Contacts of the helix formed by residues 82 - 96 (chain X) in PDB entry 2O5B
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 HIS 82 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7X TRP* 5.6 1.5 - + - -
75X ILE* 3.5 31.6 + - + +
78X LYS* 3.7 15.7 - - + -
80X GLY* 3.3 16.6 + - - +
81X HIS* 1.3 76.9 - - - +
83X GLU* 1.3 62.6 + - + +
84X ALA 3.5 2.9 - - - -
85X GLU* 3.5 12.5 + - + +
86X LEU* 2.9 49.1 + - + +
134X ALA 5.6 0.7 - - - -
137X LEU* 4.0 26.2 - - + +
138X PHE* 4.5 9.2 - - + -
141X ASP* 2.6 30.4 + - + -
158X SO4 3.8 1.7 + - - -
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Residues in contact with GLU 83 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81X HIS 3.6 2.8 + - - -
82X HIS* 1.3 80.2 - - + +
84X ALA* 1.3 59.8 + - - +
86X LEU* 4.5 7.8 - - - +
87X LYS* 3.0 37.5 + - + +
145X LYS* 2.9 43.0 + - - -
158X SO4 3.6 28.7 + - - +
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Residues in contact with ALA 84 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78X LYS* 6.0 1.3 - - - +
82X HIS 3.5 0.4 - - - -
83X GLU* 1.3 80.4 - - - +
85X GLU* 1.3 65.7 + - - +
87X LYS* 5.1 1.3 - - - -
88X PRO* 3.1 25.7 - - - +
158X SO4 4.7 2.4 + - - -
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Residues in contact with GLU 85 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74X GLY* 4.9 2.7 - - - +
75X ILE* 4.1 29.3 - - + +
78X LYS* 3.2 47.5 + - + +
81X HIS 3.9 0.5 - - - +
82X HIS* 3.5 18.0 - - + +
84X ALA* 1.3 85.6 + - - +
86X LEU* 1.3 62.6 + - - +
88X PRO* 3.6 10.9 - - - +
89X LEU* 3.9 12.1 - - - +
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Residues in contact with LEU 86 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75X ILE* 4.3 8.5 - - + -
82X HIS* 2.9 53.9 + - + +
83X GLU* 3.4 9.8 + - - +
85X GLU* 1.3 74.3 - - + +
87X LYS* 1.3 65.9 + - - +
89X LEU* 3.1 8.9 + - + +
90X ALA* 2.9 22.4 + - + +
138X PHE* 3.9 33.7 - - + +
141X ASP* 3.5 36.8 - - + +
142X ILE* 3.9 12.6 - - + +
145X LYS* 4.7 5.8 - - + -
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Residues in contact with LYS 87 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83X GLU* 3.0 33.7 + - + +
84X ALA* 4.8 1.3 - - - +
86X LEU* 1.3 77.6 - - - +
88X PRO* 1.4 64.6 - - + +
90X ALA* 3.5 3.7 + - - +
91X GLN* 3.0 62.4 + - - +
145X LYS* 3.6 30.7 - - + +
148X GLU* 5.8 2.6 + - - -
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Residues in contact with PRO 88 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84X ALA 3.1 28.0 - - - +
85X GLU 3.6 8.5 - - - +
87X LYS* 1.4 93.2 - - + +
89X LEU* 1.3 55.5 + - - +
91X GLN* 3.8 12.9 - - + +
92X SER* 3.0 29.5 + - - -
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Residues in contact with LEU 89 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71X ALA* 5.5 3.6 - - + -
75X ILE* 4.3 15.9 - - + -
85X GLU 3.9 11.0 + - - +
86X LEU* 3.1 12.2 + - + +
88X PRO* 1.3 78.8 - - - +
90X ALA* 1.3 66.4 + - - +
92X SER* 4.7 0.4 - - - -
93X HIS* 2.8 56.6 + - + -
138X PHE* 4.4 11.9 - - + -
142X ILE* 5.4 2.9 - - + -
154X MNH 3.8 65.3 - - + +
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Residues in contact with ALA 90 (chain X).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86X LEU 2.9 17.7 + - - +
87X LYS 3.7 4.0 - - - +
89X LEU* 1.3 72.3 - - - +
91X GLN* 1.3 57.9 + - - +
93X HIS* 3.2 1.8 + - - -
94X ALA* 2.9 28.1 + - - +
142X ILE* 4.2 27.4 - - + +
145X LYS* 3.7 34.1 - - + -
146X TYR* 3.5 14.5 - - + -
149X LEU* 5.0 1.1 - - - -
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Residues in contact with GLN 91 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87X LYS* 3.0 45.2 + - + +
88X PRO* 3.8 11.5 - - + +
89X LEU 3.3 0.6 - - - -
90X ALA* 1.3 75.3 - - + +
92X SER* 1.3 58.1 + - - +
94X ALA* 3.4 0.5 + - - -
95X THR* 2.9 40.7 + - - +
145X LYS* 5.9 3.7 - - + +
148X GLU* 4.9 8.3 + - - -
149X LEU* 4.2 33.8 - - + +
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Residues in contact with SER 92 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88X PRO 3.0 15.1 + - - -
89X LEU 3.7 0.9 + - - -
91X GLN* 1.3 75.1 - - - +
93X HIS* 1.3 74.4 + - - +
95X THR* 5.3 0.2 - - - -
96X LYS* 3.0 19.7 + - - +
97X HIS* 3.0 31.5 + - - -
154X MNH 2.6 29.0 + - - -
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Residues in contact with HIS 93 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89X LEU* 2.8 48.8 + - + +
90X ALA* 3.2 2.4 + - - +
92X SER* 1.3 89.0 + - - +
94X ALA* 1.3 55.5 + - - +
97X HIS* 3.8 9.6 - + - -
98X LYS 2.8 23.2 + - - -
99X ILE* 2.9 30.1 + - + -
104X LEU* 5.3 5.8 - - + -
142X ILE* 5.9 0.4 - - + -
146X TYR* 3.3 19.7 - - + +
154X MNH 2.3 68.2 + + + -
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Residues in contact with ALA 94 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90X ALA 2.9 16.3 + - - +
93X HIS* 1.3 77.0 - - - +
95X THR* 1.3 59.8 + - - +
98X LYS* 3.5 10.4 + - - +
146X TYR* 3.6 20.3 + - + -
149X LEU* 3.9 19.7 - - + -
151X PHE* 3.4 50.3 - - + -
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Residues in contact with THR 95 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91X GLN* 2.9 24.3 + - - +
92X SER* 5.3 0.4 - - - -
94X ALA* 1.3 73.1 - - - +
96X LYS* 1.3 59.8 + - + +
98X LYS* 2.9 29.6 + - - +
149X LEU* 4.5 15.9 - - - +
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Residues in contact with LYS 96 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92X SER* 3.0 19.8 + - - +
95X THR* 1.3 78.6 - - + +
97X HIS* 1.3 96.4 + - + +
98X LYS* 3.2 13.5 - - - +
154X MNH 4.9 1.6 - - - +
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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