Contacts of the strand formed by residues 74 - 80 (chain Z) in PDB entry 6QXT
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 PRO 74 (chain Z).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81Y TYR* 5.1 7.1 - - + +
66Z ILE* 5.5 10.3 - - + -
67Z PHE 3.9 2.5 - - - +
68Z CYS* 3.7 11.2 - - + +
72Z ARG 3.6 1.8 - - - -
73Z LEU* 1.3 75.5 - - - +
75Z THR* 1.3 63.2 + - - +
76Z ALA 5.5 0.2 - - - +
182Z THR* 5.2 15.3 - - - +
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Residues in contact with THR 75 (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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56Y LYS* 5.3 7.6 - - - -
59Y VAL* 4.6 18.3 - - - +
80Y PRO* 3.8 2.4 - - - +
81Y TYR* 3.3 25.7 + - - +
67Z PHE* 2.6 17.4 + - - -
68Z CYS 3.9 14.8 - - - -
69Z ASP* 4.3 9.2 - - - -
73Z LEU 3.4 1.4 + - - -
74Z PRO* 1.3 74.1 - - - +
76Z ALA* 1.3 61.9 + - - +
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Residues in contact with ALA 76 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55Y VAL 5.9 0.9 - - - +
59Y VAL* 4.8 9.2 - - + -
78Y LEU* 4.9 10.1 - - + -
79Y THR 3.4 20.6 - - - +
80Y PRO* 3.7 12.8 - - + -
81Y TYR 4.8 0.4 - - - +
66Z ILE* 5.7 0.2 - - - -
67Z PHE* 2.9 40.0 + - + +
74Z PRO* 6.5 0.2 - - - -
75Z THR* 1.3 78.2 - - - +
77Z PHE* 1.3 60.7 + - - +
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Residues in contact with PHE 77 (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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78Y LEU* 4.8 2.0 - - - -
79Y THR* 2.8 37.8 + - - +
64Z LEU* 6.5 0.9 - - + -
65Z VAL 3.3 14.1 - - - +
66Z ILE* 4.3 9.9 - - + +
76Z ALA* 1.3 74.6 - - - +
78Z LEU* 1.3 65.6 + - - +
186Z SER* 5.4 11.9 - - - -
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Residues in contact with LEU 78 (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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76Y ALA* 4.7 13.0 - - + -
77Y PHE 3.8 8.5 - - - +
78Y LEU* 4.7 2.2 - - - +
64Z LEU* 5.4 3.3 - - - -
65Z VAL* 3.0 34.9 + - + +
77Z PHE* 1.3 74.7 - - - +
79Z THR* 1.3 59.2 + - - +
80Z PRO 4.1 1.3 - - - -
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Residues in contact with THR 79 (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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76Y ALA* 3.9 2.5 - - - -
77Y PHE* 2.9 39.8 + - - +
79Y THR* 4.3 16.8 - - - -
77Z PHE 3.6 0.6 + - - -
78Z LEU* 1.3 72.5 - - - +
80Z PRO* 1.3 65.1 - - - +
81Z TYR 3.7 0.3 + - - -
193Z VAL* 6.0 6.3 - - - -
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Residues in contact with PRO 80 (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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75Y THR 3.4 9.2 - - - +
76Y ALA* 3.7 9.8 - - + -
59Z VAL* 4.9 18.6 - - + +
62Z ASN* 6.6 0.2 - - - -
78Z LEU 4.1 2.0 - - - -
79Z THR* 1.3 76.1 - - - +
81Z TYR* 1.3 66.0 + - - +
82Z TYR 4.7 13.7 - - - +
83Z ALA* 4.9 9.9 + - + +
193Z VAL* 5.2 12.2 - - + +
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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