Contacts of the helix formed by residues 564 - 573 (chain D) in PDB entry 5JA4
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 564 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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534D HIS* 3.6 4.7 - - - -
555D LEU* 5.8 0.2 - - - -
556D ASN* 4.0 13.7 - - - -
557D PRO 3.5 7.6 - - - +
558D ARG* 4.2 8.3 - - + -
562D GLY 4.3 1.3 - - - +
563D TRP* 1.3 81.2 - - - +
565D PRO* 1.3 71.8 - - - +
566D LEU* 3.0 8.1 + - - +
567D HIS* 2.4 61.1 + - + +
568D GLU* 3.2 7.6 + - - +
590D ASP* 3.1 37.3 + - - +
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Residues in contact with PRO 565 (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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533D LEU* 3.9 23.3 - - + -
534D HIS* 3.4 33.7 - - + +
537D CYS* 3.1 37.5 - - - -
555D LEU* 3.7 19.3 - - + -
557D PRO* 3.5 23.1 - - + -
564D THR* 1.3 87.1 - - - +
566D LEU* 1.3 56.0 + - - +
567D HIS 3.4 0.2 - - - -
568D GLU* 3.7 2.2 + - + -
569D ALA* 3.2 15.1 + - - +
581D LEU* 4.6 3.4 - - + +
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Residues in contact with LEU 566 (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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555D LEU* 5.4 2.4 - - + +
556D ASN* 6.1 0.2 - - - +
564D THR* 3.0 8.8 + - - +
565D PRO* 1.3 77.3 - - - +
567D HIS* 1.3 61.2 + - - +
569D ALA* 4.3 9.6 - - + -
570D CYS* 2.9 42.8 + - - -
578D VAL* 4.7 3.6 - - + -
581D LEU* 4.8 10.8 - - + -
582D LEU* 3.4 33.2 - - + -
587D ALA* 3.8 15.5 - - + +
588D VAL* 3.5 37.5 - - - +
601D PRO* 3.5 23.1 - - + -
617D LEU* 4.3 1.8 - - + -
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Residues in contact with HIS 567 (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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18B HIS* 3.5 16.3 - - + +
562D GLY 5.2 0.2 - - - -
563D TRP* 3.4 25.4 - + + -
564D THR* 2.4 48.8 + - + +
566D LEU* 1.3 79.3 - - - +
568D GLU* 1.3 52.5 + - - +
570D CYS* 3.6 4.5 - - - +
571D ASN* 2.6 37.8 + - - +
590D ASP* 3.3 30.2 + - + -
591D PRO 3.8 9.6 + - - -
592D GLY* 5.3 0.4 - - - -
599D ILE 2.8 29.4 + - - -
600D THR 4.3 0.2 - - - -
601D PRO* 3.5 16.5 - - + +
604D ASP* 3.8 9.2 - - - +
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Residues in contact with GLU 568 (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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18B HIS* 2.9 27.5 + - - +
20B LYS* 2.9 31.4 + - - -
534D HIS* 3.8 15.9 - - + +
537D CYS* 3.9 8.9 - - - +
538D ILE* 3.3 37.3 - - + +
563D TRP* 3.8 9.4 - - - +
564D THR 3.7 10.5 - - - +
565D PRO* 3.8 7.0 - - + +
566D LEU 3.3 0.2 - - - -
567D HIS* 1.3 76.7 - - - +
569D ALA* 1.3 58.6 + - - +
571D ASN* 3.6 0.4 - - - +
572D TYR* 2.9 47.6 + - - +
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Residues in contact with ALA 569 (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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537D CYS* 3.8 13.0 + - + -
565D PRO 3.2 10.7 + - - +
566D LEU* 3.7 6.1 - - + +
567D HIS 3.2 0.4 - - - -
568D GLU* 1.3 79.7 - - - +
570D CYS* 1.3 62.2 + - - +
572D TYR* 3.8 0.6 - - - -
573D GLY* 2.9 27.5 + - - -
574D HIS* 4.1 3.6 - - - +
577D ILE* 4.8 1.8 - - + -
578D VAL* 3.4 17.7 - - + +
581D LEU* 3.4 33.7 - - + -
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Residues in contact with CYS 570 (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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566D LEU* 2.9 42.8 + - - +
567D HIS* 3.7 3.6 - - - +
569D ALA* 1.3 75.3 - - - +
571D ASN* 1.3 63.8 + - - +
573D GLY* 3.2 3.6 + - - -
578D VAL* 4.3 2.2 - - - -
582D LEU* 5.1 0.9 - - - -
601D PRO* 3.7 29.4 - - + +
604D ASP* 4.8 0.7 - - + -
605D ALA* 4.3 9.9 - - + +
610D HIS* 3.0 18.7 + - - -
613D VAL* 4.0 15.8 - - - +
617D LEU* 3.4 31.2 - - + -
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Residues in contact with ASN 571 (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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16B LYS 3.0 24.2 + - - -
17B ARG* 2.6 60.2 + - - +
18B HIS* 3.6 27.8 + - + -
567D HIS 2.6 21.6 + - - +
568D GLU* 3.6 3.4 - - - +
570D CYS* 1.3 72.4 - - - +
572D TYR* 1.3 63.1 + - + +
604D ASP* 3.0 25.2 + - - +
608D CYS* 3.4 13.2 - - - -
610D HIS* 2.9 12.6 - - - -
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Residues in contact with TYR 572 (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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17B ARG* 3.6 45.1 + - + +
18B HIS* 5.3 1.9 + - - -
538D ILE* 3.9 35.1 - - + +
568D GLU* 2.9 47.7 + - - +
571D ASN* 1.3 82.5 - - - +
573D GLY* 1.3 68.7 + - - +
574D HIS* 3.5 28.4 + - + +
610D HIS* 3.3 10.2 + - - -
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Residues in contact with GLY 573 (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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569D ALA 2.9 18.8 + - - -
570D CYS 3.2 2.0 + - - -
572D TYR* 1.3 82.3 - - - +
574D HIS* 1.3 61.5 + - - -
575D LEU 3.4 3.1 - - - -
610D HIS* 3.2 28.3 + - - +
613D VAL* 4.1 11.2 - - - +
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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