Contacts of the strand formed by residues 71 - 77 (chain n) 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 n).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41k GLN* 5.1 15.9 - - + -
88k LEU 4.0 2.5 - - - -
89k TYR* 4.1 11.2 - - + +
11n MET 3.8 0.5 - - - +
12n PHE* 3.5 3.5 - - - +
13n ASP* 2.9 43.0 + - + +
69n LYS 4.6 3.4 - - - +
70n GLY* 1.3 74.5 - - - +
72n ILE* 1.3 60.9 + - - +
73n THR 4.5 0.2 + - - -
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Residues in contact with ILE 72 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41k GLN* 6.3 1.3 - - - -
86k ILE 4.9 0.4 - - - -
87k TYR* 3.0 8.9 - - - +
88k LEU* 2.9 46.1 + - + +
10n LEU* 6.2 1.8 - - + -
11n MET 3.2 8.3 - - - +
12n PHE* 5.2 3.4 - - + -
62n LEU* 6.1 6.3 - - + +
66n ASN* 5.9 4.3 - - + -
71n ASN* 1.3 75.0 - - - +
73n THR* 1.3 61.8 + - - +
74n ILE* 6.3 0.4 - - + -
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Residues in contact with THR 73 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40k HIS* 6.0 3.1 - - - -
41k GLN* 5.3 7.6 - - - -
44k VAL* 4.2 16.6 - - - -
87k TYR* 4.2 9.4 - - - -
9n ILE 3.5 1.0 - - - +
10n LEU* 3.2 7.4 - - - +
11n MET* 2.9 46.3 + - - +
72n ILE* 1.3 74.1 - - - +
74n ILE* 1.3 60.3 + - - +
75n LEU 4.2 0.2 - - - -
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Residues in contact with ILE 74 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84k ARG 5.5 0.2 - - - -
85k MET* 3.0 10.4 - - - +
86k ILE* 2.6 55.1 + - + +
87k TYR* 4.8 0.2 - - - +
8n MET* 6.5 1.6 - - + -
9n ILE 3.4 4.5 - - - +
10n LEU* 4.8 3.1 - - + +
72n ILE* 5.7 1.1 - - + -
73n THR* 1.3 73.8 - - - +
75n LEU* 1.3 61.2 + - - +
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Residues in contact with LEU 75 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9k ILE* 5.4 11.9 - - + -
81k GLN 5.2 1.8 - - - +
82k PHE* 6.4 0.9 - - - -
85k MET* 4.4 11.4 - - + +
7n ARG 3.6 1.6 - - - +
8n MET* 3.7 3.5 - - - +
9n ILE* 2.9 45.9 + - + +
73n THR 5.8 0.2 - - - -
74n ILE* 1.3 76.2 - - - +
76n THR* 1.3 64.6 + - - +
77n VAL* 6.2 0.4 - - + -
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Residues in contact with THR 76 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77k VAL* 4.3 7.3 - - - +
81k GLN* 3.1 44.9 + - - +
84k ARG* 5.0 11.4 + - - -
85k MET* 5.1 1.4 - - - +
6n MET* 5.7 9.2 - - - -
7n ARG 3.6 5.6 - - - -
8n MET* 5.1 0.7 - - - +
75n LEU* 1.3 73.1 - - - +
77n VAL* 1.3 60.7 + - - +
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Residues in contact with VAL 77 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75k LEU* 5.0 13.0 - - + -
76k THR 4.3 16.6 - - - +
77k VAL* 5.2 4.3 - - + +
81k GLN* 5.2 1.8 - - - -
6n MET* 4.5 1.0 - - - -
7n ARG* 2.8 43.9 + - + +
9n ILE* 5.6 6.3 - - + -
75n LEU* 5.2 1.8 - - + +
76n THR* 1.3 74.8 - - - +
78n THR* 1.3 65.5 + - - +
81n GLN* 4.5 4.0 - - + -
82n PHE* 4.6 6.5 - - - +
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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