Contacts of the helix formed by residues 85 - 98 (chain a) in PDB entry 5A0Q
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 THR 85 (chain a).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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83a MET 3.8 1.8 + - - -
84a THR* 1.3 74.7 - - - +
86a GLY* 1.3 55.8 + - - +
88a ILE* 3.2 12.0 + - + +
89a ALA* 3.1 23.7 + - - +
110a ILE* 3.7 18.8 - - + +
112a GLY* 3.3 46.8 + - - +
113a LEU 3.9 9.4 + - - -
114a ASP* 4.7 8.4 - - - -
120a ALA* 3.7 20.9 - - + -
122a TYR* 4.0 9.2 - - + -
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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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103S TYR 4.2 2.7 - - - +
104S ASN* 4.6 8.5 + - - +
84a THR* 3.3 10.2 - - - +
85a THR* 1.3 75.6 - - - +
87a ALA* 1.3 64.2 + - - +
89a ALA* 3.4 9.4 + - - +
90a ALA* 3.3 21.7 + - - +
122a TYR* 4.6 10.5 + - - -
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Residues in contact with ALA 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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103S TYR* 3.5 27.1 + - + +
105S GLU* 3.7 23.8 - - + +
75a TYR* 5.6 0.2 - - + -
83a MET* 3.5 18.6 - - - -
84a THR* 3.2 19.8 + - - +
86a GLY* 1.3 77.1 - - - +
88a ILE* 1.4 55.5 + - - +
90a ALA 3.5 2.1 + - - -
91a MET* 3.0 30.9 + - - +
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Residues in contact with ILE 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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50a THR* 4.1 30.7 - - + +
68a ILE* 5.2 6.3 - - + -
72a LEU* 5.2 7.0 - - + -
83a MET* 3.5 29.4 - - + +
84a THR 3.4 12.8 - - - +
85a THR* 3.2 14.7 + - + +
87a ALA* 1.4 73.6 - - - +
89a ALA* 1.3 58.1 + - - +
91a MET* 4.0 14.8 - - + -
92a LEU* 2.9 41.5 + - + +
110a ILE* 3.8 33.9 - - + -
124a PHE* 5.0 0.2 - - - -
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Residues in contact with ALA 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 THR 3.1 11.7 + - - +
86a GLY* 3.6 10.3 - - - +
87a ALA 3.3 0.4 - - - -
88a ILE* 1.3 76.6 - - - +
90a ALA* 1.4 57.3 + - - +
91a MET 3.8 0.2 + - - -
93a SER* 3.8 2.9 + - - -
110a ILE* 5.6 1.1 - - - +
122a TYR* 3.5 41.3 - - + -
124a PHE* 3.7 14.7 - - - -
130a TYR* 3.0 37.6 - - + +
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Residues in contact with ALA 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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101S PHE 4.2 1.9 - - - +
102S THR 3.2 7.4 - - - +
103S TYR 3.8 9.6 - - - -
104S ASN* 3.4 35.2 - - + +
57Z ARG* 3.8 17.2 + - - +
86a GLY 3.3 6.4 + - - +
88a ILE 3.2 0.2 - - - -
89a ALA* 1.4 77.0 - - + +
91a MET* 1.3 59.7 + - - +
93a SER* 3.4 15.8 + - - -
94a THR* 3.5 12.6 - - - +
130a TYR* 4.8 8.3 - - + -
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Residues in contact with MET 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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102S THR* 3.1 11.4 - - + +
103S TYR* 3.7 11.4 - - + -
68a ILE* 4.8 15.0 - - + +
71a ARG* 3.3 42.8 - - + +
72a LEU* 5.5 0.4 - - - -
83a MET* 3.9 26.0 - - + -
87a ALA 3.0 18.7 + - - +
88a ILE* 3.3 15.5 + - + +
90a ALA* 1.3 75.4 - - - +
92a LEU* 1.3 81.5 + - + +
93a SER 3.2 1.3 - - - -
94a THR* 2.7 22.8 + - - -
95a ILE* 3.1 30.9 + - + +
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Residues in contact with LEU 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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52a ILE* 4.2 3.4 - - + -
64a LEU* 4.9 4.3 - - + -
68a ILE* 3.4 35.0 - - + -
88a ILE* 2.9 25.0 + - + +
91a MET* 1.3 85.3 - - + +
93a SER* 1.4 60.7 + - - +
95a ILE* 3.1 8.3 + - + +
96a LEU* 3.0 48.2 + - + +
108a ASN* 4.5 9.6 - - + +
110a ILE* 4.1 23.3 - - + -
124a PHE* 3.5 26.7 - - + -
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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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53Z SER* 6.0 0.7 - - - -
57Z ARG* 5.3 4.2 - - - -
89a ALA 3.8 2.3 + - - -
90a ALA 3.4 14.6 + - - -
92a LEU* 1.4 77.6 - - - +
94a THR* 1.3 61.0 + - - +
96a LEU* 3.3 3.8 + - - +
97a TYR* 2.8 39.5 + - - -
124a PHE* 3.9 9.9 - - - -
127a VAL 3.9 0.2 - - - +
128a GLY* 4.0 21.3 - - - -
130a TYR* 3.8 33.7 - - - -
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Residues in contact with THR 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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101S PHE* 3.9 35.7 - - + +
102S THR* 4.1 13.7 - - - +
54Z PHE* 4.1 15.2 - - + -
57Z ARG* 4.7 5.2 - - - +
71a ARG* 5.0 0.7 + - - -
90a ALA 3.5 17.3 - - - +
91a MET* 2.7 19.9 + - - -
93a SER* 1.3 76.2 - - - +
95a ILE* 1.4 60.4 + - - +
97a TYR* 3.3 9.1 + - - +
98a SER* 3.0 28.2 + - - -
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Residues in contact with ILE 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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64a LEU* 3.6 29.4 - - + -
67a ILE* 4.2 22.0 - - + -
68a ILE* 4.7 7.4 - - + -
71a ARG* 3.5 33.9 - - + +
91a MET* 3.1 40.8 + - + +
92a LEU* 3.1 10.6 + - + +
94a THR* 1.4 75.8 - - - +
96a LEU* 1.3 59.9 + - - +
98a SER* 2.8 26.1 + - - +
99a ARG 4.0 1.7 + - - -
104a TYR* 4.6 9.1 - - + -
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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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64a LEU* 4.2 27.8 - - + -
92a LEU* 3.0 35.2 + - + +
93a SER 3.6 5.2 - - - +
94a THR 3.3 0.2 - - - -
95a ILE* 1.3 76.6 - - - +
97a TYR* 1.3 56.6 + - - +
99a ARG 2.7 27.8 - - - +
100a ARG* 3.8 3.8 - - - +
104a TYR* 4.5 18.1 - - + +
106a VAL* 4.9 2.0 - - + +
108a ASN* 4.4 4.5 - - - +
124a PHE* 3.7 7.0 - - + -
125a ASP 3.3 24.5 - - - +
126a PRO* 3.8 22.7 - - + +
127a VAL* 3.8 7.1 - - - -
128a GLY* 3.6 17.3 - - - -
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Residues in contact with TYR 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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50Z ALA* 1.8 65.8 + - + +
51Z ASP* 4.4 3.8 - - - -
53Z SER* 4.5 3.6 - - - -
54Z PHE* 3.7 50.7 - + + -
55Z TRP* 6.1 3.1 - + - -
93a SER* 2.8 31.8 + - - -
94a THR 3.6 7.4 - - - +
96a LEU* 1.3 75.5 - - - +
98a SER* 1.4 61.3 + - - +
99a ARG 3.1 1.8 + - - -
100a ARG* 3.0 50.7 + - - +
101a PHE* 6.1 0.2 - - - -
127a VAL 2.6 17.3 - - - -
128a GLY* 3.8 7.6 - - - -
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Residues in contact with SER 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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94a THR 3.0 13.8 + - - -
95a ILE* 2.8 24.4 + - - +
96a LEU 3.3 0.2 - - - -
97a TYR* 1.4 75.2 - - - +
99a ARG* 1.3 59.7 + - - +
100a ARG 3.7 0.8 + - - -
104a TYR* 5.1 1.2 - - - -
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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