Contacts of the helix formed by residues 571 - 580 (chain D) in PDB entry 6G52
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 571 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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567D PRO 3.5 8.5 + - - -
568D SER 5.2 0.6 + - - -
569D LEU 4.3 0.4 - - - -
570D ILE* 1.3 78.4 - - - +
572D GLU* 1.3 64.1 + - - +
573D LYS* 3.8 6.4 + - - +
574D ILE* 3.1 27.8 + - - +
575D LEU* 2.9 18.5 + - - +
723D SER* 3.4 17.6 + - - -
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Residues in contact with GLU 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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555D HIS* 3.5 25.8 + - + +
567D PRO* 4.6 13.0 + - + +
570D ILE 3.7 1.7 + - - -
571D SER* 1.3 73.4 - - - +
573D LYS* 1.3 64.7 + - - +
575D LEU* 3.0 11.3 + - - +
576D LEU* 2.9 34.8 + - + +
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Residues in contact with LYS 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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571D SER* 3.3 6.4 + - - +
572D GLU* 1.3 79.4 - - - +
574D ILE* 1.3 60.8 - - + +
576D LEU* 3.2 12.9 + - - +
577D ARG* 2.9 26.7 + - - +
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Residues in contact with ILE 574 (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 ILE* 4.0 8.2 - - + +
571D SER* 3.1 20.9 + - - +
573D LYS* 1.3 75.6 - - + +
575D LEU* 1.3 62.8 + - - +
577D ARG* 3.8 9.0 - - + +
578D LEU* 2.9 31.1 + - + +
719D GLY* 3.6 29.4 - - - +
722D ALA* 3.4 21.3 - - + +
723D SER* 3.4 31.6 - - - +
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Residues in contact with LEU 575 (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 HIS* 3.3 31.9 - - + +
558D LEU* 4.6 11.4 - - + -
559D ALA* 4.9 3.6 - - + +
565D PHE* 4.1 35.9 - - + +
567D PRO* 5.5 0.4 - - + -
570D ILE* 3.5 45.5 - - + +
571D SER 2.9 7.7 + - - +
572D GLU* 3.2 11.0 - - - +
574D ILE* 1.3 76.2 - - - +
576D LEU* 1.3 57.8 + - - +
578D LEU* 4.5 2.9 - - + -
579D LEU* 2.9 56.2 + - + +
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Residues in contact with LEU 576 (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 HIS* 3.4 35.4 - - + +
572D GLU* 2.9 33.1 + - + +
573D LYS* 3.4 13.2 - - - +
575D LEU* 1.3 76.8 - - - +
577D ARG* 1.3 56.9 + - - +
579D LEU* 3.9 4.5 - - - +
580D LYS* 2.9 29.7 + - - +
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Residues in contact with ARG 577 (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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573D LYS 2.9 16.0 + - - +
574D ILE* 4.1 10.1 - - + +
576D LEU* 1.3 76.7 - - - +
578D LEU* 1.3 58.8 + - - +
580D LYS* 3.2 8.0 + - - +
581D TYR* 2.8 29.6 + - - +
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Residues in contact with LEU 578 (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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565D PHE* 5.0 5.2 - - + -
570D ILE* 6.2 3.8 - - + -
574D ILE* 2.9 24.6 + - + +
575D LEU* 3.9 5.4 - - + +
577D ARG* 1.3 75.2 - - - +
579D LEU* 1.3 70.8 + - + +
581D TYR* 3.1 29.9 - - + +
584D VAL* 3.9 6.1 - - - +
711D ILE* 3.8 43.3 - - + -
715D GLN* 3.7 42.0 - - + +
716D TYR* 5.4 2.2 - - + -
719D GLY* 5.3 6.5 - - - -
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Residues in contact with LEU 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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551D LEU* 5.6 2.9 - - + +
554D ALA* 6.0 3.8 - - + -
555D HIS* 5.1 15.0 - - + +
558D LEU* 4.4 11.0 - - + -
565D PHE* 5.6 0.2 - - + -
575D LEU* 2.9 51.0 + - + +
576D LEU* 4.0 4.5 - - - +
578D LEU* 1.3 86.9 - - + +
580D LYS* 1.3 60.3 + - - +
581D TYR 3.1 7.0 + - - +
584D VAL* 4.0 10.2 - - + +
585D ILE* 4.4 20.4 - - + +
709D ILE* 3.6 39.9 - - + -
711D ILE* 4.7 5.8 - - + -
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Residues in contact with LYS 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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576D LEU 2.9 20.7 + - - +
577D ARG* 3.2 8.9 + - - +
579D LEU* 1.3 73.6 - - - +
581D TYR* 1.3 65.2 + - - +
582D PRO* 3.6 3.6 - - - +
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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