Contacts of the helix formed by residues 566 - 571 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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564A MET 3.0 1.2 - - - -
565A GLN* 1.3 82.3 - - - +
567A ILE* 1.3 59.0 + - - +
569A GLY* 3.1 19.2 + - - -
570A MET* 3.2 26.3 + - - +
594A LYS* 3.7 12.2 + - - +
598A GLU* 3.9 1.9 - - - +
697A ASP* 3.0 22.1 + - - -
700A ASN* 3.6 20.5 + - - +
999A THR* 4.5 19.3 - - - -
815D ARG* 5.8 0.2 - - - -
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Residues in contact with ILE 567 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
550A TYR* 4.2 10.3 - - + +
564A MET* 3.0 31.3 + - + +
566A SER* 1.3 72.4 - - - +
568A PRO* 1.3 68.1 - - + +
569A GLY 3.1 1.1 - - - -
570A MET* 2.7 20.0 + - - +
571A HIS* 3.3 27.4 + - - +
652A TRP* 4.0 13.7 - - + -
695A ILE* 4.0 16.4 - - + -
999A THR* 4.6 11.4 - - + +
1002A TYR* 3.9 24.9 - - + -
1003A THR* 3.4 22.7 + - + +
1006A LEU* 4.5 9.9 - - + -
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Residues in contact with PRO 568 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
550A TYR* 5.1 5.8 - - + -
564A MET* 3.3 27.8 - - + +
565A GLN 3.7 8.1 - - - +
567A ILE* 1.3 95.5 - - + +
569A GLY* 1.3 61.9 + - - +
571A HIS* 3.7 23.6 + - + +
578A VAL* 4.1 22.2 - - + +
580A CYS* 4.4 8.1 - - - -
595A VAL* 4.3 19.3 - - + +
598A GLU* 3.9 10.2 - - + +
599A ALA* 4.4 17.3 - - + +
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Residues in contact with GLY 569 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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566A SER 3.1 6.1 + - - -
567A ILE 3.1 1.0 - - - -
568A PRO* 1.3 81.8 - - - +
570A MET* 1.3 60.7 + - - +
571A HIS 3.6 5.2 + - - +
598A GLU* 3.2 38.8 + - - +
815D ARG* 3.3 28.2 + - - +
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Residues in contact with MET 570 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
566A SER* 3.2 23.1 + - - +
567A ILE 2.7 13.4 + - - +
569A GLY* 1.3 71.7 - - - -
571A HIS* 1.3 63.2 + - - +
572A ASN 3.7 0.3 + - - -
999A THR* 3.4 33.9 - - - +
1000A LYS* 3.4 55.7 + - + +
1003A THR* 3.5 25.6 - - - +
1004A MET* 5.8 0.3 - - - +
1007A GLU* 4.3 0.9 - - - +
729D ILE* 6.3 2.7 - - + -
730D ASP* 5.5 3.6 - - - +
815D ARG* 5.1 10.1 - - + +
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Residues in contact with HIS 571 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548A VAL* 5.3 2.6 - - + +
550A TYR* 2.7 31.2 + - - -
567A ILE* 3.3 21.4 + - - +
568A PRO* 4.0 10.5 - - + +
569A GLY 3.5 7.1 - - - +
570A MET* 1.3 80.9 - - - +
572A ASN* 1.3 59.7 + - - +
573A PRO* 3.3 12.4 - - - +
576A PHE* 4.5 14.0 - + + +
578A VAL* 3.3 37.0 - - + -
1000A LYS* 5.4 0.7 + - - -
1003A THR* 3.9 9.8 - - + +
1006A LEU* 4.7 5.2 - - + -
1007A GLU* 3.0 35.2 + - + +
1010A TYR* 3.9 15.5 - + - -
793D SER* 4.9 0.3 + - - -
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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