Contacts of the strand formed by residues 74 - 80 (chain p) 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 PRO 74 (chain p).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81o TYR* 5.0 6.9 - - - +
66p ILE* 5.5 9.9 - - + -
67p PHE 3.9 2.9 - - - +
68p CYS* 3.7 10.1 - - + -
72p ARG 3.6 2.0 - - - -
73p LEU* 1.3 75.3 - - - +
75p THR* 1.3 62.6 + - - +
76p ALA 5.5 0.2 - - - +
182p THR* 5.2 15.7 - - - +
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Residues in contact with THR 75 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56o LYS* 5.3 7.4 - - - -
59o VAL* 4.6 18.7 - - - +
80o PRO* 3.8 2.3 - - - +
81o TYR* 3.3 25.5 + - - +
82o TYR 5.2 0.2 + - - -
67p PHE* 2.6 17.2 + - - -
68p CYS 3.9 15.9 - - - -
69p ASP* 4.2 8.5 - - - -
73p LEU 3.4 1.6 + - - -
74p PRO* 1.3 74.8 - - - +
76p ALA* 1.3 60.0 + - - +
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Residues in contact with ALA 76 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55o VAL 5.8 1.3 - - - +
59o VAL* 4.8 9.9 - - + -
78o LEU* 4.9 9.6 - - + -
79o THR 3.4 20.2 - - - +
80o PRO* 3.7 12.1 - - + -
65p VAL 4.5 0.2 - - - +
66p ILE* 5.7 0.2 - - - -
67p PHE* 2.9 40.6 + - + +
74p PRO* 5.5 0.4 - - - +
75p THR* 1.3 79.5 - - - +
77p PHE* 1.3 59.9 + - - +
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Residues in contact with PHE 77 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78o LEU* 4.8 1.3 - - - -
79o THR* 2.8 37.7 + - - +
64p LEU* 6.5 0.4 - - + -
65p VAL 3.3 14.1 - - - +
66p ILE* 4.3 9.6 - - + +
76p ALA* 1.3 75.2 - - - +
78p LEU* 1.3 65.5 + - - +
79p THR* 5.5 0.2 - - - -
186p SER* 5.4 12.1 - - - -
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Residues in contact with LEU 78 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76o ALA* 4.7 12.8 - - + -
77o PHE 3.8 7.9 - - - +
78o LEU* 4.7 1.8 - - - +
64p LEU* 5.4 2.9 - - - -
65p VAL* 3.0 35.0 + - + +
77p PHE* 1.3 74.1 - - - +
79p THR* 1.3 59.2 + - - +
80p PRO 4.1 1.5 - - - -
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Residues in contact with THR 79 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76o ALA* 3.9 2.7 - - - -
77o PHE* 2.9 37.3 + - - +
79o THR* 4.3 17.5 - - - -
77p PHE 3.6 0.6 + - - -
78p LEU* 1.3 74.0 - - - +
80p PRO* 1.3 64.2 - - - +
81p TYR* 3.7 0.5 + - - -
193p VAL* 6.0 6.3 - - - -
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Residues in contact with PRO 80 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75o THR 3.4 7.9 - - - +
76o ALA* 3.7 10.2 - - + -
59p VAL* 4.9 19.3 - - + +
78p LEU 4.1 1.8 - - - -
79p THR* 1.3 75.6 - - - +
81p TYR* 1.3 65.9 + - - +
82p TYR* 4.7 13.4 - - - +
83p ALA* 4.9 10.1 + - + +
193p VAL* 5.3 12.3 - - + +
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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