Contacts of the helix formed by residues 600 - 608 (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 600 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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567D HIS* 4.1 0.7 - - - -
589D ASP* 4.5 4.2 - - - +
590D ASP 3.5 14.0 + - - -
591D PRO* 4.9 2.6 - - - +
598D GLY 3.9 3.8 + - - -
599D ILE* 1.3 78.2 - - - +
601D PRO* 1.3 75.6 - - - +
602D LEU* 3.5 10.8 + - + +
603D HIS* 3.1 43.0 - - + +
604D ASP* 2.9 23.7 + - - +
623D SER* 4.2 23.0 - - - -
626D LEU* 4.8 6.1 - - + -
628D THR* 4.6 1.9 - - - -
634D PRO* 6.0 0.2 - - + -
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Residues in contact with PRO 601 (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* 3.5 20.0 - - + +
567D HIS* 3.5 15.9 - - + +
570D CYS* 3.7 11.4 - - + +
588D VAL 3.2 23.1 - - - +
590D ASP* 3.1 26.7 - - + +
600D THR* 1.3 90.7 - - - +
602D LEU* 1.3 51.0 + - - +
604D ASP* 3.1 9.8 + - + +
605D ALA* 2.7 34.8 + - - +
617D LEU* 3.6 20.4 - - + -
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Residues in contact with LEU 602 (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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600D THR* 3.3 10.0 + - + +
601D PRO* 1.3 74.7 - - - +
603D HIS* 1.3 61.3 + - - +
605D ALA* 3.2 5.0 + - - +
606D LEU* 2.8 44.2 + - + +
614D ALA* 3.7 38.1 - - + +
617D LEU* 4.3 15.2 - - + +
618D LEU* 4.4 20.6 - - + -
622D ALA* 6.5 0.2 - - - -
623D SER* 5.5 10.1 - - - +
624D VAL* 5.0 10.5 - - - +
634D PRO* 4.2 19.7 - - + -
660D MET* 5.3 2.0 - - - -
664D LEU* 4.1 23.1 - - + -
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Residues in contact with HIS 603 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
599D ILE* 3.8 12.1 - - + +
600D THR* 3.1 38.4 - - + +
602D LEU* 1.3 75.7 - - + +
604D ASP* 1.3 57.3 + - - +
606D LEU* 3.2 8.7 + - - +
607D ASN* 2.9 34.0 + - - +
626D LEU* 4.8 2.0 - - + -
628D THR* 3.1 38.1 + - - -
630D LYS* 6.0 2.2 - - + -
632D LEU* 4.3 4.7 - - + -
633D SER* 3.6 14.4 - - - -
634D PRO* 3.3 34.2 - - + +
637D THR* 3.0 32.2 + - - +
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Residues in contact with ASP 604 (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* 4.3 3.1 - - - +
18B HIS* 2.4 33.9 + - - -
563D TRP* 3.8 1.7 - - - -
567D HIS* 3.8 17.7 - - + +
570D CYS* 4.8 2.0 - - + -
571D ASN* 3.0 30.4 + - - -
599D ILE* 3.6 13.4 - - + +
600D THR 2.9 14.0 + - - +
601D PRO* 3.2 13.0 - - + +
603D HIS* 1.3 75.6 - - - +
605D ALA* 1.3 62.1 + - - +
607D ASN* 3.1 10.0 + - - +
608D CYS* 3.1 23.1 + - - -
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Residues in contact with ALA 605 (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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570D CYS* 4.3 13.8 - - + +
601D PRO 2.7 18.7 + - - +
602D LEU* 3.7 4.5 - - - +
604D ASP* 1.3 73.3 - - - +
606D LEU* 1.3 59.6 + - - +
608D CYS* 3.4 2.3 + - - +
609D GLY* 2.9 21.8 + - - -
610D HIS* 3.1 20.9 + - + +
613D VAL* 4.1 15.9 - - + -
614D ALA* 4.3 6.5 - - + +
617D LEU* 3.9 20.9 - - + -
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Residues in contact with LEU 606 (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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602D LEU* 2.8 42.4 + - + +
603D HIS* 3.7 4.3 - - - +
604D ASP 3.2 0.2 - - - -
605D ALA* 1.3 76.1 - - - +
607D ASN* 1.3 62.3 + - - +
608D CYS 3.6 0.2 + - - -
609D GLY* 3.6 5.1 + - - +
611D PHE* 4.7 10.1 - - + -
614D ALA* 3.7 27.6 - - + -
634D PRO* 3.4 27.8 - - + +
637D THR* 4.0 12.3 - - + -
638D LEU* 4.1 12.5 - - + +
641D TRP* 3.4 26.0 - - - +
660D MET* 4.2 17.3 - - + -
664D LEU* 3.8 18.8 - - + -
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Residues in contact with ASN 607 (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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14B GLY 3.5 3.5 - - - +
15B ALA* 3.8 0.7 - - - -
16B LYS* 3.7 47.6 + - + +
599D ILE* 4.1 19.2 - - - +
603D HIS* 2.9 18.9 + - - +
604D ASP* 3.1 13.5 + - - +
606D LEU* 1.3 78.7 - - - +
608D CYS* 1.3 59.2 + - - +
609D GLY 3.4 0.2 - - - -
637D THR* 3.3 20.5 - - - +
641D TRP* 3.0 22.9 + - - +
645D TYR* 5.0 0.5 - - - -
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Residues in contact with CYS 608 (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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13B GLY 5.7 0.2 - - - -
14B GLY 3.4 20.4 + - - +
15B ALA* 3.7 17.8 - - + +
16B LYS 3.7 8.1 - - - -
571D ASN* 3.4 38.8 - - - +
604D ASP* 3.1 17.3 + - - +
605D ALA 3.4 1.8 + - - +
607D ASN* 1.3 78.1 - - - +
609D GLY* 1.3 64.7 + - - +
610D HIS* 3.1 38.7 + - + +
641D TRP* 4.6 0.5 - - - -
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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