Contacts of the strand formed by residues 666 - 669 (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 TYR 666 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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648D ILE* 3.8 27.4 - - + -
649D GLN 3.3 3.8 + - - +
650D ALA* 3.3 7.8 - - + -
651D MET* 2.8 35.4 + - - +
664D MET* 4.5 0.2 - - - +
665D ASP* 1.3 85.6 - - + +
667D ILE* 1.3 55.2 + - - +
684D GLU* 3.7 5.0 - - - +
685D LYS* 3.3 24.2 - - + +
686D LEU 4.2 0.9 - - - -
687D ALA* 4.1 10.3 - - + -
1013D MET* 3.6 37.8 + - + -
1016D HIS* 4.1 3.5 - - - -
1023D PRO* 3.4 33.7 - - + +
1024D ASP 3.2 19.5 - - - -
1026D MET* 3.1 36.7 - - + +
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Residues in contact with ILE 667 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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651D MET* 3.8 15.0 - - + +
655D TYR 5.2 3.8 - - - +
657D GLY 3.7 23.6 - - - +
658D THR* 4.6 2.9 - - - -
666D TYR* 1.3 75.8 - - - +
668D ILE* 1.3 72.0 + - - +
669D THR* 3.7 9.8 + - + +
682D TYR* 4.1 20.9 - - + -
684D GLU* 3.7 22.6 - - + +
685D LYS 3.1 11.6 + - - +
686D LEU* 3.8 22.7 - - + -
687D ALA* 2.9 25.1 + - - +
941D LEU* 4.2 16.6 - - + -
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Residues in contact with ILE 668 (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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627D VAL* 5.1 0.9 - - + -
650D ALA* 4.2 15.5 - - + -
651D MET 3.0 23.0 + - - +
652D TRP* 3.8 34.2 - - + +
653D LEU 4.9 1.9 + - - -
667D ILE* 1.3 75.4 - - - +
669D THR* 1.3 65.3 + - - +
687D ALA 3.5 2.5 - - - -
689D MET* 4.0 24.0 - - + -
693D PHE* 3.4 22.0 - - + -
1006D LEU* 4.2 18.2 - - + -
1009D LEU* 4.1 17.5 - - + -
1010D TYR* 4.4 14.6 - - + +
1013D MET* 4.2 13.9 - - + -
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Residues in contact with THR 669 (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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667D ILE* 3.8 27.8 - - + +
668D ILE* 1.3 77.4 - - - +
670D ASP* 1.3 72.0 + - - +
673D THR* 3.5 11.5 - - - -
674D SER* 2.9 33.9 + - - +
682D TYR* 5.8 0.2 - - + -
686D LEU* 4.5 7.2 - - + -
687D ALA 2.9 9.3 + - - +
688D TYR* 4.6 6.3 - - + -
689D MET* 2.6 36.6 + - - +
693D PHE* 3.5 19.3 - - - -
941D LEU* 5.4 4.5 - - - -
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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