Contacts of the helix formed by residues 416 - 425 (chain A) in PDB entry 3PEY
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 416 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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388A ASN* 5.0 3.1 + - - -
408A PRO* 3.0 29.2 + - + +
409A THR 3.6 21.9 - - - +
410A LEU* 3.6 21.9 - - + +
414A GLN 3.4 0.2 + - - -
415A ALA* 1.3 71.3 - - - +
417A PRO* 1.3 65.3 - - - +
418A ALA* 3.6 8.3 + - - +
419A THR* 2.6 37.3 + - - +
420A TYR 3.1 15.4 + - - -
452A ILE* 4.7 1.8 - - - +
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Residues in contact with PRO 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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410A LEU* 5.8 0.7 - - + -
415A ALA* 3.3 16.4 - - + +
416A ASP* 1.3 86.9 - - - +
418A ALA* 1.3 63.7 + - - +
420A TYR* 3.2 2.6 + - + +
421A ILE 3.0 18.2 + - - -
451A ALA 5.3 0.9 - - - +
452A ILE* 4.0 20.4 - - + -
455A TYR* 3.4 53.4 - - + -
456A PHE* 3.3 19.2 - - + -
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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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242A ASP* 4.6 2.9 - - - +
273A THR* 4.0 26.0 - - + +
275A ALA* 6.1 5.8 - - + +
392A ARG* 4.3 10.1 - - - +
416A ASP* 3.3 6.8 + - - +
417A PRO* 1.3 78.9 - - - +
419A THR* 1.3 64.5 + - - +
421A ILE* 3.2 10.5 + - - +
422A HIS* 3.0 29.7 + - - -
455A TYR* 5.2 3.9 - - + +
456A PHE* 4.3 2.2 - - - -
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Residues in contact with THR 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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243A ASN* 5.8 0.2 + - - -
388A ASN* 3.4 38.0 + - + +
391A ALA* 4.2 6.7 - - + -
392A ARG* 5.3 7.6 + - - +
408A PRO* 3.7 13.0 - - + -
416A ASP* 2.6 34.1 + - - -
418A ALA* 1.3 74.8 - - - +
420A TYR* 1.3 66.9 + - - +
422A HIS* 3.8 6.0 - - - +
423A ARG* 2.8 30.2 + - + +
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Residues in contact with TYR 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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306A GLN* 2.6 40.7 + - - +
307A LEU 5.6 0.9 + - - -
404A ASN* 3.5 30.1 - - - -
407A LEU* 5.7 0.9 - - + -
408A PRO* 3.6 19.8 - - + +
416A ASP 3.1 8.9 + - - +
417A PRO 3.2 9.2 + - - +
419A THR* 1.3 78.0 - - - +
421A ILE* 1.3 70.4 - - + +
423A ARG* 3.3 4.2 + - - +
424A ILE* 3.0 46.6 + - + +
436A ALA* 5.1 1.4 - - - +
438A SER* 3.5 14.0 + - - -
449A LEU* 4.0 11.3 - - + +
452A ILE* 3.5 36.8 - - + -
459A ILE* 4.4 1.1 - - + -
461A MET* 3.6 14.6 - - + +
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Residues in contact with ILE 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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140A SER* 4.7 5.1 + - - -
272A ALA* 5.4 2.5 - - + -
273A THR* 3.6 26.9 - - + -
299A VAL* 4.0 18.2 - - + +
300A ASN* 3.5 31.0 - - - +
301A VAL 5.6 0.7 - - - +
417A PRO 3.0 5.5 + - - -
418A ALA 3.4 9.4 - - - +
420A TYR* 1.3 96.9 - - + +
422A HIS* 1.3 69.6 + - + +
424A ILE* 3.6 9.5 - - + +
425A GLY* 3.1 19.8 + - - -
456A PHE* 3.6 35.7 - - + -
459A ILE* 4.4 1.8 - - + -
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Residues in contact with HIS 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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140A SER* 5.8 1.5 - - - -
240A GLU* 3.3 23.7 + - - -
271A SER* 3.9 2.9 - - - -
272A ALA* 3.7 25.6 - - + +
273A THR* 2.8 31.3 + - + +
391A ALA* 3.1 15.0 - - + +
392A ARG* 3.3 39.0 + - + +
418A ALA 3.0 29.7 + - - +
419A THR* 3.8 5.6 - - - +
421A ILE* 1.3 75.9 - - + +
423A ARG* 1.3 66.0 + - - +
425A GLY 3.1 4.5 + - - -
426A ARG* 2.9 36.5 + - - +
1002A BEF 4.9 2.8 - - - -
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Residues in contact with ARG 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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336A PHE* 3.5 38.7 - - + +
337A VAL 3.7 21.6 + - - -
338A ALA* 4.7 4.0 - - - +
388A ASN* 2.9 29.5 + - - +
391A ALA* 3.5 22.6 + - + -
402A VAL* 3.6 10.4 - - + +
404A ASN* 3.0 25.4 + - - +
406A ASP 2.9 27.9 + - - -
407A LEU 4.8 0.6 - - - -
408A PRO* 3.6 27.4 - - - +
419A THR* 2.8 28.8 + - - +
420A TYR* 3.6 3.4 - - - +
422A HIS* 1.3 72.5 - - - +
424A ILE* 1.3 62.8 + - - +
426A ARG* 3.0 22.0 + - - +
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Residues in contact with ILE 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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300A ASN* 4.3 1.1 - - - +
304A ILE* 3.4 18.6 - - + +
306A GLN* 3.4 41.7 - - + +
402A VAL* 4.0 9.4 - - + +
404A ASN* 3.8 22.0 - - - +
420A TYR* 3.0 35.2 + - + +
421A ILE* 3.6 17.9 - - + +
423A ARG* 1.3 75.8 - - - +
425A GLY* 1.3 59.9 + - - +
426A ARG 3.0 5.1 + - - -
427A THR* 3.1 25.8 + - - +
436A ALA* 3.5 25.6 - - + -
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Residues in contact with GLY 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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140A SER* 3.5 24.4 + - - -
304A ILE* 3.8 4.0 - - - -
421A ILE 3.1 10.9 + - - -
422A HIS 3.1 9.1 + - - -
424A ILE* 1.3 73.0 - - - +
426A ARG* 1.3 69.4 + - - +
427A THR 3.1 11.9 - - - +
429A ARG* 2.8 24.9 + - - +
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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