Contacts of the helix formed by residues 566 - 571 (chain D) in PDB entry 4AY6
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 566 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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815A ARG* 5.7 0.2 - - - -
564D MET 2.8 3.6 + - - -
565D GLN* 1.3 79.3 - - - +
567D ILE* 1.3 64.6 + - - +
569D GLY* 3.2 13.5 + - - -
570D MET* 3.2 34.6 + - - +
594D LYS* 3.6 19.5 + - - +
598D GLU* 4.0 1.6 - - - +
697D ASP* 3.0 21.6 + - - -
700D ASN* 3.8 13.9 + - - +
999D THR* 4.4 10.3 - - - -
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Residues in contact with ILE 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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550D TYR* 4.2 9.6 - - + +
564D MET* 2.8 37.0 + - + +
566D SER* 1.3 73.5 - - - +
568D PRO* 1.3 62.6 - - + +
570D MET* 2.7 25.2 + - - +
571D HIS* 3.4 27.0 + - - +
652D TRP* 3.9 14.8 - - + -
695D ILE* 3.9 24.5 - - + -
999D THR* 4.8 10.5 - - + +
1002D TYR* 4.0 15.7 - - + -
1003D THR* 3.6 23.2 + - + +
1006D LEU* 4.5 10.5 - - + -
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Residues in contact with PRO 568 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
550D TYR* 5.1 5.2 - - + -
564D MET* 3.4 24.2 - - + +
565D GLN 3.8 6.5 - - - +
566D SER 3.7 1.8 - - - -
567D ILE* 1.3 93.5 - - + +
569D GLY* 1.3 62.5 + - - +
570D MET 3.3 0.3 + - - -
571D HIS* 3.5 25.9 + - + +
578D VAL* 4.1 22.4 - - + +
580D CYS* 4.4 8.3 - - - -
595D VAL* 4.1 21.8 - - + +
598D GLU* 4.1 8.5 - - + +
599D ALA* 4.3 18.2 - - + +
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Residues in contact with GLY 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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815A ARG* 3.4 33.1 + - - +
566D SER 3.2 5.2 + - - -
567D ILE 3.1 1.4 - - - -
568D PRO* 1.3 79.9 - - - +
570D MET* 1.3 59.5 + - - +
571D HIS 3.4 6.1 + - - +
598D GLU* 3.3 35.1 + - - +
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Residues in contact with MET 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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729A ILE* 6.2 3.6 - - + -
730A ASP* 5.3 6.1 - - - +
815A ARG* 5.1 10.8 - - + +
566D SER* 3.2 25.3 + - - +
567D ILE 2.7 16.9 + - - +
569D GLY* 1.3 72.0 - - - +
571D HIS* 1.3 63.5 + - - +
572D ASN 3.7 0.9 + - - -
999D THR* 3.3 34.5 - - - +
1000D LYS* 3.5 56.2 + - + +
1003D THR* 3.6 21.0 - - - +
1004D MET* 5.7 0.5 - - - +
1007D GLU* 4.3 1.2 - - - +
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Residues in contact with HIS 571 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
793A SER* 4.7 0.5 + - - -
548D VAL* 5.3 2.7 - - + +
550D TYR* 2.8 32.1 + + - -
567D ILE* 3.4 23.6 + - - +
568D PRO* 3.8 10.1 - - + +
569D GLY 3.3 7.5 - - - +
570D MET* 1.3 80.1 - - - +
572D ASN* 1.3 60.5 + - - +
573D PRO* 3.2 12.7 - - - +
576D PHE* 4.5 13.0 - + + +
578D VAL* 3.4 36.3 - - + -
1000D LYS* 5.6 0.2 + - - -
1003D THR* 3.9 9.8 - - + +
1006D LEU* 4.6 4.7 - - + -
1007D GLU* 2.9 35.9 + - + +
1010D TYR* 3.9 14.8 - + - -
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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