Contacts of the helix formed by residues 83 - 97 (chain D) in PDB entry 2ONK
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 GLY 83 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81D PHE* 3.4 10.3 - - - -
82D PRO* 1.3 85.6 - - - +
84D LYS* 1.3 66.4 + - - +
85D SER* 2.6 2.3 + - - -
86D VAL* 2.6 27.2 + - - +
87D VAL* 4.3 7.9 - - - -
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Residues in contact with LYS 84 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75D ILE 4.4 0.4 - - - -
76D LEU* 2.7 46.1 + - + +
77D ALA 5.1 1.0 + - - -
78D ARG 4.8 1.8 + - - -
79D LYS 3.1 21.2 + - - -
80D SER* 4.1 16.7 - - - -
81D PHE* 2.9 49.2 - - + +
82D PRO 3.5 0.2 - - - -
83D GLY* 1.3 71.0 - - - +
85D SER* 1.3 57.2 + - - +
87D VAL* 2.8 5.1 + - - -
88D GLU* 2.6 54.7 + - + +
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Residues in contact with SER 85 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248C ARG* 4.2 8.1 + - - +
82D PRO 4.4 6.5 + - - -
83D GLY 2.6 6.2 + - - -
84D LYS* 1.3 75.4 - - - +
86D VAL* 1.3 63.0 + - - -
88D GLU* 3.7 12.2 + - - +
89D GLY* 3.2 16.5 + - - -
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Residues in contact with VAL 86 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83D GLY* 2.6 19.1 + - - +
85D SER* 1.3 72.4 - - - +
87D VAL* 1.3 63.6 + - + +
88D GLU 3.0 1.6 - - - -
89D GLY* 2.7 24.1 + - - -
90D ILE* 2.9 34.2 + - + +
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Residues in contact with VAL 87 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17C LEU* 3.8 33.5 - - + +
72D LEU* 3.9 18.8 - - + -
76D LEU* 4.1 11.9 - - + -
81D PHE* 3.9 25.1 - - + -
83D GLY* 3.6 4.7 + - - -
84D LYS* 2.8 16.2 + - - +
86D VAL* 1.3 79.4 - - + +
88D GLU* 1.3 60.1 + - - +
90D ILE* 3.5 5.5 + - + +
91D VAL* 3.3 23.2 + - + +
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Residues in contact with GLU 88 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248C ARG* 4.8 9.7 + - - +
76D LEU* 4.2 22.3 - - + +
84D LYS* 2.6 48.6 + - + +
85D SER* 3.9 12.4 + - - +
87D VAL* 1.3 72.8 - - - +
89D GLY* 1.3 60.7 + - - +
91D VAL* 3.4 9.6 + - - +
92D ASP* 3.0 28.7 + - - +
148D LYS* 4.1 20.4 + - - +
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Residues in contact with GLY 89 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248C ARG* 4.1 14.8 - - - +
85D SER 3.2 8.9 + - - -
86D VAL* 2.7 13.7 + - - -
88D GLU* 1.3 70.7 - - - +
90D ILE* 1.3 65.0 + - - -
91D VAL 3.1 1.3 - - - -
92D ASP* 2.8 17.8 + - - +
93D LEU* 3.0 12.9 + - - +
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Residues in contact with ILE 90 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17C LEU* 3.6 43.5 - - + +
20C VAL* 3.3 22.7 - - + +
21C LEU* 3.9 33.0 - - + -
86D VAL* 2.9 34.3 + - + +
87D VAL* 3.8 8.5 - - + +
89D GLY* 1.3 73.9 - - - +
91D VAL* 1.3 62.0 + - - +
93D LEU* 3.1 21.3 + - + +
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Residues in contact with VAL 91 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17C LEU* 4.1 5.2 - - + -
20C VAL* 5.1 4.8 - - - +
72D LEU* 3.6 31.0 - - + -
76D LEU* 4.5 10.1 - - + -
87D VAL 3.3 15.1 + - - +
88D GLU* 3.4 11.0 - - - +
89D GLY 3.1 0.4 - - - -
90D ILE* 1.3 79.8 - - - +
92D ASP* 1.3 60.9 + - - +
93D LEU 3.7 0.2 + - - -
94D PRO* 3.8 5.7 - - - +
140D VAL* 5.3 2.4 - - + +
141D PRO* 3.1 28.8 - - + +
144D ILE* 3.9 31.4 - - + -
145D ASN* 4.2 10.8 - - - +
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Residues in contact with ASP 92 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248C ARG* 3.4 21.6 + - - +
88D GLU* 3.0 17.7 + - - +
89D GLY* 2.8 10.0 + - - +
91D VAL* 1.3 82.2 - - - +
93D LEU* 1.3 67.1 + - - +
94D PRO* 3.3 2.2 - - - -
95D VAL* 2.9 32.5 + - + +
96D VAL* 3.9 7.5 + - + +
141D PRO* 4.5 2.8 - - - +
145D ASN* 3.9 24.9 + - - +
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Residues in contact with LEU 93 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20C VAL* 3.4 29.6 - - + +
21C LEU* 3.9 22.0 - - + -
24C VAL* 3.9 25.1 - - + -
241C LEU* 3.8 29.2 - - + -
89D GLY 3.0 7.6 + - - +
90D ILE* 3.1 18.3 + - + +
92D ASP* 1.3 74.2 - - - +
94D PRO* 1.3 63.0 - - + +
95D VAL 2.7 0.2 + - - -
96D VAL* 2.7 36.3 + - + +
97D ILE* 3.4 19.2 + - + +
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Residues in contact with PRO 94 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20C VAL* 3.4 20.6 - - + -
198C SER* 4.9 1.2 + - - -
91D VAL 3.8 6.5 - - - +
92D ASP 3.5 0.2 - - - -
93D LEU* 1.3 93.4 - - + +
95D VAL* 1.3 58.5 + - - +
96D VAL 3.1 1.0 + - - -
97D ILE* 3.5 18.6 - - + +
137D PHE* 3.0 51.6 - - + +
138D VAL* 4.5 12.9 - - - +
141D PRO* 3.6 28.3 - - + -
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Residues in contact with VAL 95 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142C ILE* 6.1 5.6 - - + -
191C MET* 5.2 13.2 - - + +
194C ALA* 3.5 32.2 - - + +
195C ARG* 5.1 3.7 - - + +
198C SER* 3.6 4.9 + - - -
92D ASP* 2.9 28.4 + - + +
93D LEU 2.7 3.2 + - - -
94D PRO* 1.3 75.0 - - - +
96D VAL* 1.3 60.6 + - + +
97D ILE 3.6 0.2 - - - -
141D PRO* 4.1 24.0 - - + -
142D ILE* 6.3 1.6 - - + -
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Residues in contact with VAL 96 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194C ALA* 4.7 5.2 - - + -
197C ILE* 4.2 5.7 - - - +
198C SER* 3.5 5.1 + - - -
240C SER* 3.2 29.1 + - - -
241C LEU* 5.6 3.8 - - + -
244C PHE* 3.2 53.6 - - + -
92D ASP* 4.1 10.5 - - + +
93D LEU* 2.7 14.0 + - + +
95D VAL* 1.3 85.7 - - + +
97D ILE* 1.3 59.3 + - + +
98D PRO* 3.3 11.6 - - - +
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Residues in contact with ILE 97 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24C VAL* 3.4 45.1 - - + -
198C SER* 3.5 4.8 + - - -
237C ILE* 4.9 13.7 - - + +
240C SER* 5.4 2.7 - - - -
241C LEU* 6.2 0.9 - - + -
93D LEU* 3.4 23.3 + - + +
94D PRO* 3.5 16.3 + - + +
96D VAL* 1.3 80.0 - - + +
98D PRO* 1.3 71.8 - - + +
99D HIS* 3.5 3.6 + - - -
101D VAL* 3.6 32.5 - - + -
102D ALA* 3.6 17.1 - - - +
105D ALA* 6.0 0.7 - - + -
137D PHE* 3.9 12.8 - - + -
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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