Contacts of the helix formed by residues 83 - 97 (chain I) 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 I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81I PHE* 3.4 9.9 - - - -
82I PRO* 1.3 84.4 - - - +
84I LYS* 1.3 67.8 + - - +
85I SER* 2.6 2.4 + - - -
86I VAL* 2.6 26.7 + - - +
87I VAL* 4.3 7.6 - - - -
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Residues in contact with LYS 84 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75I ILE 4.4 0.7 - - - -
76I LEU* 2.7 45.5 + - + +
77I ALA 5.1 0.8 + - - -
78I ARG 4.8 1.4 + - - -
79I LYS 3.1 21.6 + - - -
80I SER* 4.1 17.3 - - - -
81I PHE* 2.9 48.6 - - + +
82I PRO 4.9 0.4 - - - +
83I GLY* 1.3 71.8 - - - +
85I SER* 1.3 57.5 + - - +
86I VAL 2.8 0.9 + - - -
87I VAL* 2.8 4.3 + - - -
88I GLU* 2.6 54.5 + - + +
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Residues in contact with SER 85 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248H ARG* 4.4 7.3 + - - +
82I PRO 4.4 6.6 + - - -
83I GLY 2.6 6.1 + - - -
84I LYS* 1.3 75.6 - - - +
86I VAL* 1.3 62.2 + - - -
88I GLU* 3.9 12.0 + - - +
89I GLY* 3.2 16.5 + - - -
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Residues in contact with VAL 86 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83I GLY* 2.6 19.3 + - - +
85I SER* 1.3 72.3 - - - +
87I VAL* 1.3 62.2 + - + +
88I GLU 3.0 1.1 - - - -
89I GLY* 2.7 24.0 + - - -
90I ILE* 2.9 34.1 + - + +
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Residues in contact with VAL 87 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17H LEU* 3.8 32.4 - - + +
72I LEU* 3.9 19.5 - - + -
76I LEU* 4.1 11.7 - - + -
81I PHE* 3.9 24.7 - - + -
83I GLY* 4.3 4.5 - - - -
84I LYS* 2.8 16.0 + - - +
86I VAL* 1.3 79.5 - - + +
88I GLU* 1.3 61.1 + - - +
90I ILE* 3.5 6.0 + - + +
91I VAL* 3.3 23.3 + - + +
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Residues in contact with GLU 88 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248H ARG* 4.7 8.5 + - - +
76I LEU* 4.2 22.5 - - + +
84I LYS* 2.6 47.7 + - - +
85I SER* 3.9 12.5 + - - +
87I VAL* 1.3 73.7 - - - +
89I GLY* 1.3 59.2 + - - +
91I VAL* 3.4 9.5 + - - +
92I ASP* 3.0 29.6 + - - +
148I LYS* 4.4 16.9 + - - +
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Residues in contact with GLY 89 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248H ARG* 4.1 14.1 - - - +
85I SER 3.2 9.3 + - - -
86I VAL* 2.7 13.9 + - - -
88I GLU* 1.3 72.4 - - - +
90I ILE* 1.3 64.9 + - - -
92I ASP* 2.8 17.6 + - - +
93I LEU* 3.0 12.2 + - - +
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Residues in contact with ILE 90 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17H LEU* 3.5 44.0 - - + +
20H VAL* 3.4 11.8 - - + +
21H LEU* 3.9 32.5 - - + -
86I VAL* 2.9 34.7 + - + +
87I VAL* 3.8 9.0 - - + +
89I GLY* 1.3 74.1 - - - +
91I VAL* 1.3 62.8 + - - +
93I LEU* 3.1 30.4 + - + +
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Residues in contact with VAL 91 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17H LEU* 4.1 5.6 - - + -
20H VAL* 5.1 4.7 - - - +
72I LEU* 3.6 31.2 - - + -
76I LEU* 4.5 10.3 - - + -
87I VAL 3.3 15.8 + - - +
88I GLU* 3.4 11.2 - - - +
89I GLY 3.1 0.8 - - - -
90I ILE* 1.3 79.4 - - - +
92I ASP* 1.3 65.7 + - - +
93I LEU 3.7 0.3 + - - -
94I PRO* 3.8 6.8 - - - +
140I VAL* 5.4 2.4 - - + +
141I PRO* 3.2 27.9 - - + +
144I ILE* 4.0 30.1 - - + -
145I ASN* 4.4 5.8 - - - +
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Residues in contact with ASP 92 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248H ARG* 3.2 23.8 + - - +
88I GLU* 3.0 17.5 + - - +
89I GLY* 2.8 9.1 + - - +
91I VAL* 1.3 84.3 - - - +
93I LEU* 1.3 67.8 + - - +
94I PRO* 3.3 2.2 - - - -
95I VAL* 2.9 31.7 + - + +
96I VAL* 3.9 7.4 + - + +
141I PRO* 4.5 3.5 - - - +
145I ASN* 4.2 21.5 + - - +
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Residues in contact with LEU 93 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20H VAL* 3.4 24.5 - - + +
21H LEU* 3.8 24.7 - - + -
24H VAL* 4.0 13.7 - - + -
241H LEU* 3.6 31.4 - - + -
89I GLY 3.0 7.2 + - - +
90I ILE* 3.3 22.7 - - + +
92I ASP* 1.3 75.6 - - - +
94I PRO* 1.3 61.8 - - + +
95I VAL 2.7 0.3 + - - -
96I VAL* 2.7 35.5 + - + +
97I ILE* 3.4 26.4 + - + +
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Residues in contact with PRO 94 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20H VAL* 3.2 21.5 - - + -
198H SER* 4.8 1.0 + - - -
91I VAL 3.8 14.4 - - - +
92I ASP 3.5 0.2 - - - -
93I LEU* 1.3 94.3 - - + +
95I VAL* 1.3 60.7 + - - +
96I VAL 3.2 1.1 + - - -
97I ILE* 3.5 18.6 - - + +
137I PHE* 3.0 51.3 - - + +
138I VAL* 4.5 11.6 - - - +
141I PRO* 3.8 17.0 - - + -
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Residues in contact with VAL 95 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142H ILE* 6.2 3.8 - - + -
191H MET* 5.3 11.7 - - + +
194H ALA* 3.5 33.3 - - + +
195H ARG* 5.2 2.0 - - - +
198H SER* 3.6 5.1 + - - -
92I ASP* 2.9 29.8 + - + +
93I LEU 2.7 3.4 + - - -
94I PRO* 1.3 74.4 - - - +
96I VAL* 1.3 61.4 + - + +
141I PRO* 4.2 22.4 - - + -
142I ILE* 6.5 0.4 - - + -
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Residues in contact with VAL 96 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194H ALA* 4.7 4.5 - - + -
197H ILE* 4.1 5.4 - - - +
198H SER* 3.6 5.2 + - - -
240H SER* 3.1 36.9 + - - -
241H LEU* 4.6 7.4 - - + +
244H PHE* 3.1 46.2 - - + -
92I ASP* 4.1 9.6 - - + +
93I LEU* 2.7 14.1 + - - +
95I VAL* 1.3 86.7 - - + +
97I ILE* 1.3 59.5 + - + +
98I PRO* 3.3 12.1 - - - +
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Residues in contact with ILE 97 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24H VAL* 3.3 46.9 - - + -
198H SER* 3.5 4.6 + - - -
237H ILE* 4.6 13.0 - - + +
240H SER* 5.3 2.5 - - - -
241H LEU* 5.9 2.2 - - + -
93I LEU* 3.4 22.4 + - + +
94I PRO* 3.5 16.0 + - + +
95I VAL 3.6 0.2 - - - -
96I VAL* 1.3 80.2 - - + +
98I PRO* 1.3 72.4 - - + +
99I HIS* 3.4 3.6 + - - -
101I VAL* 3.5 31.6 - - + -
102I ALA* 3.6 16.8 - - - +
105I ALA* 6.0 0.7 - - + -
137I PHE* 3.9 13.0 - - + -
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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