Contacts of the strand formed by residues 400 - 415 (chain A) in PDB entry 2YWE
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 ILE 400 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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376A VAL* 4.2 13.5 - - + -
377A LYS 3.8 4.9 - - - +
378A LYS* 4.4 1.3 - - + +
379A LYS* 5.2 0.4 - - - -
393A PHE* 3.3 39.0 - - + -
394A PRO* 4.2 18.2 - - + +
396A ASN 4.0 7.9 - - - +
397A ALA* 3.2 24.7 + - + +
398A GLY 4.4 4.1 - - - +
399A LEU* 1.3 77.4 - - - +
401A GLU* 1.3 63.5 + - - +
402A TYR* 3.6 13.5 - - - +
403A VAL* 3.6 25.4 - - + -
485A LEU 5.6 1.6 - - - +
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Residues in contact with GLU 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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377A LYS* 2.7 46.9 + - + +
379A LYS* 3.1 55.7 + - + +
400A ILE* 1.3 74.1 - - - +
402A TYR* 1.3 69.0 + - + +
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Residues in contact with TYR 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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375A ARG 5.0 2.2 - - - -
377A LYS* 3.0 58.9 + - + +
384A VAL* 3.5 26.0 - - + +
400A ILE* 3.5 5.1 - - - +
401A GLU* 1.3 87.2 - - + +
403A VAL* 1.3 71.8 + - - +
404A GLU* 4.0 34.2 + - + -
482A PRO* 5.3 9.4 - - + -
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Residues in contact with VAL 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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374A TYR* 4.3 5.8 - - + -
375A ARG 3.4 9.4 - - - +
376A VAL* 4.0 13.7 - - + -
393A PHE* 3.9 28.0 - - + -
400A ILE* 3.6 19.7 - - + -
402A TYR* 1.3 80.5 - - - +
404A GLU* 1.3 70.5 + - - +
482A PRO* 3.3 4.4 - - - +
483A SER 2.9 34.3 + - - +
485A LEU* 3.7 36.2 - - + +
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Residues in contact with GLU 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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374A TYR* 3.6 8.3 - - - +
375A ARG* 2.9 50.2 + - + +
384A VAL* 5.9 0.2 - - - +
402A TYR* 4.0 28.7 + - + -
403A VAL* 1.3 79.1 - - - +
405A GLU* 1.3 61.1 + - - +
480A TYR* 3.8 28.7 - - + +
481A ARG 3.3 10.8 - - - +
482A PRO* 3.9 25.5 - - + +
485A LEU* 4.5 0.2 - - - -
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Residues in contact with GLU 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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372A VAL* 5.0 0.2 - - + -
374A TYR* 3.8 16.7 - - + -
404A GLU* 1.3 74.3 - - - +
406A PRO* 1.3 74.3 - - + +
407A PHE* 3.5 16.4 - - + -
430A ARG* 2.9 32.1 + - - -
451A PRO* 3.3 11.7 - - - +
453A SER* 2.8 30.0 + - - -
480A TYR* 3.4 6.2 - - - -
481A ARG 3.1 22.9 + - - -
483A SER* 3.0 20.5 + - - +
485A LEU* 3.7 12.8 - - + +
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Residues in contact with PRO 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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296A MET* 5.7 4.9 - - + +
372A VAL* 3.8 27.8 - - + -
373A ILE 3.5 20.6 - - - +
405A GLU* 1.3 90.1 - - + +
407A PHE* 1.3 59.9 + - - +
451A PRO* 3.6 4.9 - - - +
452A LEU* 2.9 40.1 + - + -
453A SER 4.6 0.6 + - - +
477A PHE* 3.6 24.2 - - + -
479A GLY 3.7 6.3 - - - +
480A TYR* 3.6 13.9 - - + +
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Residues in contact with PHE 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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405A GLU* 3.5 33.7 - - + -
406A PRO* 1.3 73.4 - - - +
408A VAL* 1.3 66.7 + - - +
430A ARG* 4.7 8.5 - - + -
432A ILE* 5.6 4.7 - - + -
449A GLU* 4.5 2.9 - - + -
450A MET* 3.4 24.7 - - - -
451A PRO* 3.8 26.0 - - + -
477A PHE* 3.6 5.0 - - - -
478A ILE* 2.9 35.2 + - + +
479A GLY 2.8 12.3 + - - +
481A ARG* 3.7 52.0 - - + -
482A PRO 5.9 0.2 - - - -
483A SER* 3.9 11.4 - - - -
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Residues in contact with VAL 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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407A PHE* 1.3 79.7 - - - +
409A LEU* 1.3 59.7 + - - +
410A VAL* 3.7 22.4 - - + -
448A TYR 3.6 0.2 - - - +
449A GLU* 3.4 3.6 - - - -
450A MET 2.9 40.3 + - - +
452A LEU* 4.2 23.8 - - + -
455A ILE* 4.4 12.6 - - + -
475A TYR* 3.8 31.4 - - + -
476A GLU 3.1 13.0 - - - +
477A PHE* 3.9 13.7 - - + -
478A ILE* 3.9 7.0 - - - +
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Residues in contact with LEU 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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408A VAL* 1.3 71.6 - - - +
410A VAL* 1.3 62.4 + - - +
411A THR* 3.9 11.2 + - + +
434A LYS* 4.6 5.2 - - + -
447A GLU* 4.4 25.6 - - + +
448A TYR 3.5 19.5 - - - +
449A GLU* 4.1 18.6 - - + +
474A ASP 3.9 0.2 - - - +
475A TYR* 3.0 4.4 - - - -
476A GLU* 2.8 44.7 + - + +
478A ILE* 3.8 21.4 - - + +
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Residues in contact with VAL 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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408A VAL* 3.7 24.9 - - + -
409A LEU* 1.3 72.3 - - - +
411A THR* 1.3 63.3 + - - +
412A ILE* 3.9 25.7 - - + +
446A LEU 3.5 1.0 - - - +
447A GLU* 3.2 5.0 - - - +
448A TYR* 2.6 50.3 + - + +
450A MET* 3.9 24.2 - - + -
455A ILE* 4.3 7.4 - - + -
459A PHE* 4.5 8.1 - - + -
473A TYR* 4.2 16.2 - - + -
474A ASP 3.3 11.2 - - - +
475A TYR* 3.9 5.2 - - + -
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Residues in contact with THR 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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112A ALA* 3.8 11.5 + - - +
115A VAL* 6.5 1.1 - - + -
116A ALA* 5.4 2.1 - - - +
409A LEU* 5.0 11.7 - - + +
410A VAL* 1.3 76.3 - - - +
412A ILE* 1.3 60.3 + - - +
445A TYR* 3.4 33.9 - - + +
446A LEU 3.2 4.3 - - - -
447A GLU* 4.2 8.5 - - + +
473A TYR* 3.0 6.9 - - - +
474A ASP* 2.8 52.6 + - - +
475A TYR* 6.1 0.2 - - - -
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Residues in contact with ILE 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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410A VAL* 3.9 15.7 - - + +
411A THR* 1.3 80.3 - - - +
413A ILE* 1.3 75.9 + - - +
414A THR* 4.4 9.6 - - + -
422A ILE* 4.1 20.4 - - + -
426A CYS* 3.8 29.4 - - - -
444A VAL 3.6 0.9 - - - +
445A TYR* 3.3 6.6 - - - -
446A LEU* 2.8 45.4 + - + +
448A TYR* 4.7 10.5 - - + -
459A PHE* 4.3 2.0 - - + -
463A ILE* 4.1 20.0 - - + -
471A ALA* 4.8 0.4 - - + -
472A SER 3.3 10.8 - - - +
473A TYR* 3.7 12.8 - - + -
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Residues in contact with ILE 413 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110A ILE* 3.9 16.8 - - + +
111A GLU* 3.4 29.8 - - - +
112A ALA* 3.4 9.4 - - + +
115A VAL* 4.0 14.6 - - + -
412A ILE* 1.3 77.7 - - - +
414A THR* 1.3 63.5 + - - +
439A LEU* 3.7 23.6 - - + -
443A THR* 3.7 24.2 - - + -
444A VAL 3.5 2.7 - - - +
445A TYR* 4.2 10.8 - - + -
470A PHE 4.1 2.3 - - - +
471A ALA* 3.2 2.4 - - - +
472A SER* 2.8 49.2 + - - +
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Residues in contact with THR 414 (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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412A ILE* 4.4 7.6 - - + -
413A ILE* 1.3 78.8 - - - +
415A PRO* 1.3 91.3 + - - +
418A TYR* 3.6 8.5 - - - +
419A VAL* 4.2 17.5 - - + -
422A ILE* 3.6 24.4 - - + +
443A THR* 3.6 6.0 - - - -
444A VAL* 2.9 36.2 + - + +
446A LEU* 4.8 6.3 - - + -
470A PHE 4.7 0.2 - - - -
471A ALA* 3.7 14.2 - - - +
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Residues in contact with PRO 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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144A ARG* 6.3 0.7 - - - +
414A THR* 1.3 105.2 + - - +
416A LYS* 1.3 64.9 + - - +
417A GLU* 3.1 31.1 + - + +
418A TYR* 3.1 14.1 + - + -
419A VAL 3.9 0.5 + - - -
442A ASN 3.3 9.0 - - - +
443A THR* 4.6 2.9 - - - +
470A PHE* 3.8 40.4 - - + +
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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