Contacts of the helix formed by residues 83 - 97 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81H PHE* 3.4 9.2 - - - -
82H PRO* 1.3 84.8 - - - +
84H LYS* 1.3 66.6 + - - +
85H SER* 2.6 2.4 + - - -
86H VAL* 2.6 26.6 + - - +
87H VAL* 4.3 7.9 - - - -
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Residues in contact with LYS 84 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75H ILE 4.4 0.7 - - - -
76H LEU* 2.7 44.6 + - + +
77H ALA 5.1 0.6 + - - -
78H ARG 4.8 1.8 + - - -
79H LYS 3.1 20.8 + - - -
80H SER* 4.1 16.4 - - - -
81H PHE* 2.9 49.4 - - + +
82H PRO 3.5 0.4 - - - +
83H GLY* 1.3 69.9 - - - +
85H SER* 1.3 57.3 + - - +
87H VAL* 2.8 5.9 + - - -
88H GLU* 2.6 55.5 + - + +
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Residues in contact with SER 85 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82H PRO 4.4 6.2 + - - -
83H GLY 2.6 5.4 + - - -
84H LYS* 1.3 75.6 - - - +
86H VAL* 1.3 62.7 + - - -
88H GLU* 3.7 12.4 + - - +
89H GLY* 3.2 15.9 + - - -
248I ARG* 4.0 10.2 + - - +
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Residues in contact with VAL 86 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83H GLY* 2.6 19.1 + - - +
85H SER* 1.3 72.4 - - - +
87H VAL* 1.3 63.8 + - + +
88H GLU 3.0 1.6 - - - -
89H GLY* 2.6 24.4 + - - -
90H ILE* 2.9 33.8 + - + +
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Residues in contact with VAL 87 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72H LEU* 3.9 18.8 - - + -
76H LEU* 4.1 12.3 - - + -
81H PHE* 3.9 24.9 - - + -
83H GLY* 4.3 4.5 - - - -
84H LYS* 2.8 15.8 + - - +
86H VAL* 1.3 80.2 - - + +
88H GLU* 1.3 60.9 + - - +
90H ILE* 3.5 6.0 + - + +
91H VAL* 3.3 22.3 + - + +
17I LEU* 3.8 33.2 - - + -
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Residues in contact with GLU 88 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76H LEU* 4.2 21.9 - - + +
84H LYS* 2.6 47.6 + - - +
85H SER* 3.9 13.3 + - - +
87H VAL* 1.3 72.6 - - - +
89H GLY* 1.3 61.3 + - - +
91H VAL* 3.4 10.0 - - - +
92H ASP* 3.0 29.1 + - - +
148H LYS* 3.9 21.3 + - - +
248I ARG* 4.7 10.0 + - - +
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Residues in contact with GLY 89 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85H SER 3.2 8.6 + - - -
86H VAL* 2.6 14.9 + - - -
88H GLU* 1.3 72.3 - - - +
90H ILE* 1.3 56.8 + - - -
92H ASP* 2.8 25.3 + - - +
93H LEU* 3.0 12.5 + - - +
248I ARG* 4.0 16.6 - - - +
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Residues in contact with ILE 90 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86H VAL* 2.9 34.7 + - + +
87H VAL* 3.8 7.6 - - - +
89H GLY* 1.3 73.3 - - - +
91H VAL* 1.3 63.6 + - - +
93H LEU* 3.1 23.9 + - + +
17I LEU* 3.6 42.6 - - + +
20I VAL* 3.3 17.9 - - + +
21I LEU* 3.9 33.2 - - + -
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Residues in contact with VAL 91 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72H LEU* 3.6 31.2 - - + -
76H LEU* 4.5 10.5 - - + -
87H VAL 3.3 15.4 + - - +
88H GLU* 3.4 11.2 - - - +
89H GLY 3.1 0.6 - - - -
90H ILE* 1.3 79.2 - - - +
92H ASP* 1.3 59.9 + - - +
93H LEU 3.7 0.3 + - - -
94H PRO* 3.7 4.9 - - - +
140H VAL* 5.6 1.2 - - - +
141H PRO* 3.0 30.5 - - + +
144H ILE* 4.0 20.6 - - + -
145H ASN* 3.9 21.5 - - - +
17I LEU* 4.0 5.6 - - + -
20I VAL* 5.0 5.5 - - - +
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Residues in contact with ASP 92 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88H GLU* 3.0 17.2 + - - +
89H GLY* 2.8 11.2 + - - +
91H VAL* 1.3 82.5 - - - +
93H LEU* 1.3 66.4 + - - +
94H PRO* 3.3 1.8 - - - -
95H VAL* 2.9 32.4 + - + +
96H VAL* 3.9 7.8 + - + +
141H PRO* 4.7 2.3 - - - +
145H ASN* 3.9 25.8 + - - +
248I ARG* 3.4 20.7 + - - +
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Residues in contact with LEU 93 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89H GLY 3.0 7.6 + - - +
90H ILE* 3.1 22.8 + - + +
92H ASP* 1.3 73.3 - - - +
94H PRO* 1.3 62.6 - - + +
95H VAL 2.7 0.2 + - - -
96H VAL* 2.7 36.3 + - + +
97H ILE* 3.4 18.4 + - + +
20I VAL* 3.5 24.2 - - + +
21I LEU* 3.8 24.0 - - + -
24I VAL* 3.9 22.7 - - + -
241I LEU* 3.7 30.1 - - + -
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Residues in contact with PRO 94 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91H VAL 3.7 6.1 - - - +
92H ASP 3.5 0.2 - - - -
93H LEU* 1.3 93.0 - - + +
95H VAL* 1.3 59.8 + - - +
96H VAL 3.1 0.8 + - - -
97H ILE* 3.5 19.9 - - + +
137H PHE* 3.2 46.1 - - + +
138H VAL* 4.6 13.1 - - + +
141H PRO* 3.5 32.1 - - + -
20I VAL* 3.3 21.5 - - + -
198I SER* 5.1 0.7 + - - -
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Residues in contact with VAL 95 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92H ASP* 2.9 31.1 + - + +
93H LEU 2.7 3.4 + - - -
94H PRO* 1.3 74.0 - - - +
96H VAL* 1.3 60.7 + - + +
141H PRO* 4.3 19.5 - - + -
142H ILE* 6.3 2.0 - - + -
142I ILE* 6.0 5.6 - - + -
191I MET* 5.3 12.1 - - + +
194I ALA* 3.7 23.7 - - + +
195I ARG* 5.2 4.3 - - + +
198I SER* 3.6 12.6 + - - -
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Residues in contact with VAL 96 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92H ASP* 4.1 9.4 - - + +
93H LEU* 2.7 14.0 + - + +
95H VAL* 1.3 86.2 - - + +
97H ILE* 1.3 60.1 + - + +
98H PRO* 3.3 12.0 - - - +
194I ALA* 4.8 4.5 - - + -
197I ILE* 4.4 4.9 - - - +
198I SER* 3.6 6.7 + - - -
240I SER* 3.1 37.8 + - - -
241I LEU* 5.5 4.0 - - + -
244I PHE* 3.2 46.9 - - + -
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Residues in contact with ILE 97 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93H LEU* 3.4 24.3 + - + +
94H PRO* 3.5 16.2 + - + +
96H VAL* 1.3 79.2 - - + +
98H PRO* 1.3 71.1 - - + +
99H HIS* 3.5 4.0 + - - -
101H VAL* 3.6 31.6 - - + -
102H ALA* 3.6 17.4 - - - +
105H ALA* 6.0 0.7 - - + -
137H PHE* 4.1 11.2 - - + -
24I VAL* 3.3 47.1 - - + -
198I SER* 3.7 4.5 + - - -
237I ILE* 4.7 13.5 - - + +
240I SER* 5.3 2.2 - - - -
241I LEU* 6.2 1.1 - - + -
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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
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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