Contacts of the strand formed by residues 64 - 68 (chain Z) in PDB entry 6QY3
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 LEU 64 (chain Z).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39Z ASP 3.6 6.0 + - - +
40Z ILE* 3.6 12.3 - - + +
41Z LEU* 2.8 30.8 + - - +
62Z ASN 4.1 2.2 + - - -
63Z ILE* 1.3 70.6 - - - +
65Z VAL* 1.3 59.6 + - - +
66Z ILE* 5.6 0.8 - - + +
78Z LEU 5.4 4.5 - - - +
186Z SER* 5.5 3.1 - - - +
187Z MET* 6.2 1.3 - - - -
190Z ARG* 4.3 23.8 - - + -
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Residues in contact with VAL 65 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41Z LEU* 3.4 12.1 - - + +
58Z LEU* 5.6 7.4 - - + -
63Z ILE 3.4 6.0 + - - +
64Z LEU* 1.3 73.9 - - - +
66Z ILE* 1.3 59.9 + - - +
77Z PHE* 3.3 6.4 - - - +
78Z LEU* 3.0 47.7 + - + +
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Residues in contact with ILE 66 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41Z LEU 2.9 13.5 + - - +
42Z LEU* 4.5 9.6 - - + -
43Z LEU* 3.0 31.2 + - - +
64Z LEU* 4.1 1.1 - - + +
65Z VAL* 1.3 74.3 - - - +
67Z PHE* 1.3 59.5 + - - +
68Z CYS 4.2 0.2 - - - -
74Z PRO* 5.5 10.3 - - + -
76Z ALA 4.2 2.9 - - - -
77Z PHE* 4.3 9.0 - - + +
186Z SER* 5.9 6.3 - - - -
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Residues in contact with PHE 67 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52Y THR* 5.7 8.1 - - - +
55Y VAL* 5.3 13.5 - - + -
43Z LEU* 3.9 8.1 - - + -
65Z VAL 4.3 0.2 - - - -
66Z ILE* 1.3 73.2 - - - +
68Z CYS* 1.3 55.4 + - - +
74Z PRO* 3.9 2.7 - - - +
75Z THR* 2.6 29.8 + - - -
76Z ALA* 2.9 33.1 + - + +
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Residues in contact with CYS 68 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52Y THR* 5.2 5.2 - - - +
56Y LYS* 4.6 7.6 - - - +
43Z LEU* 3.0 22.1 + - - +
44Z GLU* 3.9 11.7 - - - -
45Z THR 4.9 7.7 + - - +
46Z THR* 5.4 1.9 + - - -
66Z ILE 4.2 0.2 - - - -
67Z PHE* 1.3 76.8 - - - +
69Z ASP* 1.3 63.1 + - - +
72Z ARG 3.4 20.0 - - - +
73Z LEU 3.2 17.5 - - - +
74Z PRO* 3.7 3.6 - - + -
75Z THR* 3.5 9.1 - - - +
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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