Contacts of the strand formed by residues 64 - 68 (chain J) 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 J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39J ASP 3.6 6.2 + - - +
40J ILE* 3.6 12.1 - - + +
41J LEU* 2.8 31.1 + - - +
62J ASN 4.1 1.8 + - - -
63J ILE* 1.3 71.0 - - - +
65J VAL* 1.3 59.7 + - - +
66J ILE* 4.1 0.4 - - - -
78J LEU 5.4 4.7 - - - +
186J SER* 5.5 2.9 - - - +
187J MET* 6.2 1.3 - - - -
190J ARG* 4.3 24.2 - - + -
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Residues in contact with VAL 65 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41J LEU* 3.4 11.2 - - + +
58J LEU* 5.6 7.2 - - + -
63J ILE 3.4 6.7 + - - +
64J LEU* 1.3 72.8 - - - +
66J ILE* 1.3 60.1 + - - +
77J PHE* 3.3 6.8 - - - +
78J LEU* 3.0 47.1 + - + +
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Residues in contact with ILE 66 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41J LEU 2.9 12.9 + - - +
42J LEU* 3.8 10.3 - - + -
43J LEU* 3.0 30.6 + - - +
64J LEU* 4.1 1.1 - - + +
65J VAL* 1.3 74.1 - - - +
67J PHE* 1.3 60.1 + - - +
68J CYS 4.2 0.2 - - - -
74J PRO* 5.5 9.6 - - + -
76J ALA 4.2 2.9 - - - -
77J PHE* 4.3 8.1 - - + +
186J SER* 5.9 6.1 - - - -
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Residues in contact with PHE 67 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52I THR* 5.7 7.6 - - - +
55I VAL* 5.3 13.5 - - + -
43J LEU* 3.9 7.6 - - + -
66J ILE* 1.3 74.0 - - - +
68J CYS* 1.3 56.2 + - - +
74J PRO* 3.9 2.3 - - - +
75J THR* 2.6 30.3 + - - -
76J ALA* 2.9 32.3 + - + +
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Residues in contact with CYS 68 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52I THR* 5.2 4.7 - - - +
56I LYS* 4.6 8.5 - - - +
43J LEU 3.0 22.5 + - - +
44J GLU* 3.8 11.9 - - - -
45J THR 4.9 7.3 + - - +
46J THR* 5.5 2.3 - - - -
66J ILE 4.2 0.2 - - - -
67J PHE* 1.3 76.7 - - - +
69J ASP* 1.3 63.2 + - - +
72J ARG 3.4 20.0 - - - +
73J LEU 3.2 16.6 - - - +
74J PRO* 3.7 3.8 - - + -
75J THR* 3.5 9.3 - - - +
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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