Contacts of the helix formed by residues 464 - 474 (chain A) in PDB entry 3F4V
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 LYS 464 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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391A GLN* 2.9 21.4 + - - -
400A TYR* 3.4 22.4 - - - +
401A LEU* 3.7 11.0 - - - +
403A ASP* 3.5 22.0 - - - +
406A ARG* 3.5 3.1 - - - +
437A ASP* 2.8 24.4 + - - -
448A LYS* 4.3 1.6 - - - +
450A GLY 2.7 31.5 + - - +
451A ILE 2.9 17.0 + - - +
453A TYR* 3.5 39.3 - - + +
463A PRO* 1.3 75.7 - - - +
465A ALA* 1.3 66.5 - - - +
466A SER* 3.2 0.7 - - - +
467A ALA* 2.9 10.7 + - - +
468A TYR* 3.3 13.7 + - - -
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Residues in contact with ALA 465 (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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6A TRP* 3.6 14.4 - - + -
401A LEU 2.8 17.6 + - - +
402A ARG* 4.7 3.4 - - - -
403A ASP* 3.2 17.5 - - - +
404A THR* 5.2 0.9 - - - +
407A VAL* 4.0 12.8 - - + -
464A LYS* 1.3 70.5 - - - +
466A SER* 1.3 55.6 + - - +
468A TYR* 3.1 12.6 + - - +
469A TRP 2.8 24.3 + - - -
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Residues in contact with SER 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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403A ASP* 2.6 32.9 + - - -
406A ARG* 3.4 24.9 - - - -
407A VAL* 3.7 16.3 - - - +
410A TYR* 4.5 6.5 - - - -
451A ILE* 3.5 19.3 + - - +
465A ALA* 1.3 77.8 - - - +
467A ALA* 1.3 58.4 + - - +
469A TRP* 3.3 5.3 + - - +
470A PHE* 3.0 33.6 + - - -
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Residues in contact with ALA 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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80A LEU* 3.5 30.1 - - + +
451A ILE* 3.3 34.5 + - + +
452A VAL* 4.5 0.4 - - + -
463A PRO* 3.8 19.7 - - + -
464A LYS 2.9 8.5 + - - +
466A SER* 1.3 80.2 + - - +
468A TYR* 1.3 58.3 + - - +
470A PHE* 3.3 4.4 + - - +
471A ARG 3.0 22.0 + - - -
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Residues in contact with TYR 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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6A TRP* 4.0 10.3 - - + -
80A LEU* 4.7 5.2 - - + -
463A PRO* 3.6 46.6 - - + +
464A LYS 3.3 19.5 + - - -
465A ALA* 3.1 9.5 + - - +
467A ALA* 1.3 74.4 - - - +
469A TRP* 1.3 60.7 + - - +
471A ARG* 3.5 48.4 + - - +
472A ASP* 2.9 35.0 + - - +
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Residues in contact with TRP 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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6A TRP* 2.8 54.5 + + + -
7A LEU* 3.7 16.7 - - + +
10A LEU* 3.9 18.4 - - + -
407A VAL* 3.5 27.7 - - + +
410A TYR* 3.9 11.2 - + + -
411A ARG* 3.7 28.4 - - + +
414A LEU* 3.8 31.4 - - + -
465A ALA 2.8 12.9 + - - +
466A SER* 3.4 13.0 - - - +
468A TYR* 1.3 75.9 - - - +
470A PHE* 1.3 82.2 + + - +
472A ASP* 3.3 3.8 + - - +
473A MET* 2.8 44.3 + - + +
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Residues in contact with PHE 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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21A PHE* 4.9 2.9 - + - -
22A GLY 5.9 0.2 - - - -
80A LEU 3.9 1.8 - - - -
82A PHE* 3.6 39.9 - + + -
410A TYR* 3.6 54.3 - + + -
414A LEU* 4.0 11.0 - - + -
430A TYR* 4.2 15.9 - + - -
432A ALA* 4.2 10.5 - - + -
451A ILE* 4.3 8.3 - - + -
466A SER 3.0 24.7 + - - -
467A ALA* 3.3 7.8 + - - +
469A TRP* 1.3 92.7 - + - +
471A ARG* 1.3 68.0 + - - +
473A MET* 3.1 6.6 + - + -
474A LEU* 2.8 41.7 + - + +
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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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79A SER* 3.4 22.6 + - - +
80A LEU* 3.3 26.7 + - + +
81A ASN* 2.9 35.7 + - - +
467A ALA 3.0 13.9 + - - +
468A TYR* 3.3 42.9 + - - +
470A PHE* 1.3 77.4 - - - +
472A ASP* 1.3 74.1 + - - +
475A LYS* 3.3 9.2 + - - +
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Residues in contact with ASP 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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6A TRP* 3.2 29.5 + - - +
7A LEU* 3.9 22.2 - - + +
11A SER* 6.0 0.2 - - - -
468A TYR* 2.9 17.8 + - - +
469A TRP 3.6 4.3 - - - +
471A ARG* 1.3 90.2 + - - +
473A MET* 1.3 64.8 + - - +
475A LYS* 3.1 45.6 + - - +
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Residues in contact with MET 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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7A LEU* 3.8 15.9 - - + +
10A LEU* 3.7 28.7 - - + +
11A SER* 3.3 38.7 - - - +
12A ARG 3.5 4.3 + - - -
15A PHE* 4.7 6.5 - - + -
21A PHE* 3.9 21.8 - - + -
414A LEU* 4.1 20.6 - - + -
469A TRP* 2.8 32.2 + - + +
470A PHE* 3.1 8.9 + - + +
472A ASP* 1.3 78.5 - - - +
474A LEU* 1.3 82.3 + - + +
475A LYS* 3.7 2.4 + - - +
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Residues in contact with LEU 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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12A ARG* 2.8 29.7 + - + +
21A PHE* 3.4 40.4 - - + -
80A LEU 4.1 2.5 - - - +
81A ASN* 3.6 33.8 - - + +
82A PHE* 3.7 37.2 - - + -
470A PHE* 2.8 26.3 + - + +
473A MET* 1.3 98.2 - - + +
475A LYS* 1.3 69.1 + - - +
476A HIS* 3.3 3.1 + - - -
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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