Contacts of the helix formed by residues 462 - 474 (chain A) in PDB entry 3EHN
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 ASN 462 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51A ILE* 4.6 6.2 - - - +
70A ASP* 4.9 2.6 - - - +
80A TYR* 3.7 6.9 + - - -
149A ARG* 4.3 12.1 + - - +
224A ARG* 4.8 3.8 - - - +
354A TYR* 3.5 22.9 + - + +
355A TRP* 3.5 24.7 + - - +
360A GLU* 5.4 0.2 + - - -
459A LEU* 2.9 36.8 + - + +
460A TYR* 3.7 0.8 - - - +
461A PRO* 1.3 66.8 - - - +
463A ALA* 1.3 64.3 + - - +
464A VAL 3.3 2.1 + - - -
465A GLU* 3.6 25.9 + - - +
466A ALA* 3.3 17.0 + - - +
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Residues in contact with ALA 463 (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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70A ASP* 3.7 17.6 + - + +
74A SER* 3.4 17.5 - - - +
75A GLY* 3.4 24.9 - - - +
78A ILE* 3.5 4.6 - - - +
80A TYR* 3.7 15.3 - - + -
81A PHE* 4.4 2.7 - - + -
461A PRO 2.6 13.5 + - - +
462A ASN* 1.3 70.9 - - - +
464A VAL* 1.3 63.6 + - - +
467A TRP* 3.1 25.6 + - - +
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Residues in contact with VAL 464 (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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69A THR 3.5 24.9 - - - +
70A ASP* 3.7 7.7 + - - +
74A SER* 3.6 9.6 - - - +
109A PHE* 4.0 7.0 - - + -
149A ARG* 3.5 52.3 - - + +
152A ASP* 5.4 0.2 - - + -
153A VAL* 4.0 24.0 - - + -
462A ASN* 3.3 2.0 + - - -
463A ALA* 1.3 76.0 - - - +
465A GLU* 1.3 58.8 + - - +
467A TRP* 3.9 3.9 - - + +
468A THR* 2.8 38.8 + - - +
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Residues in contact with GLU 465 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A LEU* 4.9 0.7 - - - +
149A ARG* 6.0 2.2 - - - +
152A ASP* 4.9 0.2 - - - +
224A ARG* 3.1 39.5 + - - +
228A ARG* 2.7 40.3 + - - -
360A GLU* 3.9 12.9 - - - +
455A LYS* 4.7 1.3 + - - -
459A LEU* 3.9 19.3 - - + -
462A ASN* 3.3 26.7 + - - +
464A VAL* 1.3 76.5 - - - +
466A ALA* 1.3 60.6 + - - +
468A THR* 3.3 3.6 + - - -
469A GLU* 2.9 45.5 + - + +
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Residues in contact with ALA 466 (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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78A ILE* 3.3 23.5 - - + +
80A TYR* 3.3 28.7 - - + +
456A TYR* 4.1 14.7 - - + +
459A LEU* 3.8 12.9 - - + +
462A ASN 3.3 6.1 + - - +
465A GLU* 1.3 79.6 - - - +
467A TRP* 1.3 57.1 + - - +
469A GLU* 3.2 6.2 + - - +
470A TYR* 2.9 27.7 + - - +
475A PHE 5.1 0.7 - - - +
476A PRO* 5.8 0.5 - - - +
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Residues in contact with TRP 467 (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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69A THR 5.8 0.7 - - - -
74A SER* 3.4 30.1 - - - -
77A TYR* 3.9 21.6 - + - -
78A ILE* 3.3 25.7 - - + +
109A PHE* 5.8 0.7 - + - -
153A VAL* 3.9 31.6 - - + -
463A ALA 3.1 16.7 + - - +
464A VAL* 3.9 6.7 - - + +
466A ALA* 1.3 79.5 - - - +
468A THR* 1.3 60.6 + - - +
470A TYR* 3.3 2.0 + - + +
471A ARG* 3.1 63.9 + - + +
499A VAL* 4.0 13.0 - - + +
500A PRO* 3.3 22.6 + - + -
502A ARG* 4.4 8.3 - - - -
503A PHE* 4.3 28.3 - + - -
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Residues in contact with THR 468 (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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152A ASP* 3.5 15.2 + - - +
228A ARG* 3.5 38.8 - - - +
464A VAL* 2.8 25.2 + - - +
465A GLU* 3.6 8.0 - - - -
466A ALA 3.2 0.2 - - - -
467A TRP* 1.3 76.3 - - - +
469A GLU* 1.3 63.9 + - - +
471A ARG* 2.8 25.3 + - - +
472A ARG* 3.0 21.3 + - - +
535A TRP* 3.7 21.1 - - + -
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Residues in contact with GLU 469 (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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227A VAL* 5.1 0.6 - - - +
228A ARG* 2.8 26.6 + - - -
364A LEU* 5.8 0.4 - - - -
452A ILE* 3.9 17.4 - - + +
455A LYS* 2.6 36.4 + - + +
459A LEU* 5.0 2.2 - - + -
465A GLU* 2.9 28.1 + - + +
466A ALA* 3.2 7.2 + - - +
468A THR* 1.3 76.5 - - - +
470A TYR* 1.3 56.9 + - - +
472A ARG* 2.7 43.2 + - - -
473A THR* 2.9 35.4 + - - +
475A PHE 4.1 1.8 - - - -
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Residues in contact with TYR 470 (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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78A ILE* 4.5 6.1 - - + -
456A TYR* 6.4 0.2 - - + -
466A ALA 2.9 13.3 + - - +
467A TRP* 3.6 10.3 - + - +
468A THR 3.2 0.2 - - - -
469A GLU* 1.3 77.1 - - - +
471A ARG* 1.3 63.5 + - + +
474A GLY* 2.6 53.3 + - - -
475A PHE 3.3 16.5 + - - +
476A PRO* 3.4 28.9 - - + -
477A TYR* 4.8 1.6 - + - -
478A LEU* 3.5 29.9 + - + -
496A ASP 5.4 0.2 + - - -
498A ARG* 3.8 23.1 + - + +
499A VAL* 3.5 34.5 - - + -
540A ARG* 4.1 12.1 + - - -
541A PRO 5.5 2.3 + - - -
542A LYS* 6.2 0.5 - - - +
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Residues in contact with ARG 471 (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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152A ASP 2.7 31.0 + - - -
153A VAL* 4.8 0.6 - - - +
467A TRP* 3.1 68.6 + - + +
468A THR* 2.8 31.6 + - - +
470A TYR* 1.3 77.8 - - - +
472A ARG* 1.3 57.4 + - - +
499A VAL* 4.2 9.6 - - + -
500A PRO 3.5 8.7 - - - +
501A GLU* 2.9 37.6 + - - +
502A ARG* 4.0 2.2 - - - +
533A LEU* 3.6 7.1 - - - +
535A TRP* 3.6 18.8 - - + -
536A VAL* 3.3 9.7 - - - +
540A ARG* 2.6 37.4 + - - +
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Residues in contact with ARG 472 (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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227A VAL* 3.5 21.3 + - - +
228A ARG* 3.3 38.3 - - - +
231A PHE* 3.6 19.1 - - + -
367A GLU* 2.9 41.2 + - - -
452A ILE* 4.0 0.4 - - - +
468A THR 3.0 15.6 + - - +
469A GLU* 2.7 39.9 + - - +
470A TYR 3.1 0.2 - - - -
471A ARG* 1.3 80.3 - - - +
473A THR* 1.3 76.6 + - - +
535A TRP* 3.4 29.6 - - + +
536A VAL* 4.3 0.2 - - - +
537A ARG* 3.0 30.9 + - - +
540A ARG* 4.1 1.6 - - - -
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Residues in contact with THR 473 (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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231A PHE* 4.5 7.0 - - + -
367A GLU* 4.6 1.1 - - - +
448A LEU* 4.5 4.5 - - + -
452A ILE* 3.6 26.7 - - + +
469A GLU* 2.9 20.3 + - - +
472A ARG* 1.3 120.7 - - - +
474A GLY* 1.3 60.8 + - - +
475A PHE* 3.2 19.2 + - - +
537A ARG* 2.9 36.0 + - - +
540A ARG* 3.8 2.7 - - - -
541A PRO* 3.4 4.5 - - - +
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Residues in contact with GLY 474 (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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470A TYR* 2.6 44.8 + - - -
473A THR* 1.3 72.3 - - - +
475A PHE* 1.3 67.9 + - - +
477A TYR* 3.9 13.3 - - - -
540A ARG* 3.5 19.1 - - - +
541A PRO* 4.2 11.6 - - - +
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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