Contacts of the helix formed by residues 529 - 545 (chain A) in PDB entry 1ZD4
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 529 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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518A ILE* 3.6 29.4 - - + -
519A GLU 4.4 4.7 - - - -
520A ASP* 3.7 21.4 + - - -
521A CYS* 3.9 13.9 - - + -
525A THR 2.9 14.2 + - - +
528A ASP* 1.3 107.1 + - - +
530A PRO* 1.3 59.3 - - - +
532A GLU* 2.8 42.1 - - + +
533A VAL* 2.9 21.7 + - - +
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Residues in contact with PRO 530 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A LEU* 3.7 30.1 - - + -
227A PRO* 4.0 6.7 - - + -
274A TYR* 3.5 29.2 - - + -
275A GLN* 4.4 4.7 - - - +
526A GLN 3.1 19.4 - - - +
527A MET 3.3 11.2 - - - +
528A ASP 3.3 10.1 - - - +
529A LYS* 1.3 88.7 - - - +
531A THR* 1.3 62.7 + - - +
532A GLU* 4.7 0.2 - - - +
533A VAL* 3.5 1.9 + - + +
534A ASN* 2.8 33.2 + - - -
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Residues in contact with THR 531 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A PRO 4.7 5.9 + - - -
226A LEU* 5.2 2.1 - - - +
227A PRO* 3.8 20.1 - - - +
529A LYS 3.3 0.8 - - - -
530A PRO* 1.3 77.5 - - - +
532A GLU* 1.3 79.6 + - - +
534A ASN* 3.4 5.7 + - - +
535A GLN* 3.1 24.2 + - + +
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Residues in contact with GLU 532 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518A ILE* 4.0 28.9 - - + -
529A LYS* 2.8 48.1 - - + +
530A PRO* 4.7 0.2 - - - +
531A THR* 1.3 86.1 + - + +
533A VAL* 1.3 57.2 + - - +
535A GLN* 3.3 9.7 + - - +
536A ILE* 2.8 38.9 + - + +
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Residues in contact with VAL 533 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A TRP* 5.4 0.2 - - + -
275A GLN* 4.1 16.6 - - - +
356A LEU* 4.2 19.3 - - + -
490A VAL* 6.2 0.4 - - - -
518A ILE* 3.7 9.9 - - + -
525A THR* 3.4 34.8 - - + +
526A GLN* 4.6 2.2 - - + +
529A LYS 2.9 20.6 + - - +
530A PRO* 3.6 6.5 - - + +
531A THR 3.2 0.2 - - - -
532A GLU* 1.3 77.7 - - - +
534A ASN* 1.3 59.0 + - - +
536A ILE* 3.3 5.1 + - - +
537A LEU* 2.8 51.0 + - + +
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Residues in contact with ASN 534 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227A PRO* 4.0 12.5 - - - +
274A TYR 3.0 19.2 - - - +
275A GLN* 2.5 40.7 - - - +
278A ALA* 3.3 24.0 - - + +
279A LEU* 5.3 3.1 - - + -
530A PRO 2.8 14.7 + - - +
531A THR* 3.8 5.4 - - - +
533A VAL* 1.3 74.0 - - - +
535A GLN* 1.3 57.2 + - - +
537A LEU* 4.8 3.6 - - - -
538A ILE* 2.8 46.4 + - + +
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Residues in contact with GLN 535 (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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531A THR* 3.1 13.4 + - + +
532A GLU* 3.4 11.5 - - - +
534A ASN* 1.3 79.6 - - - +
536A ILE* 1.3 78.5 + - - +
538A ILE* 4.2 4.9 - - - +
539A LYS* 3.1 50.5 + - - +
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Residues in contact with ILE 536 (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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488A LEU* 4.6 9.0 - - + -
490A VAL* 4.0 30.1 - - + -
515A ARG 5.4 0.7 - - - +
516A GLY* 4.7 9.9 - - - -
517A HIS 4.1 13.2 - - - +
518A ILE* 3.8 32.8 - - + -
532A GLU* 2.8 27.6 + - + +
533A VAL* 3.6 5.4 - - - +
535A GLN* 1.3 89.1 - - - +
537A LEU* 1.3 63.4 + - + +
539A LYS* 3.4 7.5 - - + +
540A TRP* 3.0 21.7 + - - +
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Residues in contact with LEU 537 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A TRP* 4.7 9.6 - - + -
275A GLN* 5.1 4.7 - - + -
279A LEU* 4.3 19.7 - - + -
330A ILE* 4.3 41.5 - - + -
354A ALA* 4.6 4.9 - - + -
356A LEU* 4.6 12.8 - - + -
488A LEU* 4.3 21.3 - - + -
490A VAL* 4.8 1.8 - - + -
533A VAL* 2.8 42.7 + - + +
534A ASN* 3.9 2.5 - - - +
536A ILE* 1.3 71.0 - - + +
538A ILE* 1.3 56.3 + - - +
540A TRP* 3.1 8.2 + - + +
541A LEU* 2.7 41.7 + - + +
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Residues in contact with ILE 538 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A ALA* 4.1 16.6 - - + +
279A LEU* 3.6 19.0 - - + +
282A ALA* 3.9 29.2 - - + -
284A TYR* 5.4 0.2 - - + -
534A ASN* 2.8 34.8 + - + +
535A GLN* 4.2 4.0 - - - +
537A LEU* 1.3 71.4 - - - +
539A LYS* 1.3 62.7 + - - +
541A LEU* 3.3 8.3 + - - +
542A ASP* 2.7 45.6 + - - +
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Residues in contact with LYS 539 (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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535A GLN* 3.1 38.3 + - - +
536A ILE* 3.4 8.3 - - + +
538A ILE* 1.3 81.1 - - - +
540A TRP* 1.3 63.3 + - - +
542A ASP* 3.4 5.1 + - - +
543A SER* 3.1 23.3 + - - +
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Residues in contact with TRP 540 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328A VAL* 3.9 8.3 - - + -
330A ILE* 4.4 3.8 - - + -
352A ALA* 3.5 33.4 - - + -
353A VAL 3.3 28.7 - - - -
354A ALA* 3.5 20.2 - - + -
486A PRO* 3.8 7.2 - - + -
487A ALA 3.8 9.3 + - - +
488A LEU* 3.2 38.2 - - + +
514A LYS* 4.5 10.3 - - + -
536A ILE 3.0 10.3 + - - +
537A LEU* 3.5 13.9 - - + +
539A LYS* 1.3 82.4 - - - +
541A LEU* 1.3 88.5 + - + +
543A SER* 3.2 5.9 + - - -
544A ASP* 2.9 52.1 + - + +
545A ALA* 3.8 0.6 + - + -
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Residues in contact with LEU 541 (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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259A VAL* 4.2 12.1 - - + -
279A LEU* 3.7 33.0 - - + -
284A TYR* 2.9 44.5 + - + +
328A VAL* 4.0 12.1 - - + -
330A ILE* 4.5 4.7 - - + -
537A LEU* 2.7 29.3 + - + +
538A ILE* 3.6 5.2 - - - +
540A TRP* 1.3 98.6 - - + +
542A ASP* 1.3 57.6 + - - +
545A ALA* 2.9 38.2 + - + +
546A ARG 3.0 8.3 + - - -
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Residues in contact with ASP 542 (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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282A ALA 4.3 5.5 - - - +
284A TYR* 2.8 28.3 + - - -
538A ILE* 2.7 34.7 + - - +
539A LYS* 3.4 4.8 + - - +
541A LEU* 1.3 76.3 - - - +
543A SER* 1.3 61.8 + - - +
546A ARG* 4.1 17.3 + - - +
547A ASN* 4.5 4.2 + - - -
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Residues in contact with SER 543 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514A LYS* 3.9 11.3 + - - +
539A LYS* 3.1 18.2 + - - +
540A TRP* 3.2 8.1 + - - -
542A ASP* 1.3 81.3 - - - +
544A ASP* 1.3 77.2 + - - +
547A ASN* 5.4 5.8 + - - -
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Residues in contact with ASP 544 (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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351A ARG* 3.4 20.7 + - - -
352A ALA* 5.2 0.7 - - - -
486A PRO* 3.7 32.2 - - + +
487A ALA 5.3 0.5 - - - +
514A LYS* 3.0 38.3 + - - +
540A TRP* 2.9 26.5 + - + +
543A SER* 1.3 96.4 + - - +
545A ALA* 1.3 60.9 + - - +
547A ASN* 4.6 7.2 + - - +
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Residues in contact with ALA 545 (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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257A PRO* 5.8 2.8 - - + +
284A TYR* 4.6 4.0 - - + -
328A VAL* 4.1 19.5 - - + -
351A ARG* 2.7 38.9 + - - +
352A ALA* 4.6 6.3 - - + -
540A TRP* 3.8 1.3 + - + -
541A LEU* 2.9 39.3 + - + +
544A ASP* 1.3 77.8 - - + +
546A ARG* 1.3 63.7 + - - +
547A ASN 3.1 1.3 - - - -
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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
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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