Contacts of the strand formed by residues 76 - 86 (chain A) in PDB entry 5N8A
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 VAL 76 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4A GLN* 4.8 7.0 - - + +
5A LEU* 4.0 11.4 - - + -
24A ILE* 3.5 27.4 - - + -
25A LEU 3.5 5.8 - - - +
26A GLN* 4.3 3.1 - - + -
74A ASN 4.2 2.0 - - - +
75A CYS* 1.3 75.6 - - - +
77A CYS* 1.3 64.1 - - - +
101A VAL* 3.7 2.1 - - - +
102A LEU* 2.8 32.2 + - + -
103A LYS* 3.0 21.1 + - + +
108A VAL* 3.8 18.6 - - + -
112A ILE* 4.0 23.8 - - + -
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Residues in contact with CYS 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A PRO 3.8 0.5 - - - +
24A ILE* 3.4 3.5 - - - -
25A LEU* 2.9 37.2 + - - +
27A VAL* 4.3 12.6 - - - -
46A MET* 3.5 31.2 - - - -
71A LEU* 4.5 7.2 - - + -
75A CYS* 4.8 0.9 - - - -
76A VAL* 1.3 75.8 - - - +
78A GLN* 1.3 57.9 + - - +
79A ILE* 3.9 12.2 + - - +
99A LEU* 4.1 12.3 - - + -
100A GLU 3.1 20.6 - - - +
101A VAL* 4.1 7.4 - - + -
102A LEU* 4.1 4.5 - - - +
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Residues in contact with GLN 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A LYS* 2.9 35.5 + - - +
23A PRO 3.5 3.6 - - - +
24A ILE* 4.0 22.3 - - + +
77A CYS* 1.3 72.6 - - - +
79A ILE* 1.3 66.8 + - - +
80A HIS* 3.5 30.2 + - + +
99A LEU* 3.2 4.5 - - - -
100A GLU* 2.8 35.6 + - + +
102A LEU* 4.0 19.8 - - + +
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Residues in contact with ILE 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A ILE 4.3 0.9 - - - +
22A LYS* 3.1 27.2 - - - +
23A PRO* 2.9 26.0 + - + +
25A LEU* 3.9 20.6 - - + -
46A MET* 4.3 3.8 - - + -
77A CYS* 3.9 19.1 - - - +
78A GLN* 1.3 74.1 - - - +
80A HIS* 1.3 61.8 + - - +
81A ARG 3.9 7.4 - - - +
82A PHE* 3.7 30.0 - - + -
96A LEU* 3.8 33.4 - - + -
98A GLU 3.8 4.0 - - - +
99A LEU* 3.8 21.8 - - + -
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Residues in contact with HIS 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A ILE 5.5 1.3 - - - +
22A LYS* 2.9 46.0 + - + +
78A GLN* 3.5 43.7 + - + +
79A ILE* 1.3 74.1 - - - +
81A ARG* 1.3 62.5 + - - +
82A PHE* 5.5 0.9 - - - -
98A GLU* 2.9 28.1 + - + +
99A LEU 4.3 0.9 - - - -
100A GLU* 3.2 43.8 + - + +
102A LEU* 6.0 0.2 - - - +
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Residues in contact with ARG 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A THR 6.0 1.1 - - - -
61A GLN* 3.8 15.8 + - - +
79A ILE* 3.6 2.8 - - - +
80A HIS* 1.3 80.5 - - - +
82A PHE* 1.3 70.5 + - - +
83A ILE* 5.3 5.7 - - + +
97A MET* 2.9 57.6 + - + +
98A GLU* 2.9 50.1 + - + +
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Residues in contact with PHE 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A ILE* 3.8 31.6 - - + -
18A ASP 3.3 22.9 - - - -
19A THR* 3.4 43.8 + - + +
21A ILE* 3.5 26.0 - - + -
23A PRO* 4.3 9.4 - - + -
79A ILE* 3.7 24.5 - - + -
80A HIS 5.5 0.2 - - - -
81A ARG* 1.3 80.4 - - - +
83A ILE* 1.3 74.2 + - - +
84A VAL* 4.4 0.7 - - + -
94A VAL* 3.8 17.7 - - + -
95A ILE 3.2 17.7 - - - +
96A LEU* 4.2 6.1 - - + -
97A MET* 4.2 2.5 - - - -
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Residues in contact with ILE 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A THR* 5.0 3.4 - - - -
81A ARG* 5.3 7.0 - - + +
82A PHE* 1.3 81.1 - - - +
84A VAL* 1.3 64.0 + - - +
85A ASN* 3.6 30.7 - - - +
94A VAL* 3.6 3.5 - - - +
95A ILE* 2.8 45.6 + - + -
97A MET* 3.5 37.5 - - + -
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Residues in contact with VAL 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A ILE* 3.9 33.7 - - + +
14A MET* 5.8 0.9 - - - -
17A GLY* 5.5 4.3 - - - -
19A THR* 4.5 11.5 - - + +
82A PHE* 4.4 10.1 - - + -
83A ILE* 1.3 80.6 - - - +
85A ASN* 1.3 75.3 + - - +
86A THR* 4.4 2.0 - - - +
92A ARG* 3.9 36.6 - - + +
93A VAL 3.4 8.1 - - - +
94A VAL* 4.5 7.6 - - + -
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Residues in contact with ASN 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A ILE* 3.6 13.6 + - - +
84A VAL* 1.3 81.6 - - - +
86A THR* 1.3 62.3 + - - +
87A LEU* 4.0 4.7 + - + -
91A ARG 4.0 0.2 - - - +
92A ARG* 3.5 1.4 - - - -
93A VAL* 2.8 47.0 + - + +
95A ILE* 3.2 29.4 - - + +
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Residues in contact with THR 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A VAL* 4.4 3.1 - - - +
85A ASN* 1.3 73.6 - - - +
87A LEU* 1.3 75.9 + - - +
90A GLY* 3.8 22.9 - - - +
91A ARG 3.6 3.8 - - - +
92A ARG* 3.0 34.6 + - + +
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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