Contacts of the helix formed by residues 116 - 125 (chain C) in PDB entry 4OA5
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 GLU 116 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89C LYS* 4.4 6.4 - - + +
115C GLY* 1.3 72.5 - - - -
117C ALA* 1.3 70.1 + - - +
118C LEU* 3.0 38.7 + - - +
119C ALA* 3.2 14.6 + - + +
120C GLN* 3.0 18.4 + - - +
138C ASN* 4.2 4.3 + - - -
145C TYR* 4.1 5.0 + - - -
301C SAH 2.8 33.0 + - + +
140E SER* 4.7 9.3 - - - +
182E ASN* 3.7 42.2 + - + +
185E ALA* 6.3 1.6 - - + -
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Residues in contact with ALA 117 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63C VAL* 3.6 23.1 - - + -
87C ILE* 3.8 14.6 - - + -
116C GLU* 1.3 73.3 - - - +
118C LEU* 1.3 58.4 + - - +
121C LEU* 2.7 38.9 + - + +
145C TYR* 3.5 28.9 - - + +
301C SAH 2.9 21.4 + - + +
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Residues in contact with LEU 118 (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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116C GLU* 3.0 19.3 + - - +
117C ALA* 1.3 77.2 - - - +
119C ALA* 1.3 62.6 + - - +
121C LEU* 3.8 8.8 - - + +
122C ASN* 3.1 21.5 + - - +
141C SER* 5.0 1.6 - - - +
144C ALA* 4.0 24.9 - - + +
145C TYR* 4.3 18.4 - - + -
148C TRP* 6.1 1.6 - - + -
312C IOD 3.4 34.5 - - + -
140E SER 4.7 4.7 - - - +
141E SER* 4.6 9.2 - - - +
143E LEU* 3.6 16.0 - - + +
144E ALA* 3.8 21.3 - - + +
147E ASN* 5.3 10.7 + - - +
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Residues in contact with ALA 119 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116C GLU* 3.2 17.5 + - + +
118C LEU* 1.3 78.9 - - - +
120C GLN* 1.3 69.6 + - - +
122C ASN* 3.2 16.5 + - - +
123C THR* 3.4 12.6 + - - +
143E LEU* 3.4 19.6 - - + +
182E ASN 6.0 0.2 - - - +
185E ALA* 4.5 28.5 - - + +
186E SER* 4.9 3.1 - - - +
189E ALA* 5.3 3.3 - - + +
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Residues in contact with GLN 120 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87C ILE* 3.7 34.3 - - + -
113C LEU* 3.5 25.5 - - + +
114C HIS 3.5 20.9 + - - +
115C GLY* 3.8 17.9 - - - +
116C GLU 3.0 16.9 + - - +
119C ALA* 1.3 82.7 + - - +
121C LEU* 1.3 63.0 + - - +
123C THR* 2.8 36.4 + - - +
124C LEU* 3.2 9.2 + - - +
185E ALA* 6.4 0.4 - - - +
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Residues in contact with LEU 121 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61C VAL* 3.6 30.3 - - + -
63C VAL* 4.4 11.0 - - + -
87C ILE* 3.7 12.5 - - + +
117C ALA 2.7 26.7 + - - +
118C LEU* 3.8 9.6 - - + +
120C GLN* 1.3 71.2 - - - +
122C ASN* 1.3 63.7 + - - +
124C LEU* 3.0 15.2 + - + +
125C LYS 3.2 6.6 + - - -
133C ILE* 4.8 1.1 - - + -
145C TYR* 3.8 31.9 - - + -
148C TRP* 3.1 59.8 + - + +
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Residues in contact with ASN 122 (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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118C LEU 3.1 14.3 + - - +
119C ALA 3.3 12.1 - - - +
120C GLN 3.2 0.2 - - - -
121C LEU* 1.3 77.2 - - - +
123C THR* 1.3 62.0 + - + +
125C LYS* 3.3 51.2 + - - +
126C GLU* 4.6 2.4 - - - +
148C TRP* 4.4 1.5 - - - +
143E LEU* 3.9 28.7 - - + +
146E LEU* 6.0 0.4 - - - +
147E ASN* 4.7 11.9 + - - +
150E LYS* 5.1 1.0 - - - +
189E ALA* 3.6 21.3 - - + +
193E GLU* 4.9 9.2 - - - +
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Residues in contact with THR 123 (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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113C LEU* 4.3 4.7 - - - +
119C ALA 3.6 13.7 - - - +
120C GLN* 2.8 34.5 + - - +
122C ASN* 1.3 79.4 - - + +
124C LEU* 1.3 67.1 + - - +
125C LYS 3.5 0.3 + - - -
126C GLU* 3.9 18.4 + - - +
127C MET* 5.3 3.1 - - - +
189E ALA* 6.5 0.9 - - + -
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Residues in contact with LEU 124 (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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61C VAL* 3.9 26.9 - - + -
85C TYR* 3.8 33.9 - - + -
87C ILE* 4.3 9.0 - - + -
113C LEU* 3.8 21.3 - - + -
120C GLN 3.2 11.6 + - - +
121C LEU* 3.0 11.7 + - + +
123C THR* 1.3 80.6 + - - +
125C LYS* 1.3 64.4 + - - +
126C GLU 3.1 3.4 - - - -
127C MET* 3.0 42.0 + - + +
130C PHE* 3.4 23.0 - - + -
148C TRP* 4.2 7.0 - - + -
317C IOD 4.5 3.6 - - + -
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Residues in contact with LYS 125 (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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121C LEU 3.2 10.5 + - - +
122C ASN* 3.3 43.7 - - - +
123C THR 3.3 0.4 - - - -
124C LEU* 1.3 77.6 - - - +
126C GLU* 1.3 83.8 + - - +
128C ALA* 3.1 24.3 + - - +
148C TRP* 4.1 5.4 - - + +
152C TYR* 3.3 44.8 + - + +
147E ASN* 5.3 1.3 - - - +
150E LYS* 3.8 8.1 - - - +
193E GLU* 3.1 27.8 + - - -
199E LYS* 5.3 8.1 - - - +
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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