Contacts of the strand formed by residues 71 - 78 (chain N) in PDB entry 5XVO
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 71 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40M HIS* 3.7 28.9 - - + +
41M GLN* 3.8 18.3 + - + +
87M TYR* 3.8 31.0 - - + -
89M HIS 3.3 11.0 - - - +
90M GLY* 4.3 8.5 - - - -
91M GLU 4.3 5.8 - - - +
12N PHE* 3.3 4.2 - - - -
13N ASP* 2.7 46.2 + - + +
70N GLY* 1.3 72.1 - - - -
72N ILE* 1.3 64.6 + - - +
73N THR* 4.0 5.2 - - + -
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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
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87M TYR 3.7 0.3 - - - -
88M LEU* 3.0 51.5 + - + +
89M HIS* 2.9 20.0 + - + +
10N LEU* 4.3 12.1 - - + -
11N MET 3.5 9.4 - - - +
12N PHE* 3.9 9.0 - - + -
14N MET* 4.1 7.4 - - + -
28N PHE* 4.1 21.1 - - + -
67N PRO* 3.5 37.5 - - + -
69N ARG 3.6 17.9 - - - +
70N GLY 4.6 0.2 - - - -
71N LEU* 1.3 80.0 - - - +
73N THR* 1.3 65.1 + - - +
74N LEU* 5.3 0.2 - - + -
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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
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40M HIS* 3.0 38.7 + - + +
41M GLN* 3.0 11.2 + - - +
85M MET* 3.9 13.7 - - + -
86M ILE 3.4 4.5 - - - +
87M TYR* 3.8 27.6 - - + -
9N LEU 3.7 0.5 - - - +
10N LEU* 3.4 4.3 - - - +
11N MET* 3.0 39.4 + - - +
71N LEU* 4.0 7.6 - - + -
72N ILE* 1.3 78.3 - - - +
74N LEU* 1.3 65.4 + - - +
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Residues in contact with LEU 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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84M ARG 4.8 0.2 - - - +
85M MET* 3.4 9.3 - - - +
86M ILE* 3.0 61.3 + - + +
88M LEU* 4.4 17.9 - - + -
8N LEU* 4.0 15.3 - - + -
9N LEU 3.2 3.4 - - - +
10N LEU* 3.4 43.5 - - + -
11N MET* 5.3 0.2 - - - -
59N LEU* 4.6 12.1 - - + -
62N LEU* 3.9 24.9 - - + -
72N ILE* 5.3 1.6 - - + -
73N THR* 1.3 76.4 - - - +
75N LEU* 1.3 63.0 + - - +
76N ASN* 5.9 0.7 - - - +
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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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9M LEU* 4.3 23.8 - - + -
75M LEU* 6.1 0.2 - - + -
77M VAL* 4.4 26.2 - - + -
81M GLN 4.3 11.7 - - - +
82M PHE* 4.4 16.2 - - + -
85M MET* 3.4 45.8 - - + +
7N ARG 3.6 0.9 - - - +
8N LEU* 3.6 5.3 - - - -
9N LEU* 2.8 52.0 + - + +
11N MET* 4.3 11.2 - - + -
74N LEU* 1.3 74.3 - - - +
76N ASN* 1.3 64.5 + - - +
77N VAL* 3.8 4.7 + - + +
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Residues in contact with ASN 76 (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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81M GLN* 3.7 27.2 + - + +
86M ILE* 5.5 4.6 - - - +
6N MET* 4.1 18.5 - - + +
7N ARG 3.5 9.7 - - - +
8N LEU* 3.6 18.1 - - - +
49N LEU* 4.6 0.5 - - - +
55N ASN* 3.2 40.4 + - - +
59N LEU* 4.6 7.9 - - - +
74N LEU 5.9 0.4 - - - -
75N LEU* 1.3 73.6 - - - +
77N VAL* 1.3 65.4 + - - +
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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
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75M LEU* 4.8 10.8 - - + -
77M VAL* 4.6 17.9 - - + -
81M GLN* 4.5 7.2 - - - +
6N MET* 3.4 6.4 - - - +
7N ARG* 2.6 73.9 + - + +
9N LEU* 5.4 5.6 - - + -
75N LEU* 4.7 11.4 - - + +
76N ASN* 1.3 80.7 - - - +
78N THR* 1.3 63.2 + - - +
81N GLN* 3.5 18.8 - - + +
82N PHE* 4.2 13.2 - - + +
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Residues in contact with THR 78 (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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81M GLN* 5.0 1.3 - - - +
5N TYR 4.0 7.9 - - - +
6N MET* 4.4 6.1 - - + +
77N VAL* 1.3 76.2 - - - +
79N GLU* 1.3 65.1 + - - +
80N LYS* 3.6 3.4 + - - -
81N GLN* 2.9 50.5 + - - +
82N PHE 3.1 10.4 + - - -
22Q A 3.2 53.7 + - + +
23Q A 5.3 0.9 - - - +
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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