Contacts of the helix formed by residues 397 - 413 (chain A) in PDB entry 5YDJ
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 397 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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396A VAL* 1.3 76.6 - - - +
398A ARG* 1.3 53.9 + - - +
399A GLU* 3.7 13.3 + - - +
400A GLU* 3.1 26.3 + - - +
401A ALA* 2.8 36.6 + - - +
454A VAL* 4.1 0.4 - - - -
455A VAL* 5.8 1.3 - - - -
804A SO4 3.4 18.4 - - - -
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Residues in contact with ARG 398 (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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318A PHE* 3.8 29.1 - - + -
320A GLY* 6.2 1.0 - - - -
396A VAL 3.9 0.8 + - - -
397A SER* 1.3 71.7 - - - +
399A GLU* 1.3 53.0 + - - +
401A ALA* 3.9 0.7 - - - -
402A THR* 2.8 42.0 + - + +
454A VAL* 3.8 12.1 - - + +
455A VAL* 3.4 29.4 - - + +
456A ASP* 5.2 3.4 - - - +
804A SO4 2.7 34.9 + - - +
320B GLY 4.4 12.0 + - - -
321B THR* 4.3 13.9 - - - +
322B PRO* 3.6 29.8 - - - +
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Residues in contact with GLU 399 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397A SER* 3.2 8.6 - - - +
398A ARG* 1.3 87.0 + - - +
400A GLU* 1.3 58.2 + - - +
402A THR* 2.7 18.5 + - - -
403A LEU* 3.6 18.6 + - - +
804A SO4 3.0 42.5 + - - -
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Residues in contact with GLU 400 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396A VAL* 3.9 10.3 - - + -
397A SER* 3.1 18.9 + - - +
399A GLU* 1.3 74.3 - - - +
401A ALA* 1.3 60.7 + - - +
403A LEU* 3.2 13.5 + - - +
404A ARG* 3.0 70.3 + - - +
407A ARG* 3.2 28.5 + - - -
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Residues in contact with ALA 401 (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 PHE 5.9 0.7 - - - +
318A PHE* 2.9 42.2 + - + +
396A VAL* 3.9 21.9 - - + +
397A SER 2.8 23.3 + - - +
398A ARG* 4.1 0.4 - - - +
400A GLU* 1.3 71.7 - - - +
402A THR* 1.3 63.1 + - - +
404A ARG* 3.6 7.4 + - - +
405A ALA* 3.3 14.4 + - - +
451A PHE* 4.8 4.8 - - + -
454A VAL* 4.6 3.8 - - + -
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Residues in contact with THR 402 (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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318A PHE* 3.5 13.9 + - + -
319A LEU* 3.5 40.2 - - + +
320A GLY* 4.7 1.3 - - - -
398A ARG* 2.8 19.0 + - + +
399A GLU* 2.7 27.2 + - - -
401A ALA* 1.3 74.7 - - - +
403A LEU* 1.3 65.3 + - - +
405A ALA 3.5 0.7 + - - -
406A LEU* 3.3 29.8 + - - +
421A LEU* 6.0 1.3 - - + -
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Residues in contact with LEU 403 (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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399A GLU 3.6 15.7 + - - +
400A GLU* 3.2 19.6 + - - +
402A THR* 1.3 85.6 + - - +
404A ARG* 1.3 58.3 + - - +
406A LEU* 3.3 18.1 + - + +
407A ARG* 2.9 49.8 + - - +
418A PRO* 6.1 2.7 - - + -
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Residues in contact with ARG 404 (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 VAL* 3.7 18.8 - - - +
400A GLU* 3.0 53.0 + - - +
401A ALA* 4.1 4.7 - - - +
402A THR 3.4 0.4 - - - -
403A LEU* 1.3 72.4 - - - +
405A ALA* 1.3 61.0 + - - +
407A ARG* 3.3 30.0 + - - +
408A LEU* 2.9 23.4 + - - +
444A LEU* 4.1 21.5 - - - +
448A GLU* 4.7 10.3 + - - +
449A PHE 3.3 25.1 + - - +
450A PRO* 3.2 23.9 + - + +
451A PHE* 3.4 24.7 - - + -
452A VAL* 5.3 0.2 - - - +
522A TYR* 5.7 1.2 + - - -
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Residues in contact with ALA 405 (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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317A LEU* 3.7 21.1 - - + -
318A PHE 3.2 27.4 - - - +
319A LEU* 3.4 23.1 - - + -
401A ALA 3.3 4.6 + - - +
402A THR 3.7 0.7 - - - +
403A LEU 3.4 0.2 - - - -
404A ARG* 1.3 78.8 - - - +
406A LEU* 1.3 57.3 + - - +
408A LEU* 3.4 2.9 + - - +
409A ALA* 3.0 27.5 + - - +
424A ALA* 5.9 0.4 - - - +
428A LEU* 4.4 5.5 - - - +
451A PHE* 3.8 10.6 - - + -
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Residues in contact with LEU 406 (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 LEU* 4.0 7.2 - - + -
402A THR* 3.3 20.5 + - - +
403A LEU* 3.5 22.9 - - + +
404A ARG 3.3 0.4 - - - -
405A ALA* 1.3 75.4 - - - +
407A ARG* 1.3 59.2 + - - +
409A ALA* 3.4 3.4 + - - -
410A GLU* 2.8 26.1 + - - +
416A HIS* 3.3 41.2 - - - +
417A GLU 3.8 14.1 - - - +
418A PRO* 4.0 28.0 - - + -
421A LEU* 3.9 15.7 - - + -
424A ALA* 5.0 7.6 - - + -
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Residues in contact with ARG 407 (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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400A GLU* 3.2 30.6 + - - -
403A LEU* 2.9 33.1 + - - +
404A ARG* 3.3 29.3 + - - +
406A LEU* 1.3 71.9 - - - +
408A LEU* 1.3 54.7 + - - +
410A GLU* 3.3 13.6 + - - +
411A ALA* 2.8 37.2 + - - +
443A THR 5.7 2.4 + - - -
444A LEU* 5.4 6.5 - - - +
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Residues in contact with LEU 408 (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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313A SER* 3.7 30.3 - - - +
317A LEU* 3.7 17.0 - - + -
404A ARG 2.9 14.2 + - - +
405A ALA 3.5 7.6 - - - +
407A ARG* 1.3 76.9 - - - +
409A ALA* 1.3 57.5 + - - +
411A ALA* 3.3 3.9 + - - +
412A VAL* 2.9 42.6 + - + +
428A LEU* 4.2 16.2 - - + -
436A LEU* 3.3 31.4 - - + +
439A ASN 3.5 21.5 - - - +
440A GLU* 4.0 9.9 - - + -
451A PHE* 3.9 6.7 - - + -
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Residues in contact with ALA 409 (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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405A ALA 3.0 16.7 + - - +
406A LEU* 3.6 7.6 - - - +
408A LEU* 1.3 76.2 - - - +
410A GLU* 1.3 53.0 + - - +
412A VAL* 4.7 0.9 - - - -
413A GLY 3.0 9.7 + - - -
414A CYS* 2.7 50.3 + - + +
415A PRO 3.9 14.8 - - - +
416A HIS* 4.1 2.0 - - + -
424A ALA* 4.5 5.2 - - + -
428A LEU* 4.1 20.8 - - + +
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Residues in contact with GLU 410 (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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406A LEU 2.8 21.6 + - - +
407A ARG* 3.3 13.8 + - - +
409A ALA* 1.3 74.2 - - - +
411A ALA* 1.3 59.4 + - - +
413A GLY* 3.4 12.0 + - - -
414A CYS 4.3 0.2 - - - -
416A HIS* 3.0 48.6 + - + +
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Residues in contact with ALA 411 (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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407A ARG 2.8 20.2 + - - +
408A LEU 3.8 3.1 - - - +
410A GLU* 1.3 75.1 - - - +
412A VAL* 1.3 62.4 + - - +
413A GLY* 3.6 0.5 + - - -
439A ASN* 4.1 32.0 - - + +
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Residues in contact with VAL 412 (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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408A LEU* 2.9 35.2 + - + +
409A ALA* 4.1 4.9 - - - +
411A ALA* 1.3 76.0 - - - +
413A GLY* 1.3 57.5 + - - +
414A CYS* 5.1 2.9 - - + -
428A LEU* 5.1 0.9 - - + -
431A LYS* 3.5 45.9 + - + -
435A VAL* 4.3 13.0 - - + +
436A LEU* 3.9 24.7 - - + -
439A ASN* 4.1 20.4 - - + +
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Residues in contact with GLY 413 (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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409A ALA 3.0 2.6 + - - -
410A GLU 3.4 7.1 + - - -
411A ALA 3.3 3.2 - - - -
412A VAL* 1.3 80.3 - - - +
414A CYS* 1.3 64.6 + - - +
415A PRO* 5.0 0.3 - - - +
416A HIS* 6.3 0.2 - - - -
431A LYS* 4.4 9.2 + - - -
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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