - + -
397A VAL* 3.2 41.7 - - + -
413A MET* 4.0 25.8 - - + +
414A LEU* 4.1 17.5 - - + -
417A TYR* 3.6 21.3 - - + -
418A GLY 2.7 18.4 + - - +
419A VAL 2.9 2.2 + - - +
421A ALA* 1.3 71.4 - - - +
423A VAL* 1.3 63.8 + - - +
425A ALA* 3.5 2.9 + - + +
426A PHE* 3.0 45.9 + - + -
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Residues in contact with VAL 423 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A MET* 3.6 37.5 - - + -
300A LEU* 4.0 13.5 - - + -
304A ILE* 4.1 7.4 - - + -
419A VAL* 2.8 35.2 + - + +
420A GLU 3.7 3.4 - - - +
422A LEU* 1.3 73.5 - - - +
424A ASP* 1.3 59.0 + - - +
426A PHE* 2.9 3.3 + - - +
427A SER* 2.7 38.3 + - - +
568A VAL* 4.4 6.1 - - + -
576A PRO* 4.3 9.4 - - + -
577A TYR 3.9 1.8 - - - +
578A VAL* 3.7 24.5 - - + -
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Residues in contact with ASP 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 GLU 3.2 14.1 + - - +
421A ALA* 3.7 8.5 - - - +
423A VAL* 1.3 80.2 - - - +
425A ALA* 1.3 62.3 + - - +
427A SER* 4.0 0.7 - - - -
428A ARG* 2.7 66.9 + - - +
576A PRO* 3.8 11.3 - - + +
577A TYR* 3.4 29.5 + - - +
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Residues in contact with ALA 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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396A ARG 3.8 25.1 - - - +
397A VAL* 3.8 27.8 - - + -
398A GLY 4.8 1.6 - - - +
421A ALA 3.1 17.1 + - - +
422A LEU* 3.7 7.0 - - + +
423A VAL 3.1 0.8 - - - -
424A ASP* 1.3 81.6 + - - +
426A PHE* 1.3 63.7 + - + +
428A ARG* 3.6 5.6 + - - +
429A GLN* 3.4 18.4 + - - +
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Residues in contact with PHE 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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196A LEU* 3.5 15.2 + - + +
197A MET* 3.4 31.9 + - + +
200A PHE* 3.3 39.3 - + - -
297A GLY* 4.3 6.7 - - - -
300A LEU* 3.6 26.0 - - + -
301A TYR* 6.0 0.4 - + - -
395A PHE* 4.6 7.9 - + + -
396A ARG 5.4 1.8 - - - -
397A VAL* 5.1 11.7 - - + -
407A PHE* 3.9 25.6 - + - -
422A LEU* 3.0 37.4 + - + +
423A VAL* 2.9 5.4 + - - +
425A ALA* 1.3 76.4 - - + +
427A SER* 1.3 61.6 + - - +
428A ARG 2.8 10.9 + - - -
429A GLN* 3.1 20.5 + - - +
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Residues in contact with SER 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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195A ASN* 2.9 27.2 + - - +
197A MET* 3.2 20.5 - - - +
423A VAL* 2.7 16.5 + - - +
424A ASP 4.2 0.4 - - - -
426A PHE* 1.3 72.1 - - - +
428A ARG* 1.3 57.5 + - - +
577A TYR* 3.2 46.9 + - - -
578A VAL* 3.2 20.8 - - - +
579A SER 3.4 0.7 + - - -
582A VAL* 3.7 8.8 - - - -
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Residues in contact with ARG 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 ASP* 2.7 51.5 + - - +
425A ALA* 4.0 5.6 - - - +
426A PHE 2.8 3.0 + - - -
427A SER* 1.3 81.6 - - - +
429A GLN* 1.3 60.8 + - - +
430A PRO* 3.6 4.2 - - - +
577A TYR* 4.1 20.9 - - + +
582A VAL* 3.6 18.5 - - - +
583A PRO* 4.4 17.4 - - + +
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Residues in contact with GLN 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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195A ASN* 3.5 3.5 - - - +
196A LEU* 3.1 46.5 + - + +
392A PRO* 2.8 36.8 - - - +
394A SER 3.1 9.2 + - - +
395A PHE* 3.6 1.6 - - - -
396A ARG* 2.8 41.4 + - + +
425A ALA 3.4 12.5 + - - +
426A PHE* 3.1 4.6 + - - +
428A ARG* 1.3 78.3 - - - +
430A PRO* 1.3 74.9 + - + +
582A VAL* 5.3 0.2 - - - -
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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