Contacts of the helix formed by residues 481 - 496 (chain A) in PDB entry 4KZI
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 ASP 481 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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479A PHE 3.9 0.2 + - - -
480A GLY* 1.3 70.9 - - - -
482A TRP* 1.3 63.4 + - - +
483A ILE 3.1 0.2 - - - -
484A ASP* 2.9 30.8 + - + +
485A SER* 3.1 14.0 + - - +
568A GLN* 4.8 5.8 - - - +
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Residues in contact with TRP 482 (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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406A PHE* 3.8 28.9 - + - -
410A LEU* 4.7 3.6 - - + -
444A LEU* 4.5 13.5 - - + -
447A PHE* 4.0 20.6 - + - -
448A ILE* 3.8 26.0 - - + -
479A PHE* 3.4 37.4 + + - +
480A GLY 2.9 1.2 + - - -
481A ASP* 1.3 78.6 - - - +
483A ILE* 1.3 57.3 + - - +
485A SER* 3.1 2.4 + - - -
486A ILE* 2.8 48.8 + - + +
565A LEU* 3.0 21.6 + - + +
568A GLN* 3.5 40.1 + - + +
569A GLY* 3.5 28.5 - - - -
572A ARG* 4.6 4.9 - - + -
573A ILE* 6.0 1.1 - - + -
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Residues in contact with ILE 483 (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 LEU* 4.2 6.7 - - + -
462A LEU* 3.8 37.9 - - + -
464A PHE* 4.9 0.9 - - + -
472A ARG* 4.2 13.0 - - + +
475A CYS* 3.9 27.4 - - + -
476A ALA* 4.6 2.9 - - - +
479A PHE* 3.9 37.5 - - + +
480A GLY 3.3 12.8 + - - +
481A ASP 3.1 1.0 - - - -
482A TRP* 1.3 79.7 - - - +
484A ASP* 1.3 77.0 + - - +
486A ILE* 3.2 16.2 + - + +
487A LEU* 2.9 24.1 + - - +
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Residues in contact with ASP 484 (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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472A ARG* 3.2 40.3 + - - +
476A ALA* 6.1 2.0 - - - +
480A GLY 4.9 0.5 - - - +
481A ASP* 2.9 23.2 + - + +
483A ILE* 1.3 81.5 - - - +
485A SER* 1.3 64.2 + - - +
487A LEU* 3.2 9.0 + - - +
488A ALA* 3.0 21.0 + - - +
491A ARG* 4.8 1.9 + - - -
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Residues in contact with SER 485 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481A ASP* 3.1 10.1 + - - +
482A TRP 3.1 5.4 + - - -
484A ASP* 1.3 76.3 - - - +
486A ILE* 1.3 63.2 + - - +
488A ALA* 3.4 9.7 + - - +
489A PHE* 3.0 23.4 + - - +
561A GLU* 5.1 0.5 - - - +
565A LEU* 3.5 23.0 - - - +
568A GLN* 3.2 25.4 + - - -
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Residues in contact with ILE 486 (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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447A PHE* 4.9 2.0 - - + -
448A ILE* 4.4 20.9 - - + +
451A LEU* 4.0 31.6 - - + -
452A ALA* 4.3 11.5 - - + +
455A SER* 6.4 0.2 - - - -
462A LEU* 4.8 6.1 - - + -
479A PHE* 5.0 0.4 - - + -
482A TRP* 2.8 65.1 + - + +
483A ILE* 3.2 23.1 + - + +
485A SER* 1.3 72.7 - - - +
487A LEU* 1.3 57.7 + - - +
489A PHE* 3.2 7.1 + - - +
490A SER* 2.9 25.3 + - - -
565A LEU* 4.3 8.3 - - + -
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Residues in contact with LEU 487 (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* 4.6 6.5 - - - -
457A PRO* 3.8 28.7 - - + +
460A GLY* 4.7 7.6 - - - -
461A LYS 4.3 10.8 - - - +
462A LEU* 3.9 28.3 - - + -
472A ARG* 3.9 39.3 - - + -
483A ILE 2.9 17.2 + - - +
484A ASP* 3.2 9.6 + - - +
486A ILE* 1.3 75.6 - - - +
488A ALA* 1.3 65.1 + - - +
490A SER* 3.1 5.9 + - - -
491A ARG* 3.0 43.6 + - - +
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Residues in contact with ALA 488 (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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484A ASP 3.0 12.8 + - - +
485A SER* 3.5 12.3 - - - +
487A LEU* 1.3 73.8 - - - +
489A PHE* 1.3 63.4 + - - +
491A ARG* 3.1 23.3 + - - +
492A SER* 3.1 20.8 + - - -
561A GLU* 4.2 7.8 - - - +
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Residues in contact with PHE 489 (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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448A ILE* 4.4 4.0 - - + -
449A LEU* 4.1 21.5 - - + -
452A ALA* 3.6 23.8 - - + -
485A SER 3.0 7.2 + - - +
486A ILE 3.4 7.9 - - - +
487A LEU 3.1 0.2 - - - -
488A ALA* 1.3 73.8 - - - +
490A SER* 1.3 61.3 + - - +
492A SER* 3.3 2.2 + - - -
493A LEU* 2.8 41.9 + - + +
555A LEU* 6.6 0.2 - - + -
558A LYS* 4.0 35.7 - - + -
561A GLU* 3.5 25.5 + - + +
562A LEU* 3.9 31.4 - - + -
565A LEU* 3.5 30.5 - - + -
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Residues in contact with SER 490 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452A ALA* 2.6 37.8 + - - +
455A SER* 4.1 4.2 + - - -
457A PRO* 3.4 21.7 - - - +
486A ILE 2.9 12.9 + - - -
487A LEU* 3.2 17.7 - - - -
489A PHE* 1.3 77.1 - - - +
491A ARG* 1.3 57.8 + - - +
493A LEU* 3.3 1.6 + - - +
494A HIS* 2.8 38.6 + - - -
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Residues in contact with ARG 491 (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 PRO* 3.3 42.8 + - + +
458A GLY* 5.6 0.6 - - - -
460A GLY* 5.8 0.6 - - - -
472A ARG* 6.2 1.0 - - - +
484A ASP 4.8 1.6 + - - -
487A LEU* 3.0 27.3 + - - +
488A ALA* 3.1 35.9 + - - +
490A SER* 1.3 75.2 - - - +
492A SER* 1.3 63.5 + - - +
494A HIS* 3.3 5.4 + - - +
495A SER* 3.1 24.4 + - - -
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Residues in contact with SER 492 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
488A ALA 3.1 12.7 + - - -
489A PHE* 3.6 8.3 - - - -
491A ARG* 1.3 78.5 - - - +
493A LEU* 1.3 60.9 + - - +
495A SER* 2.9 24.1 + - - -
496A LEU* 3.9 4.5 + - - +
558A LYS* 2.9 45.1 + - - +
561A GLU* 3.5 18.8 + - - -
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Residues in contact with LEU 493 (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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449A LEU* 4.3 20.0 - - + +
452A ALA* 4.4 4.7 - - + -
453A TYR* 3.8 48.1 - - + +
489A PHE* 2.8 38.1 + - + +
490A SER* 3.7 3.8 - - - +
492A SER* 1.3 73.9 - - - +
494A HIS* 1.3 64.2 + - - +
496A LEU* 3.2 21.4 + - + +
497A LEU 3.9 2.6 + - - -
498A VAL* 4.2 25.1 + - + +
503A PHE* 4.5 4.0 - - + -
555A LEU* 4.4 17.3 - - + -
558A LYS* 5.1 3.8 - - + +
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Residues in contact with HIS 494 (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 ALA 3.3 14.1 - - - -
453A TYR* 3.0 39.6 - + - -
455A SER 3.1 20.6 + - - -
456A LYS* 6.5 0.4 - - + -
457A PRO* 3.9 16.6 - - + -
490A SER* 2.8 28.9 + - - +
491A ARG* 3.3 6.0 + - - +
493A LEU* 1.3 75.4 - - - +
495A SER* 1.3 61.8 + - - +
497A LEU* 3.0 26.7 + - - +
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Residues in contact with SER 495 (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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491A ARG 3.1 14.2 + - - -
492A SER* 2.9 18.7 + - - -
493A LEU 3.2 0.4 - - - -
494A HIS* 1.3 77.1 - - - +
496A LEU* 1.3 69.5 + - - +
497A LEU* 3.5 12.5 + - - +
558A LYS* 4.6 4.5 + - - -
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Residues in contact with LEU 496 (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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492A SER 4.4 6.3 - - - +
493A LEU* 3.2 13.5 + - + +
494A HIS 3.2 0.8 - - - -
495A SER* 1.3 92.6 + - - +
497A LEU* 1.3 71.1 + - - +
498A VAL* 4.0 12.4 - - + +
551A CYS* 4.9 12.6 - - - +
554A ARG* 4.2 25.6 - - + +
555A LEU* 4.0 39.3 - - + +
558A LYS* 4.1 27.1 - - + +
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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