Contacts of the helix formed by residues 451 - 467 (chain A) in PDB entry 5ULM
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 GLU 451 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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420A LYS* 2.8 27.2 + - - +
424A GLU* 5.7 0.4 - - - +
435A TYR* 3.4 24.3 + - + +
439A LEU* 3.9 11.7 - - + -
444A HIS* 5.1 8.6 + - + +
450A PHE* 1.3 69.4 + - - +
452A LEU* 1.3 56.2 + - - +
453A ARG 3.4 0.2 - - - -
454A LYS* 2.9 13.5 + - + +
455A VAL* 2.6 42.7 + - + +
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Residues in contact with LEU 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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436A ALA* 3.7 42.6 - - + +
439A LEU* 4.1 12.7 - - + +
440A LEU* 3.6 30.3 - - + -
444A HIS* 3.7 29.3 + - + +
449A SER* 3.4 18.8 - - - +
450A PHE* 3.2 3.6 - - - +
451A GLU* 1.3 76.1 - - - +
453A ARG* 1.3 59.2 + - + +
455A VAL* 3.6 3.3 + - + +
456A GLY* 3.1 21.0 + - - -
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Residues in contact with ARG 453 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448A SER 5.8 3.6 - - - +
449A SER 3.1 23.4 + - - +
450A PHE* 3.6 23.5 - - + -
452A LEU* 1.3 73.6 - - + +
454A LYS* 1.3 54.3 + - - +
456A GLY* 3.2 5.4 + - - +
457A VAL* 2.8 34.0 + - - +
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Residues in contact with LYS 454 (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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450A PHE* 4.3 12.2 - - + +
451A GLU* 3.1 25.1 - - + +
453A ARG* 1.3 73.1 - - - +
455A VAL* 1.3 61.4 + - + +
456A GLY 3.1 1.1 - - - -
457A VAL* 2.9 28.5 - - + +
458A LYS* 3.3 8.7 + - - +
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Residues in contact with VAL 455 (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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423A PHE* 4.0 24.5 - - + -
432A GLY* 3.6 24.5 - - - +
435A TYR* 3.5 34.5 - - + -
436A ALA* 4.2 9.6 - - + -
439A LEU* 4.5 4.7 - - + -
451A GLU* 2.6 29.7 + - + +
452A LEU* 3.9 5.6 - - - +
454A LYS* 1.3 70.1 - - + +
456A GLY* 1.3 57.0 + - - +
458A LYS* 3.3 2.9 + - - +
459A LEU* 2.9 39.4 + - + +
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Residues in contact with GLY 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 LEU 3.1 15.9 + - - -
453A ARG* 3.3 10.8 - - - -
454A LYS 3.1 0.4 - - - -
455A VAL* 1.3 73.3 - - - +
457A VAL* 1.3 63.9 + - - +
459A LEU* 3.5 10.6 + - - +
460A SER* 3.1 26.3 + - - -
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Residues in contact with VAL 457 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453A ARG* 2.8 14.3 + - - +
454A LYS* 2.9 33.7 - - + +
456A GLY* 1.3 73.1 - - - +
458A LYS* 1.3 62.7 + - + +
460A SER* 3.1 17.0 + - - -
461A SER* 3.2 13.8 + - - +
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Residues in contact with LYS 458 (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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423A PHE* 3.5 32.5 - - + -
427A PRO* 3.6 30.7 - - + +
454A LYS 3.3 9.8 + - - +
455A VAL 3.3 4.6 + - - +
457A VAL* 1.3 77.4 - - + +
459A LEU* 1.3 60.8 + - - +
461A SER* 3.0 15.8 + - - +
462A LEU* 3.0 38.8 + - + +
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Residues in contact with LEU 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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423A PHE* 4.5 4.5 - - + -
428A THR 4.4 2.0 - - - +
429A LEU* 3.6 33.1 - - + +
432A GLY* 4.0 28.3 - - - +
433A ILE* 4.1 15.5 - - + +
436A ALA* 4.9 0.4 - - + -
455A VAL* 2.9 39.0 + - + +
456A GLY* 3.7 9.2 - - - +
458A LYS* 1.3 76.4 - - - +
460A SER* 1.3 55.9 + - - +
462A LEU* 3.5 3.8 + - + +
463A LEU* 2.9 35.0 + - + +
484A ALA* 4.8 7.4 - - + +
487A LEU* 4.3 16.6 - - + -
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Residues in contact with SER 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 GLY 3.1 14.0 + - - -
457A VAL* 3.1 14.0 + - - -
459A LEU* 1.3 76.0 - - - +
461A SER* 1.3 56.9 + - - +
463A LEU* 3.6 11.6 + - - +
464A GLY* 3.0 21.1 + - - -
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Residues in contact with SER 461 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457A VAL* 3.2 11.5 + - - +
458A LYS* 3.0 28.2 + - - +
460A SER* 1.3 74.1 - - - +
462A LEU* 1.3 60.5 + - - +
464A GLY* 3.3 3.0 + - - +
465A LYS* 2.9 27.5 + - - +
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Residues in contact with LEU 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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423A PHE* 4.0 12.6 - - + -
427A PRO* 3.7 25.4 - - + +
428A THR* 3.5 38.1 - - - +
429A LEU* 3.8 20.4 - - + +
458A LYS* 3.0 31.5 + - + +
459A LEU* 3.8 1.6 - - + +
461A SER* 1.3 74.3 + - - +
463A LEU* 1.3 63.8 - - - +
465A LYS* 3.0 31.1 + - + +
466A LYS* 3.0 28.1 + - + +
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Residues in contact with LEU 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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429A LEU* 4.1 19.2 - - + +
459A LEU 2.9 21.0 + - - +
460A SER* 3.7 11.0 - - - +
462A LEU* 1.3 75.2 - - - +
464A GLY* 1.3 62.2 + - - +
466A LYS* 3.3 7.2 + - + +
467A GLY* 3.2 22.0 + - - +
481A PHE* 3.5 39.3 - - + +
484A ALA* 4.2 29.2 - - + +
485A SER* 4.9 6.1 - - - +
488A ALA* 5.6 6.1 - - + -
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Residues in contact with GLY 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 SER 3.0 16.0 + - - -
461A SER* 3.3 4.9 + - - -
462A LEU 3.2 0.4 - - - -
463A LEU* 1.3 76.2 - - - +
465A LYS* 1.3 60.6 + - - +
467A GLY* 3.4 12.9 + - - -
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Residues in contact with LYS 465 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427A PRO 4.9 4.6 + - - -
461A SER 2.9 14.4 + - - +
462A LEU* 3.0 32.1 + - + +
464A GLY* 1.3 77.2 - - - +
466A LYS* 1.3 78.7 + - + +
467A GLY* 3.4 0.5 + - - -
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Residues in contact with LYS 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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429A LEU* 4.4 23.8 - - + +
462A LEU* 3.0 18.0 + - - +
463A LEU* 3.3 11.6 + - + +
465A LYS* 1.3 94.0 - - + +
467A GLY* 1.3 65.0 + - - +
468A ASN 4.7 0.3 - - - +
471A LYS* 5.7 2.3 - - - +
472A LEU* 3.6 31.6 - - + +
477A GLU* 2.9 41.2 + - - +
481A PHE* 5.5 0.7 - - + -
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Residues in contact with GLY 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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463A LEU 3.2 14.1 + - - +
464A GLY* 3.4 8.9 + - - -
465A LYS 3.3 3.4 - - - -
466A LYS* 1.3 82.3 - - - +
468A ASN* 1.3 65.1 + - - +
469A LEU 3.7 0.9 + - - -
471A LYS* 6.3 0.4 - - - -
472A LEU* 4.5 1.7 - - - +
481A PHE* 4.2 12.8 - - - -
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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