Contacts of the helix formed by residues 451 - 466 (chain A) in PDB entry 1VF9
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 THR 451 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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448A GLN* 4.4 20.4 - - + -
450A TRP* 1.3 83.5 - - - +
452A VAL* 1.3 66.1 + - - +
453A GLU* 3.6 7.5 + - - +
454A GLU* 3.5 35.6 + - - +
455A SER* 3.3 22.7 + - - -
490A ARG* 4.9 1.4 + - - -
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Residues in contact with VAL 452 (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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451A THR* 1.3 78.2 - - - +
453A GLU* 1.3 69.5 + - + +
454A GLU 3.3 0.7 - - - -
455A SER* 4.0 3.6 - - - -
456A GLU* 3.3 31.9 + - - +
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Residues in contact with GLU 453 (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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451A THR* 3.5 6.8 + - - +
452A VAL* 1.3 82.0 - - + +
454A GLU* 1.3 60.8 + - + +
456A GLU* 3.6 4.3 + - - +
457A TRP* 2.8 62.6 + - + +
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Residues in contact with GLU 454 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448A GLN* 5.3 1.4 - - - +
449A LYS 5.2 0.2 - - - -
450A TRP* 3.2 32.2 - - + -
451A THR* 3.5 31.0 + - - +
452A VAL 3.3 0.4 - - - -
453A GLU* 1.3 79.0 - - - +
455A SER* 1.3 66.1 + - - +
456A GLU 3.2 0.2 + - - -
457A TRP* 3.2 23.4 + - + +
458A VAL* 3.1 26.7 + - - +
479A PHE* 3.6 15.9 - - + -
480A VAL* 5.6 5.6 - - - +
482A ARG* 2.9 38.6 + - - +
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Residues in contact with SER 455 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
450A TRP* 4.6 0.7 - - - -
451A THR 3.3 16.8 + - - -
452A VAL* 3.7 6.5 + - - -
453A GLU 3.4 0.2 - - - -
454A GLU* 1.3 78.8 - - - +
456A GLU* 1.3 67.3 + - - +
458A VAL* 3.3 9.1 + - - +
459A LYS* 3.2 21.1 + - - +
490A ARG* 2.8 42.8 + - - +
494A MET* 5.4 7.6 - - - +
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Residues in contact with GLU 456 (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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452A VAL* 3.3 27.0 + - + +
453A GLU* 3.6 9.0 - - - +
454A GLU 3.1 0.2 - - - -
455A SER* 1.3 84.7 - - - +
457A TRP* 1.3 70.0 + - + +
459A LYS* 3.1 14.4 + - + +
460A ALA* 3.1 21.8 + - - +
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Residues in contact with TRP 457 (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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453A GLU* 2.8 48.7 + - + +
454A GLU* 3.2 27.8 + - + +
456A GLU* 1.3 80.7 - - + +
458A VAL* 1.3 53.0 + - - +
460A ALA* 3.2 3.1 + - - -
461A GLY* 2.6 35.2 + - - -
473A ILE* 4.2 0.3 - - - +
477A TYR* 3.5 30.5 - + + -
478A PRO* 2.7 56.5 - - + +
479A PHE* 3.6 21.3 - + + -
480A VAL* 6.4 0.4 - - + -
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Residues in contact with VAL 458 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
450A TRP* 4.3 9.2 - - + -
454A GLU 3.1 17.9 + - - +
455A SER* 3.4 10.8 - - - +
456A GLU 3.2 0.2 - - - -
457A TRP* 1.3 76.9 - - - +
459A LYS* 1.3 64.5 + - - +
461A GLY* 2.9 3.1 + - - -
462A VAL* 2.8 33.0 + - + +
470A TRP* 4.3 0.2 - - + -
473A ILE* 4.7 4.9 - - - -
479A PHE* 3.6 11.4 - - + -
487A ILE* 3.6 31.9 - - + +
490A ARG* 5.1 5.2 - - - -
491A TRP* 3.2 39.5 - - + +
494A MET* 5.4 0.9 - - + -
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Residues in contact with LYS 459 (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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455A SER 3.2 9.0 + - - +
456A GLU* 3.1 17.2 + - - +
458A VAL* 1.3 80.0 - - - +
460A ALA* 1.3 62.5 + - - +
462A VAL* 3.3 2.6 + - - +
463A GLN* 3.2 23.9 + - + +
491A TRP* 3.9 27.7 - - + -
494A MET* 5.0 10.3 - - + -
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Residues in contact with ALA 460 (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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456A GLU 3.1 9.6 + - - +
457A TRP* 3.7 7.4 - - - +
459A LYS* 1.3 80.8 - - - +
461A GLY* 1.3 61.3 + - - +
463A GLN* 4.0 5.7 - - - +
464A LYS* 3.2 22.6 + - + +
477A TYR* 3.1 24.2 + - + +
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Residues in contact with GLY 461 (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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457A TRP 2.6 21.4 + - - -
458A VAL 2.9 1.7 + - - -
460A ALA* 1.3 74.6 - - - +
462A VAL* 1.3 57.8 + - - +
464A LYS* 4.6 1.1 - - - -
465A TYR* 3.0 22.7 + - - +
473A ILE* 3.1 38.3 - - - +
477A TYR* 3.5 13.0 + - - -
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Residues in contact with VAL 462 (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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458A VAL 2.8 22.8 + - - +
459A LYS 3.7 4.3 - - - +
461A GLY* 1.3 76.0 - - - +
463A GLN* 1.3 60.3 + - - +
464A LYS 3.1 1.8 - - - -
466A GLY* 2.5 36.6 + - - +
467A GLU* 4.0 19.3 - - + +
470A TRP* 3.6 31.6 - - + -
473A ILE* 4.4 0.9 - - - -
491A TRP* 3.7 35.0 - - + +
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Residues in contact with GLN 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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459A LYS* 3.2 14.4 + - + +
460A ALA* 3.6 6.5 + - - +
461A GLY 3.5 0.2 - - - -
462A VAL* 1.3 80.0 - - - +
464A LYS* 1.3 63.9 + - + +
466A GLY 4.4 0.4 + - - -
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Residues in contact with LYS 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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460A ALA* 3.2 19.8 + - + +
462A VAL 3.1 0.2 - - - -
463A GLN* 1.3 86.6 - - - +
465A TYR* 1.3 81.0 + - + +
477A TYR* 4.0 9.2 - - - +
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Residues in contact with TYR 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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461A GLY* 3.0 18.7 + - - +
464A LYS* 1.3 96.5 - - + +
466A GLY* 1.3 67.4 + - - +
467A GLU 4.5 0.5 - - - +
469A ASN* 3.8 36.5 - - + +
472A ALA* 3.4 32.1 - - + -
473A ILE* 4.0 9.0 - - + -
476A ASN* 3.5 25.5 + - + +
477A TYR* 4.3 15.9 - + - -
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Residues in contact with GLY 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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461A GLY 4.7 0.2 - - - +
462A VAL* 2.5 34.9 + - - -
463A GLN 4.4 0.2 - - - -
464A LYS 3.5 1.6 - - - -
465A TYR* 1.3 86.0 - - - +
467A GLU* 1.3 67.9 + - - -
468A GLY 3.4 1.0 + - - -
469A ASN 3.6 8.0 + - - +
470A TRP* 5.8 0.2 - - - -
473A ILE* 5.1 1.7 - - - +
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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