Contacts of the helix formed by residues 98 - 110 (chain C) in PDB entry 2ONL
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 CYS 98 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96C GLN* 3.0 40.9 + - - -
97C ASP* 1.3 82.5 + - - +
99C PRO* 1.3 68.1 - - + -
100C LYS* 3.2 9.2 - - - -
101C ALA* 2.6 35.7 + - - +
102C ARG* 2.7 18.5 + - - +
134C LEU* 5.5 0.2 - - - +
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Residues in contact with PRO 99 (chain C).
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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98C CYS* 1.3 94.9 - - + +
100C LYS* 1.3 50.5 + - - +
102C ARG* 3.7 9.4 - - + +
103C ARG* 2.3 76.6 + - + +
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Residues in contact with LYS 100 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98C CYS* 3.2 8.7 - - - -
99C PRO* 1.3 81.6 - - - +
101C ALA* 1.3 61.4 + - + +
103C ARG* 4.0 13.2 - - - +
104C GLU* 3.0 36.9 + - + +
209C GLY* 2.4 33.3 + - - -
210C PHE* 4.7 9.3 - - - +
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Residues in contact with ALA 101 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95C LEU* 4.1 22.2 - - + -
96C GLN 3.9 11.7 - - - +
97C ASP* 4.7 0.4 - - - -
98C CYS* 2.6 30.8 + - - +
100C LYS* 1.3 81.0 - - + +
102C ARG* 1.3 54.0 + - - -
104C GLU* 3.2 9.0 - - - +
105C VAL* 2.8 31.5 - - - +
134C LEU* 2.9 9.5 - - + +
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Residues in contact with ARG 102 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52C LEU* 6.2 0.9 - - + -
54C ILE* 3.8 29.4 - - + +
56C LYS* 4.8 4.9 - - - +
97C ASP* 2.6 30.9 + - - -
98C CYS* 2.7 16.7 + - - +
99C PRO* 3.7 8.5 - - + +
101C ALA* 1.3 72.3 - - - +
103C ARG* 1.3 59.5 + - - +
105C VAL* 2.8 23.3 - - + +
106C GLU* 2.8 17.8 + - + +
125C GLU* 3.0 37.2 - - - +
134C LEU* 4.1 5.2 - - + +
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Residues in contact with ARG 103 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99C PRO* 2.3 66.3 + - - +
100C LYS* 4.0 10.5 - - - +
102C ARG* 1.3 67.4 - - - +
104C GLU* 1.3 56.0 + - - +
106C GLU* 2.7 36.7 + - - +
107C LEU* 2.8 22.3 + - + +
213C GLU* 5.9 3.4 - - - +
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Residues in contact with GLU 104 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93C LYS* 5.2 4.5 + - - -
95C LEU* 4.3 14.0 - - - +
100C LYS* 3.0 31.1 + - + +
101C ALA* 3.2 13.5 - - - +
103C ARG* 1.3 77.8 - - - +
105C VAL* 1.3 97.8 + - - +
107C LEU* 2.9 18.1 + - + +
108C HIS* 2.8 34.3 + - - +
136C ILE* 5.8 0.2 - - - +
208C PHE* 4.3 21.8 + - - +
209C GLY* 4.2 21.6 + - - +
211C ALA 5.6 2.2 - - - +
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Residues in contact with VAL 105 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52C LEU* 5.2 2.9 - - + -
54C ILE* 4.9 4.0 - - + -
95C LEU* 4.7 0.4 - - + -
101C ALA 2.8 21.5 - - - +
102C ARG* 2.8 33.2 - - + +
104C GLU* 1.3 103.8 + - - +
106C GLU* 1.3 53.6 + - - +
108C HIS* 3.7 4.3 - - + +
109C TRP* 2.7 37.4 + - - +
123C VAL* 4.7 12.6 - - + +
134C LEU* 3.0 31.4 - - + -
136C ILE* 3.8 22.0 - - + -
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Residues in contact with GLU 106 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52C LEU* 4.3 15.7 - - + -
102C ARG* 2.8 20.7 + - + +
103C ARG* 2.7 31.2 + - - +
105C VAL* 1.3 73.0 - - - +
107C LEU* 1.3 81.5 + - - +
109C TRP* 3.6 10.3 - - + +
110C ARG* 3.0 39.1 + - + +
213C GLU* 4.3 9.2 - - - +
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Residues in contact with LEU 107 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103C ARG* 2.8 29.8 - - + +
104C GLU* 2.9 19.9 + - + +
106C GLU* 1.3 91.5 - - - +
108C HIS* 1.3 65.8 + - - +
110C ARG* 3.2 25.6 - - - +
111C ALA* 3.0 24.2 + - - +
182C ILE* 4.7 18.6 - - + +
208C PHE* 5.0 2.9 - - + -
211C ALA* 4.4 26.0 - - + +
212C LYS* 4.9 8.1 - - - -
213C GLU* 4.2 26.0 - - + +
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Residues in contact with HIS 108 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104C GLU* 2.8 22.6 + - - +
105C VAL* 3.7 7.9 - - - +
107C LEU* 1.3 72.5 - - - +
109C TRP* 1.3 65.2 + - - +
111C ALA* 2.9 21.3 + - - +
112C SER* 3.5 0.7 + - - -
117C ILE* 4.9 4.6 - - + +
118C VAL* 3.5 23.5 + - + -
120C ILE* 3.2 17.6 - - + +
136C ILE* 6.2 2.7 - - + -
138C MET* 3.1 40.0 - - + +
206C THR* 5.0 0.4 - - - -
207C ASP 4.8 7.4 - - - -
208C PHE* 3.9 43.7 + + + +
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Residues in contact with TRP 109 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49C LYS* 5.6 7.9 - - + -
50C SER 3.0 24.5 - - - -
51C GLY* 3.2 7.0 - - - -
52C LEU* 3.0 68.2 - - + +
105C VAL 2.7 21.5 + - - +
106C GLU* 3.6 10.1 - - + +
108C HIS* 1.3 67.6 - - - +
110C ARG* 1.3 87.1 + - + +
111C ALA 2.7 14.6 + - - -
112C SER* 2.8 22.4 + - - -
120C ILE* 2.9 44.8 - - + +
123C VAL* 5.7 0.9 - - + -
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Residues in contact with ARG 110 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106C GLU* 3.0 25.1 + - - +
107C LEU* 3.2 30.0 - - - +
109C TRP* 1.3 97.6 - - + +
111C ALA* 1.3 55.4 + - - +
112C SER 3.5 1.1 - - - -
113C GLN* 3.9 20.3 + - - -
176C TYR* 5.0 2.3 - - - -
180C ILE* 3.3 30.7 + - - +
181C ASN 5.4 0.6 + - - -
182C ILE* 3.5 31.7 - - + +
213C GLU* 5.2 8.3 + - - +
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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