Contacts of the helix formed by residues 578 - 587 (chain D) in PDB entry 7ATU
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 SER 578 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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576D PRO 3.5 0.4 + - - -
577D PRO* 1.3 75.8 + - - +
579D PHE* 1.3 64.3 + - - +
580D PHE 3.3 2.0 - - - -
581D PRO* 3.5 17.6 - - - +
582D ILE* 3.2 33.3 + - - +
607D LEU* 3.0 17.8 - - - +
621D LEU* 3.8 37.0 - - - +
624D LEU* 5.4 1.8 - - - -
625D ASP* 3.1 20.7 + - - -
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Residues in contact with PHE 579 (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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434D TRP* 3.5 35.2 - + - -
438D VAL* 4.0 30.1 - - + -
441D ALA* 4.2 16.8 - - + -
539D LEU* 4.6 13.9 - - + +
542D ILE* 4.1 19.3 - - + -
543D ILE* 3.6 27.4 - - + -
575D CYS* 4.5 1.8 - - - -
576D PRO* 3.4 19.0 + - + +
577D PRO 2.9 5.9 + - - -
578D SER* 1.3 78.2 - - - +
580D PHE* 1.3 62.4 + - - +
582D ILE* 3.7 7.0 + - + +
583D THR* 3.2 19.4 + - - -
604D LEU* 4.9 4.9 - - + -
607D LEU* 3.6 26.2 - - + -
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Residues in contact with PHE 580 (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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540D CYS* 4.7 11.4 - - - -
543D ILE* 3.7 24.7 - - + +
561D LEU* 4.7 3.6 - - + -
563D VAL* 4.1 5.4 - - + -
566D PHE* 3.3 48.0 - + + -
567D LEU* 4.0 12.1 - - + -
571D CYS* 4.3 20.4 - - - -
575D CYS* 4.5 6.6 - - - -
576D PRO 4.7 0.6 + - - -
579D PHE* 1.3 79.9 - - - +
581D PRO* 1.3 69.6 - - + +
583D THR* 3.1 14.7 + - - -
584D VAL* 3.1 37.4 + - + +
628D PHE* 3.5 31.9 - + - -
629D TRP* 5.8 2.9 - + + -
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Residues in contact with PRO 581 (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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578D SER* 3.5 26.9 - - - +
579D PHE 3.9 0.2 - - - +
580D PHE* 1.3 95.9 - - + +
582D ILE* 1.3 61.9 + - + +
584D VAL* 3.3 8.1 + - + +
585D ARG* 3.2 20.1 + - - +
624D LEU* 4.3 12.8 - - + +
625D ASP* 4.0 14.1 - - - +
628D PHE* 3.5 46.3 - - + -
629D TRP* 5.6 1.6 - - + +
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Residues in contact with ILE 582 (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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539D LEU* 4.6 6.5 - - + -
578D SER* 3.2 30.4 + - - +
579D PHE* 3.8 9.6 - - + +
580D PHE 3.1 0.6 - - - -
581D PRO* 1.3 74.4 - - + +
583D THR* 1.3 58.8 + - - +
585D ARG* 2.7 29.0 + - - +
586D CYS* 2.9 14.7 + - - -
595D PRO* 5.2 0.2 - - + -
600D LEU* 3.7 29.2 - - + -
603D TRP* 3.9 32.5 - - + -
604D LEU* 3.9 25.4 - - + -
607D LEU* 5.2 5.4 - - + -
621D LEU* 6.2 1.3 - - + -
624D LEU* 5.9 5.6 - - + -
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Residues in contact with THR 583 (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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536D GLY 3.3 26.0 - - - +
539D LEU* 3.3 24.6 - - + +
540D CYS* 3.5 25.6 - - - +
543D ILE* 3.1 25.2 - - + +
561D LEU* 5.3 0.7 - - + -
579D PHE 3.2 5.9 + - - -
580D PHE* 3.1 14.3 + - + -
582D ILE* 1.3 76.2 - - - +
584D VAL* 1.3 63.9 + - - +
586D CYS* 3.1 9.6 + - - +
587D CYS* 3.0 22.1 + - - +
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Residues in contact with VAL 584 (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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561D LEU* 4.4 9.2 - - + -
563D VAL* 4.0 23.1 - - + -
580D PHE* 3.1 46.7 + - + +
581D PRO* 3.5 9.6 - - + +
582D ILE 3.2 0.2 - - - -
583D THR* 1.3 75.7 - - - +
585D ARG* 1.3 59.5 + - - +
587D CYS* 3.5 7.9 + - - +
588D ASP* 3.4 19.2 + - - +
628D PHE* 4.0 20.0 - - + -
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Residues in contact with ARG 585 (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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581D PRO 3.2 11.2 + - - +
582D ILE* 2.7 18.8 + - - +
584D VAL* 1.3 69.1 - - - +
586D CYS* 1.3 62.5 + - - +
587D CYS 3.2 1.3 + - - -
588D ASP* 3.6 7.1 + - - +
593D LYS 3.6 7.8 - - - +
594D ARG* 3.4 12.6 - - - +
595D PRO* 3.4 24.6 - - + +
603D TRP* 5.4 5.4 - - + -
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Residues in contact with CYS 586 (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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532D VAL* 3.6 18.2 - - + +
533D PHE* 3.5 10.8 + - - -
535D PHE* 3.9 13.2 - - - -
536D GLY* 3.5 17.5 - - - -
582D ILE* 2.9 16.8 + - - -
583D THR* 3.4 9.9 - - - +
585D ARG* 1.3 77.3 - - - +
587D CYS* 1.3 56.5 + - - +
588D ASP 3.3 0.7 - - - -
594D ARG* 3.1 24.8 + - - +
595D PRO* 4.0 2.9 - - - -
600D LEU* 3.6 42.2 - - - -
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Residues in contact with CYS 587 (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 PHE* 3.5 24.6 - - + -
536D GLY* 3.5 34.3 - - - -
537D ILE* 3.7 23.1 - - - -
540D CYS* 4.9 0.9 - - - -
560D GLY* 4.9 0.3 - - - -
561D LEU* 4.2 31.1 + - + +
583D THR* 3.0 18.1 + - - +
584D VAL 3.5 6.5 + - - +
585D ARG 3.2 0.4 - - - -
586D CYS* 1.3 74.7 - - - +
588D ASP* 1.3 68.0 + - - +
589D LEU* 3.3 3.1 + - - +
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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