Contacts of the strand formed by residues 71 - 77 (chain x) 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 ASN 71 (chain x).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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88w LEU 3.3 8.5 - - - +
89w TYR* 4.6 9.0 - - + -
11x MET 3.7 0.3 - - - +
12x PHE* 3.4 3.6 - - - +
13x ASP* 2.9 45.3 + - + +
69x LYS 4.7 3.1 - - - +
70x GLY* 1.3 74.5 - - - +
72x ILE* 1.3 59.8 + - - +
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Residues in contact with ILE 72 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87w TYR* 3.8 1.4 - - - +
88w LEU* 2.9 41.4 + - + +
10x LEU* 5.9 3.6 - - + -
11x MET 3.0 11.0 - - - +
12x PHE* 5.0 4.5 - - + -
62x LEU* 6.1 5.4 - - + -
70x GLY 4.4 0.2 - - - -
71x ASN* 1.3 75.4 - - - +
73x THR* 1.3 60.8 + - - +
74x ILE* 4.0 2.3 + - + +
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Residues in contact with THR 73 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44w VAL* 5.6 10.1 - - - -
86w ILE 3.7 7.0 - - - -
87w TYR* 4.6 6.5 - - - +
9x ILE 3.3 1.9 - - - +
10x LEU* 3.1 8.3 - - - -
11x MET* 2.9 45.5 + - - -
72x ILE* 1.3 72.1 - - - +
74x ILE* 1.3 58.9 + - - +
75x LEU* 5.7 0.4 - - - -
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Residues in contact with ILE 74 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84w ARG 4.5 0.9 - - - +
85w MET* 3.7 2.6 - - - +
86w ILE* 2.8 47.7 + - + +
8x MET* 6.3 3.1 - - + -
9x ILE 3.2 5.6 - - - +
10x LEU* 4.7 4.3 - - + +
72x ILE* 4.0 2.1 + - + +
73x THR* 1.3 73.7 - - - +
75x LEU* 1.3 61.8 + - - +
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Residues in contact with LEU 75 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81w GLN 5.4 3.1 - - - +
84w ARG 5.2 0.7 - - - -
85w MET* 4.7 13.7 - - + +
7x ARG 3.4 2.4 - - - +
8x MET* 3.6 3.8 - - - -
9x ILE* 2.9 43.3 + - + +
73x THR 5.7 0.2 - - - +
74x ILE* 1.3 76.9 - - - +
76x THR* 1.3 63.6 + - - +
77x VAL* 5.3 1.1 - - + -
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Residues in contact with THR 76 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81w GLN* 3.3 32.2 + - - +
84w ARG* 4.9 18.5 + - - -
6x MET* 5.5 9.4 - - - -
7x ARG 3.5 4.9 - - - -
8x MET* 5.1 0.9 - - - +
75x LEU* 1.3 72.6 - - - +
77x VAL* 1.3 62.5 + - - +
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Residues in contact with VAL 77 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81w GLN* 5.5 0.7 - - - -
6x MET* 4.6 1.4 - - - -
7x ARG* 2.6 50.7 + - + +
9x ILE* 5.5 7.9 - - + -
75x LEU* 5.1 3.4 - - + +
76x THR* 1.3 75.3 - - - +
78x THR* 1.3 63.5 + - - +
81x GLN* 4.5 12.3 - - + -
82x PHE* 5.0 5.2 - - + +
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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