Contacts of the helix formed by residues 85 - 105 (chain N) in PDB entry 5OA3
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 85 (chain N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10192 C 5.6 0.4 - - - +
72N LEU* 5.8 10.5 - - + -
82N PRO* 4.9 2.5 - - + -
83N ASP 4.6 1.6 - - - +
84N LEU* 1.3 85.7 - - + +
86N GLU* 1.3 67.7 + - - +
87N ASP* 3.3 5.8 - - - +
88N LEU* 3.2 11.4 + - + +
89N TYR 3.1 16.6 + - - -
129N TYR* 3.4 52.5 - - + +
134N VAL* 4.3 20.9 - - + -
135N LEU* 5.0 5.8 - - + -
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Residues in contact with GLU 86 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9242 G 4.8 2.6 + - - -
9252 G 4.1 8.0 + - - +
9262 A 5.5 0.7 - - - +
10182 U 3.9 19.2 + - - +
10192 C 4.2 10.9 - - - +
46N THR* 3.8 27.1 - - + -
47N PRO* 4.0 26.6 - - + +
48N SER* 4.3 9.4 + - - -
72N LEU* 5.5 4.8 - - + +
82N PRO* 4.8 11.3 - - + +
84N LEU 3.4 3.0 + - - -
85N PRO* 1.3 71.1 - - + +
87N ASP* 1.3 96.4 + - - +
89N TYR* 3.1 13.2 - - + +
90N HIS* 2.9 33.8 + - + +
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Residues in contact with ASP 87 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9242 G 3.2 22.9 + - - +
9252 G 3.6 41.3 - - - +
10192 C 4.6 2.8 + - - +
85N PRO* 3.6 9.0 - - - +
86N GLU* 1.3 89.4 + - - +
88N LEU* 1.3 61.8 + - - +
90N HIS* 2.9 4.6 + - - +
91N LEU* 2.9 32.6 + - - +
125N LEU* 3.9 18.8 - - + +
129N TYR* 3.4 17.7 + - - -
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Residues in contact with LEU 88 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84N LEU* 4.8 7.2 - - + -
85N PRO* 3.2 17.2 + - + +
87N ASP* 1.3 80.3 - - - +
89N TYR* 1.3 65.0 + - - +
91N LEU* 3.5 3.8 + - + +
92N ILE* 2.9 34.7 + - + +
122N ILE* 4.4 26.9 - - + +
125N LEU* 4.1 25.7 - - + +
126N ALA* 4.4 9.9 - - + +
129N TYR* 3.6 34.1 - - + -
135N LEU* 4.0 22.9 - - + -
139N TRP* 4.8 10.5 - - + -
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Residues in contact with TYR 89 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82N PRO* 6.4 0.2 - - + -
84N LEU* 3.6 33.9 - - + +
85N PRO 3.1 6.0 + - - +
86N GLU* 3.1 22.2 - - + +
88N LEU* 1.3 74.9 - - - +
90N HIS* 1.3 75.4 + + - +
92N ILE* 2.9 10.2 + - - +
93N LYS* 2.9 50.5 + - + +
149N LEU 4.6 2.7 - - - -
150N VAL* 3.7 53.6 + - + +
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Residues in contact with HIS 90 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9252 G 3.5 30.7 - - - +
9262 A 3.8 42.4 + - - +
9272 C 5.0 4.5 - - - -
46N THR* 5.0 13.8 + - + +
49N GLN* 5.8 3.8 + - - -
86N GLU* 2.9 25.7 + - + -
87N ASP 2.9 8.5 + - - +
89N TYR* 1.3 82.6 - + - +
91N LEU* 1.3 64.5 + - - +
93N LYS* 3.0 35.9 + - - +
94N LYS* 2.9 22.8 + - - +
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Residues in contact with LEU 91 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9242 G 4.7 2.5 - - - +
9252 G 3.5 44.6 - - - +
9262 A 5.0 3.8 - - - +
87N ASP 2.9 15.5 + - - +
88N LEU* 3.8 5.6 - - + +
90N HIS* 1.3 71.7 - - - +
92N ILE* 1.3 63.5 + - - +
94N LYS* 3.1 12.9 + - + +
95N ALA* 2.9 24.4 + - - +
118N ILE* 4.2 7.4 - - + +
121N ARG* 3.8 44.4 - - + +
122N ILE* 4.1 23.1 - - + +
125N LEU* 4.6 16.4 - - + -
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Residues in contact with ILE 92 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84N LEU* 4.9 8.5 - - + -
88N LEU* 2.9 23.1 + - + +
89N TYR* 3.3 8.7 - - - +
91N LEU* 1.3 75.4 - - - +
93N LYS* 1.3 58.8 + - - +
95N ALA* 3.4 3.3 + - - +
96N VAL* 2.9 27.2 + - + +
122N ILE* 4.2 22.0 - - + +
139N TRP* 4.1 17.9 - - + -
141N TYR* 3.9 24.7 + - + -
146N ALA 3.9 17.5 - - - +
149N LEU* 4.0 26.0 - - + -
150N VAL* 3.6 18.2 - - + -
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Residues in contact with LYS 93 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89N TYR* 2.9 25.9 + - - +
90N HIS* 3.0 38.6 + - - +
92N ILE* 1.3 78.6 - - - +
94N LYS* 1.3 61.6 + - - +
96N VAL* 3.0 11.6 - - + +
97N ALA* 3.0 21.1 + - - +
150N VAL* 3.7 37.7 - - + -
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Residues in contact with LYS 94 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9262 A 4.1 22.8 + - - +
10092 A 3.8 27.4 - - - +
10102 G 2.8 44.4 + - - +
90N HIS 2.9 12.7 + - - +
91N LEU* 3.6 17.2 - - + +
93N LYS* 1.3 75.5 - - - +
95N ALA* 1.3 63.2 + - - +
97N ALA* 3.1 9.5 + - - +
98N VAL* 2.9 23.2 + - + +
118N ILE* 3.8 21.8 - - + -
121N ARG* 5.6 0.7 - - - +
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Residues in contact with ALA 95 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91N LEU 2.9 16.3 + - - +
92N ILE* 3.6 5.4 - - - +
94N LYS* 1.3 73.2 - - - +
96N VAL* 1.3 66.1 + - - +
98N VAL* 3.8 7.0 - - - +
99N ARG* 2.9 30.1 + - - +
115N LEU* 4.3 4.5 - - + +
118N ILE* 3.7 22.6 - - + +
119N GLU* 4.3 9.4 - - - +
122N ILE* 4.4 7.2 - - + -
141N TYR* 4.1 17.5 - - - +
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Residues in contact with VAL 96 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92N ILE* 2.9 22.5 + - + +
93N LYS* 3.0 18.4 - - + +
95N ALA* 1.3 77.5 - - - +
97N ALA* 1.3 63.9 + - + +
99N ARG* 3.3 7.6 + - - +
100N LYS* 2.9 28.1 + - + +
141N TYR* 5.2 0.8 + - - -
146N ALA* 3.6 36.8 - - + +
147N SER* 4.3 13.5 - - - +
150N VAL* 4.9 6.7 - - + -
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Residues in contact with ALA 97 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10082 A 4.1 25.0 - - - +
10092 A 4.2 8.3 - - - +
93N LYS 3.0 11.3 + - - +
94N LYS* 3.1 10.1 + - - +
96N VAL* 1.3 79.5 - - - +
98N VAL* 1.3 63.9 + - - +
100N LYS* 3.0 11.0 + - - +
101N HIS* 2.9 24.2 + - - +
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Residues in contact with VAL 98 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10082 A 4.0 20.0 - - - +
10092 A 4.8 18.6 - - - +
94N LYS 2.9 18.2 + - - +
95N ALA* 3.8 6.3 - - - +
97N ALA* 1.3 75.9 - - - +
99N ARG* 1.3 64.9 + - - +
101N HIS* 3.3 3.2 + - - +
102N LEU* 2.9 31.1 + - + +
111N ALA* 4.0 17.0 - - + +
114N ARG* 5.6 1.8 - - + -
115N LEU* 3.5 37.2 - - + +
118N ILE* 4.2 17.5 - - + -
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Residues in contact with ARG 99 (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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95N ALA 2.9 17.3 + - - +
96N VAL* 3.3 11.9 - - - +
98N VAL* 1.3 75.3 - - - +
100N LYS* 1.3 64.8 + - - +
102N LEU* 2.9 18.0 + - - +
103N GLU* 3.0 14.6 + - - +
115N LEU* 3.9 22.3 - - + +
119N GLU* 3.0 23.6 + - - +
141N TYR* 2.8 27.3 + - - -
143N SER* 3.2 47.4 + - - +
146N ALA* 4.6 2.4 - - - +
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Residues in contact with LYS 100 (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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96N VAL* 2.9 19.1 + - + +
97N ALA* 3.0 13.0 + - - +
99N ARG* 1.3 77.0 - - - +
101N HIS* 1.3 58.5 + - - +
103N GLU* 3.0 36.6 - - - +
104N ARG* 3.5 38.1 + - - +
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Residues in contact with HIS 101 (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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9352 G 4.1 10.5 + - - -
9362 G 5.3 1.6 - - - -
10072 C 3.3 34.0 + - - +
10082 A 3.4 34.8 + - - +
97N ALA 2.9 14.6 + - - +
98N VAL 3.8 4.0 - - - +
100N LYS* 1.3 75.8 - - - +
102N LEU* 1.3 62.5 + - - +
103N GLU 3.2 3.3 + - - -
104N ARG* 3.4 19.3 + - - +
105N ASN* 3.0 42.3 + - + -
108N ASP* 3.6 21.1 + - - +
111N ALA* 4.5 13.5 - - + +
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Residues in contact with LEU 102 (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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98N VAL* 2.9 19.0 + - + +
99N ARG* 2.9 5.1 + - - +
101N HIS* 1.3 76.4 - - - +
103N GLU* 1.3 61.0 + - - +
105N ASN 3.2 28.5 - - - +
106N ARG* 4.2 9.3 + - - +
108N ASP* 3.8 21.8 - - + +
111N ALA* 3.6 27.8 - - + +
112N LYS* 3.6 29.8 - - + +
115N LEU* 4.1 22.7 - - + -
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Residues in contact with GLU 103 (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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99N ARG 3.0 8.9 + - - +
100N LYS* 3.0 35.2 - - - +
102N LEU* 1.3 79.7 - - - +
104N ARG* 1.3 86.1 + - + +
106N ARG* 4.4 14.1 + - - +
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Residues in contact with ARG 104 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10072 C 5.8 4.2 + - - -
100N LYS* 3.5 49.1 + - - +
101N HIS* 3.4 10.8 + - - +
103N GLU* 1.3 102.0 + - + +
105N ASN* 1.3 72.8 + - - +
106N ARG* 3.8 2.4 + - - +
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Residues in contact with ASN 105 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9362 G 3.5 33.8 + - - +
9372 C 3.8 21.7 + - - +
10072 C 5.0 2.0 + - - -
101N HIS* 3.0 43.1 + - + +
102N LEU* 3.2 27.1 - - - +
104N ARG* 1.3 88.2 - - - +
106N ARG* 1.3 61.3 + - - +
107N LYS* 3.4 1.6 - - - +
108N ASP* 3.9 8.1 + - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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