Contacts of the helix formed by residues 84 - 98 (chain A) in PDB entry 5J3V
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 84 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44A PRO* 3.5 32.1 - - + +
47A ASN* 6.4 0.7 - - - +
82A ASN 3.3 11.4 - - - +
83A PHE* 1.3 86.7 - - + +
85A ASN* 1.3 67.0 + - - +
86A GLY 4.4 2.9 - - - +
87A VAL* 3.0 22.6 + - + +
88A THR* 3.0 21.7 + - - -
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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 PHE 4.3 6.2 + - - -
84A PRO* 1.3 72.0 - - - +
86A GLY* 1.3 57.5 + - - +
88A THR* 3.8 8.7 - - - -
89A ASP* 2.9 40.2 + - - +
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Residues in contact with GLY 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 PRO* 3.1 3.2 - - - +
85A ASN* 1.3 80.2 - - - +
87A VAL* 1.3 60.4 + - - +
89A ASP* 3.7 8.2 + - - +
90A PHE* 3.6 16.5 + - - +
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Residues in contact with VAL 87 (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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44A PRO 3.8 12.3 - - - +
45A ASP* 4.5 13.2 - - + -
47A ASN* 4.3 16.4 - - + -
48A ASN* 4.4 17.0 - - + +
83A PHE* 4.2 20.0 - - + -
84A PRO* 3.0 30.5 + - + +
86A GLY* 1.3 73.7 - - - +
88A THR* 1.3 65.8 + - - +
89A ASP 3.2 0.2 - - - -
90A PHE* 3.0 22.4 + - + +
91A ILE* 3.2 13.3 + - + +
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Residues in contact with THR 88 (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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80A PHE* 3.9 23.8 - - + -
83A PHE* 3.3 26.3 + - - +
84A PRO 3.0 17.1 + - - -
85A ASN* 3.9 9.1 - - - -
86A GLY 3.4 0.2 - - - -
87A VAL* 1.3 76.2 - - - +
89A ASP* 1.3 62.8 + - - +
91A ILE* 3.5 6.0 + - + +
92A LYS* 3.1 53.2 + - + +
117A ILE* 5.1 3.4 - - + -
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Residues in contact with ASP 89 (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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85A ASN* 2.9 30.5 + - - +
86A GLY* 3.9 9.0 - - - +
87A VAL 3.2 0.2 - - - -
88A THR* 1.3 78.0 - - - +
90A PHE* 1.3 61.8 + - - +
92A LYS* 3.8 13.5 + - - +
93A SER* 3.2 22.7 + - - -
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Residues in contact with PHE 90 (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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48A ASN* 3.3 37.2 - - + -
51A ILE* 3.9 25.1 - - + -
52A PHE* 5.2 8.5 - + + -
56A LYS* 4.6 14.8 - - + -
86A GLY 3.6 10.0 + - - +
87A VAL* 3.0 14.4 + - + +
89A ASP* 1.3 77.1 - - - +
91A ILE* 1.3 63.1 + - + +
93A SER* 2.6 22.4 + - - -
94A GLU* 3.1 47.3 + - + +
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Residues in contact with ILE 91 (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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47A ASN 4.4 3.4 - - - +
51A ILE* 4.0 26.0 - - + -
72A LEU* 3.7 43.1 - - + -
76A VAL* 5.4 1.6 - - + -
83A PHE* 3.8 24.7 - - + -
87A VAL* 3.2 18.1 + - + +
88A THR* 3.5 5.8 + - + +
90A PHE* 1.3 71.7 - - + +
92A LYS* 1.3 66.4 + - - +
94A GLU* 3.9 0.3 - - - -
95A CYS* 3.1 38.4 + - - -
113A LEU* 4.8 1.6 - - + -
117A ILE* 3.8 24.0 - - + -
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Residues in contact with LYS 92 (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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80A PHE* 5.5 1.5 - - - -
88A THR* 3.1 43.7 + - + +
89A ASP* 4.1 13.2 + - - +
90A PHE 3.3 0.2 - - - -
91A ILE* 1.3 76.7 - - - +
93A SER* 1.3 59.6 + - - +
95A CYS* 4.5 0.2 - - - +
96A LEU* 3.3 31.3 + - - +
117A ILE* 3.8 24.2 - - + -
122A GLU 5.7 0.2 + - - -
125A ASN* 3.2 34.6 + - - +
126A TRP* 3.4 49.9 - - + +
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Residues in contact with SER 93 (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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89A ASP 3.2 12.9 + - - -
90A PHE* 2.6 29.1 + - - -
92A LYS* 1.3 79.2 - - - +
94A GLU* 1.3 64.8 + - - +
95A CYS 3.3 0.4 - - - -
96A LEU* 3.5 5.8 + - - +
97A ASN* 2.9 36.0 + - - +
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Residues in contact with GLU 94 (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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51A ILE* 3.8 25.4 - - + +
55A THR* 3.4 24.6 + - - +
56A LYS* 4.2 14.7 - - - +
90A PHE* 3.1 50.3 + - + +
91A ILE 3.3 0.6 + - - +
93A SER* 1.3 84.2 + - - +
95A CYS* 1.3 61.0 + - - +
97A ASN* 3.4 14.6 + - - +
98A ASN* 3.0 34.3 + - - +
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Residues in contact with CYS 95 (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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51A ILE* 4.0 7.4 - - - -
55A THR* 5.4 0.2 - - - -
91A ILE* 3.1 30.6 + - - +
92A LYS* 4.5 4.0 - - - +
94A GLU* 1.3 75.7 - - - +
96A LEU* 1.3 63.9 + - - +
97A ASN 3.3 0.5 + - - -
98A ASN* 3.3 1.0 + - - -
99A ILE* 3.2 21.0 + - - +
110A VAL* 3.2 23.9 - - + +
113A LEU* 3.8 40.6 - - - -
114A ILE* 3.6 21.1 - - + -
117A ILE* 5.3 2.0 - - - -
126A TRP* 5.2 1.8 - - + -
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Residues in contact with LEU 96 (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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92A LYS 3.3 20.4 + - - +
93A SER* 3.5 6.4 + - - +
94A GLU 3.4 0.4 - - - -
95A CYS* 1.3 75.8 - - - +
97A ASN* 1.3 65.3 + - - +
99A ILE* 3.6 34.7 - - + +
114A ILE* 4.1 8.3 - - + -
126A TRP* 3.6 20.0 - - + +
128A ASP 4.4 1.8 - - - +
129A LEU* 4.0 22.0 - - + -
132A LYS* 3.7 43.3 - - + +
133A LEU* 4.6 6.7 - - + -
136A LEU* 4.8 7.5 - - + +
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Residues in contact with ASN 97 (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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93A SER* 2.9 26.9 + - - +
94A GLU* 3.5 20.9 + - - +
95A CYS 3.1 0.4 - - - -
96A LEU* 1.3 83.4 - - - +
98A ASN* 1.3 63.2 + - - +
99A ILE 3.2 8.8 + - - +
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Residues in contact with ASN 98 (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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55A THR* 3.3 30.3 + - + +
58A LYS* 3.7 26.9 - - - +
65A ARG* 5.5 0.6 - - - +
94A GLU* 3.0 27.2 + - - +
95A CYS 3.3 4.2 + - - +
97A ASN* 1.3 79.3 - - - +
99A ILE* 1.3 63.0 + - - +
100A GLY 3.4 2.8 + - - -
101A ASP* 3.5 27.7 + - + +
106A ILE* 5.9 1.5 - - + +
107A ARG* 5.0 1.2 - - - -
110A VAL* 4.0 26.7 - - + +
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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