Contacts of the helix formed by residues 434 - 451 (chain A) in PDB entry 4D2Y
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 434 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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432A CYS* 3.6 0.9 - - - -
433A THR* 1.3 94.7 + - - +
435A ALA* 1.3 58.2 + - - +
436A HIS* 3.7 9.1 + - - +
437A GLY* 3.2 19.6 + - - -
438A MET* 2.9 28.6 + - - +
526A ALA* 3.4 9.9 - - - -
529A ASN* 6.0 1.1 - - - +
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Residues in contact with ALA 435 (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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434A THR* 1.3 70.1 - - - +
436A HIS* 1.3 61.8 + - - +
438A MET* 3.2 10.3 + - - +
439A PHE* 2.8 28.4 + - - +
524A LEU* 3.7 25.6 - - + +
526A ALA* 3.5 11.7 - - + +
530A ASP 5.8 0.2 - - - +
532A GLU* 3.8 22.7 + - + +
534A PHE* 3.7 20.8 - - + -
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Residues in contact with HIS 436 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434A THR* 3.3 8.9 + - - +
435A ALA* 1.3 78.1 - - - +
437A GLY* 1.3 62.1 + - - +
439A PHE* 3.2 8.6 + + - +
440A ASN* 3.0 21.7 + - - +
532A GLU* 3.5 25.0 + - - -
534A PHE* 3.7 24.3 - + - -
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Residues in contact with GLY 437 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432A CYS* 3.6 11.9 - - - -
433A THR 5.7 0.2 - - - -
434A THR* 3.2 19.2 + - - -
436A HIS* 1.3 75.0 - - - +
438A MET* 1.3 61.5 + - - +
440A ASN* 3.2 8.4 + - - +
441A TYR* 3.1 28.7 + - - -
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Residues in contact with MET 438 (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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432A CYS* 3.4 13.2 - - - -
434A THR 2.9 15.6 + - - +
435A ALA* 3.4 8.1 - - - +
437A GLY* 1.3 72.9 - - - +
439A PHE* 1.3 67.2 + - - +
441A TYR* 3.2 2.3 + - - +
442A ILE* 2.9 28.7 + - + +
462A PHE* 3.8 32.5 - - + -
472A PHE* 3.9 7.9 - - + -
473A ARG 3.9 17.3 - - - +
474A VAL* 4.0 21.3 - - + -
524A LEU* 3.9 18.4 - - + -
525A GLN 3.4 36.1 - - - +
526A ALA* 3.8 10.1 - - - -
581A ALA* 4.7 1.6 - - + -
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Residues in contact with PHE 439 (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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435A ALA 2.8 13.5 + - - +
436A HIS* 3.4 12.1 - + - +
438A MET* 1.3 75.7 - - - +
440A ASN* 1.3 60.0 + - - +
442A ILE* 3.2 3.6 + - - -
443A CYS* 2.8 56.4 + - - -
522A LEU* 3.9 17.5 - - + -
524A LEU* 3.5 10.5 - - + +
534A PHE* 3.4 47.1 - + + -
535A GLN 3.4 26.7 - - - -
536A ILE* 4.3 1.3 - - - -
537A PRO* 3.9 8.1 - - + -
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Residues in contact with ASN 440 (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 HIS 3.0 12.6 + - - +
437A GLY* 3.4 12.2 + - - +
439A PHE* 1.3 82.8 - - + +
441A TYR* 1.3 66.3 + - - +
443A CYS* 3.3 6.0 + - - +
444A ASN* 3.0 46.5 + - - +
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Residues in contact with TYR 441 (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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427A PHE* 5.5 6.3 - - + -
428A ASP 3.9 10.7 + - - -
429A ALA* 3.7 31.0 - - + -
431A ASP* 2.5 36.6 + - - -
432A CYS* 3.9 13.5 - - + -
437A GLY* 3.1 24.6 + - - -
438A MET 3.6 6.5 - - - +
440A ASN* 1.3 80.3 - - + +
442A ILE* 1.3 59.1 + - - +
444A ASN* 3.4 10.9 + - + +
445A HIS* 2.9 28.1 + - - +
460A THR* 4.1 11.1 + - + -
462A PHE* 3.8 18.6 - + + -
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Residues in contact with ILE 442 (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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438A MET* 2.9 22.2 + - + +
439A PHE 3.7 4.0 - - - +
441A TYR* 1.3 74.3 - - - +
443A CYS* 1.3 60.7 + - - +
445A HIS* 3.2 7.0 + - + +
446A VAL* 2.8 33.8 + - + +
460A THR* 5.5 1.1 - - + -
462A PHE* 4.0 17.7 - - + -
474A VAL* 4.0 16.6 - - + -
479A LEU* 3.9 28.7 - - + -
522A LEU* 3.8 22.2 - - + -
524A LEU* 3.8 33.4 - - + -
536A ILE* 5.4 1.6 - - + -
583A PRO* 4.6 9.0 - - + -
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Residues in contact with CYS 443 (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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439A PHE* 2.8 57.4 + - - +
440A ASN* 3.7 7.0 - - - +
442A ILE* 1.3 77.3 - - - +
444A ASN* 1.3 60.3 + - - +
446A VAL* 3.3 6.0 + - - +
447A LYS* 2.9 31.3 + - - +
522A LEU* 5.8 0.2 - - - -
536A ILE* 5.0 4.5 - - - -
537A PRO* 3.7 20.0 - - - -
540A LEU* 3.8 15.7 - - + +
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Residues in contact with ASN 444 (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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427A PHE* 5.5 3.6 - - + -
440A ASN* 3.0 40.7 + - - +
441A TYR* 3.7 11.7 - - + +
443A CYS* 1.3 77.7 - - - +
445A HIS* 1.3 58.0 + - - +
447A LYS* 3.4 7.5 + - - +
448A TYR* 2.8 31.9 + - - +
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Residues in contact with HIS 445 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427A PHE* 4.4 12.6 - - - -
441A TYR 2.9 10.7 + - - +
442A ILE* 3.4 12.1 - - - +
444A ASN* 1.3 76.1 - - - +
446A VAL* 1.3 59.3 + - + +
448A TYR* 3.1 1.7 + - - +
449A ALA* 2.7 37.7 + - + +
458A ALA* 3.2 35.0 + - + +
459A ILE* 3.6 1.5 - - - -
460A THR* 2.8 30.7 + - - +
479A LEU* 4.5 14.8 - - + +
564A LEU* 5.0 1.1 - - + -
583A PRO* 3.4 22.6 + - + +
584A PHE* 4.2 2.0 - - - -
585A SER* 2.9 30.0 + - - -
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Residues in contact with VAL 446 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442A ILE* 2.8 29.1 + - + +
443A CYS* 3.7 6.7 - - - +
445A HIS* 1.3 72.8 - - - +
447A LYS* 1.3 62.7 + - - +
450A THR* 2.7 36.6 + - - +
479A LEU* 4.0 27.6 - - + -
480A ILE* 4.6 10.8 - - + -
536A ILE* 4.9 11.9 - - + -
540A LEU* 3.3 35.9 - - + +
564A LEU* 4.1 18.6 - - + -
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Residues in contact with LYS 447 (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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443A CYS 2.9 17.6 + - - +
444A ASN* 3.8 7.9 - - - +
446A VAL* 1.3 78.2 - - - +
448A TYR* 1.3 64.2 + - - +
450A THR* 4.0 2.6 - - - -
451A ASN* 3.1 21.3 + - - -
456A ARG* 4.8 0.3 + - - -
540A LEU* 3.8 32.0 - - + +
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Residues in contact with TYR 448 (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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425A GLN* 3.5 43.8 + - + +
427A PHE* 3.5 31.0 - + + -
444A ASN 2.8 18.4 + - - +
445A HIS 3.6 2.2 - - - +
447A LYS* 1.3 79.4 - - - +
449A ALA* 1.3 65.6 - - - +
451A ASN* 3.5 3.1 - - - +
456A ARG* 2.9 85.4 + - + +
457A SER 4.4 2.0 - - - -
458A ALA* 4.2 3.6 - - + -
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Residues in contact with ALA 449 (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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445A HIS* 2.7 27.0 + - + +
446A VAL 4.3 1.1 - - - +
448A TYR* 1.3 77.3 - - - +
450A THR* 1.3 59.0 + - - +
451A ASN* 4.1 0.2 - - - +
455A LEU* 3.1 10.9 - - - +
456A ARG 2.8 45.9 + - - +
458A ALA* 4.3 3.4 - - + -
564A LEU* 3.8 13.2 - - + -
585A SER* 3.4 21.8 - - - +
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Residues in contact with THR 450 (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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446A VAL* 2.7 29.3 + - - +
447A LYS* 4.0 3.1 - - - -
449A ALA* 1.3 74.3 - - - +
451A ASN* 1.3 61.0 + - - +
452A LYS* 4.1 5.2 - - - +
453A GLY 2.8 26.6 + - - +
454A ASN 3.4 1.4 + - - -
455A LEU* 3.3 19.8 - - + +
540A LEU 4.1 9.1 + - - +
542A LEU* 3.7 39.2 + - + -
563A GLY 6.5 0.4 - - - -
564A LEU* 3.9 21.3 - - + +
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Residues in contact with ASN 451 (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 LYS 3.1 15.3 + - - -
448A TYR 3.5 13.2 - - - +
449A ALA 4.1 0.7 - - - +
450A THR* 1.3 75.8 - - - +
452A LYS* 1.3 72.8 + - - +
453A GLY 3.0 1.7 + - - -
454A ASN* 2.8 52.1 + - - +
456A ARG* 3.5 36.0 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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