Contacts of the helix formed by residues 520 - 532 (chain D) in PDB entry 1ZM9
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 ALA 520 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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466D TRP* 3.3 23.4 - - - -
517D THR* 3.9 2.7 + - - +
518D LEU 2.9 9.1 + - - +
519D ALA* 1.3 76.3 - - - +
521D PRO* 1.3 72.7 - - + +
522D GLU* 2.7 34.3 - - - +
523D ALA* 3.5 5.7 + - - +
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Residues in contact with PRO 521 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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466D TRP* 5.6 1.1 - - - +
519D ALA 4.8 0.2 - - - +
520D ALA* 1.3 88.4 - - + +
522D GLU* 1.3 69.2 + - - +
523D ALA 2.9 2.5 - - - -
524D ALA* 2.7 29.0 + - + +
525D GLY 3.9 1.9 + - - -
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Residues in contact with GLU 522 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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516D LEU* 4.3 17.0 - - + +
517D THR* 3.4 26.0 + - - +
520D ALA* 2.7 36.7 - - - +
521D PRO* 1.3 76.6 - - - +
523D ALA* 1.3 63.0 + - + +
525D GLY* 4.6 2.6 + - - -
526D GLU* 4.7 3.5 + - - +
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Residues in contact with ALA 523 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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466D TRP* 4.2 9.9 - - + -
514D THR* 5.9 0.9 - - + -
516D LEU* 3.9 27.4 - - + -
517D THR 3.5 25.6 - - - +
518D LEU* 4.2 1.6 - - + +
520D ALA 3.5 5.5 + - - +
521D PRO 2.7 4.4 + - - -
522D GLU* 1.3 78.8 - - + +
524D ALA* 1.3 70.2 + - - +
525D GLY 3.3 0.9 - - - -
526D GLU* 3.0 3.5 + - - +
527D VAL* 2.7 28.3 + - + +
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Residues in contact with ALA 524 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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465D ILE* 5.9 1.3 - - + -
466D TRP* 3.4 27.8 - - + +
521D PRO* 2.7 26.5 + - + +
523D ALA* 1.3 75.5 - - - +
525D GLY* 1.3 51.3 + - - +
527D VAL* 2.7 4.0 + - - +
528D GLU* 2.7 41.6 + - - +
535D LEU* 4.1 10.3 - - + -
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Residues in contact with GLY 525 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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521D PRO 3.9 2.6 + - - -
522D GLU 4.6 2.1 + - - -
523D ALA 3.3 0.6 - - - -
524D ALA* 1.3 79.6 - - - +
526D GLU* 1.3 50.8 + - - +
528D GLU* 3.0 14.5 + - - +
529D ARG* 2.6 36.1 + - - +
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Residues in contact with GLU 526 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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514D THR* 4.3 11.7 - - - +
516D LEU* 3.5 33.9 - - + -
522D GLU 4.7 3.1 + - - +
523D ALA 3.0 4.9 + - - +
525D GLY* 1.3 72.6 - - - +
527D VAL* 1.3 69.6 + - + +
529D ARG* 3.1 52.0 + - - +
530D LEU* 3.1 22.6 + - + +
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Residues in contact with VAL 527 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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466D TRP* 3.5 20.4 - - + -
514D THR* 5.1 3.6 - - + -
518D LEU* 4.6 0.7 - - + -
523D ALA* 2.7 26.7 + - + +
524D ALA 3.1 5.6 - - - +
526D GLU* 1.3 77.8 - - + +
528D GLU* 1.3 55.4 + - + +
530D LEU* 3.0 9.2 + - + +
531D ILE* 2.6 49.7 + - + +
535D LEU* 4.3 17.0 - - + -
537D LEU* 4.5 1.3 - - + -
542D ILE* 3.2 45.1 - - + -
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Residues in contact with GLU 528 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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524D ALA* 2.7 23.9 + - - +
525D GLY* 3.5 13.2 + - - +
527D VAL* 1.3 77.5 - - - +
529D ARG* 1.3 62.4 + - - +
531D ILE* 3.4 4.2 - - - +
532D GLY* 3.0 18.7 + - - -
533D HIS 3.5 17.5 + - - +
534D PRO* 3.5 11.7 - - + +
535D LEU* 2.7 51.4 + - + +
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Residues in contact with ARG 529 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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525D GLY 2.6 20.0 + - - +
526D GLU* 3.1 38.9 + - - +
528D GLU* 1.3 74.4 - - - +
530D LEU* 1.3 67.4 + - - +
532D GLY* 3.8 6.8 + - - -
602D SER 4.8 4.6 + - - -
603D GLN* 5.1 0.4 - - - +
604D PRO* 2.9 51.1 - - + +
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Residues in contact with LEU 530 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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512D TYR* 3.7 38.3 - - + -
513D ARG 3.3 26.5 - - - +
514D THR* 4.4 10.1 - - - -
526D GLU* 3.1 27.3 + - - +
527D VAL* 3.0 10.8 + - - +
529D ARG* 1.3 80.7 - - - +
531D ILE* 1.3 69.0 + - + +
532D GLY* 3.2 1.4 + - - -
542D ILE* 5.2 3.8 - - + -
602D SER* 3.4 30.3 - - - +
603D GLN 3.7 0.9 - - - -
604D PRO* 3.5 35.5 - - + +
605D GLY 3.9 2.9 + - - -
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Residues in contact with ILE 531 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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512D TYR* 4.3 22.8 + - + -
527D VAL* 2.6 43.7 + - + +
528D GLU* 3.4 8.1 - - + +
530D LEU* 1.3 74.8 - - + +
532D GLY* 1.3 60.9 + - - +
533D HIS* 2.4 73.5 + - + +
534D PRO 3.6 8.1 - - - +
535D LEU* 4.3 8.5 - - + +
536D PRO 4.5 1.1 - - - +
537D LEU* 4.1 13.0 - - + -
540D ASP* 4.3 12.8 - - + +
541D ALA 6.0 0.2 - - - +
542D ILE* 5.7 1.3 - - + -
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Residues in contact with GLY 532 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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528D GLU 3.0 9.2 + - - -
529D ARG 4.3 4.7 - - - -
530D LEU 3.2 4.2 - - - -
531D ILE* 1.3 80.2 - - - +
533D HIS* 1.3 66.0 + - - +
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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
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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