Contacts of the helix formed by residues 141 - 152 (chain E) 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 SER 141 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118C LEU* 4.6 4.7 - - - +
312C IOD 3.2 29.5 - - - +
138E ASN* 3.1 31.9 + - - -
140E SER* 1.3 79.0 + - - +
142E TYR* 1.3 64.5 + - - +
143E LEU 3.1 3.6 - - - -
144E ALA* 3.0 13.2 + - - +
145E TYR* 3.1 30.4 + - - -
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Residues in contact with TYR 142 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135E ILE* 3.4 28.7 + - + -
136E ASP* 3.9 9.2 + - - -
137E ALA 3.3 23.4 + - - -
138E ASN 3.5 9.9 - - - -
139E LYS* 3.2 35.6 + - + +
140E SER 3.5 0.6 - - - -
141E SER* 1.3 77.8 - - - +
143E LEU* 1.3 57.5 + - - +
145E TYR* 3.2 8.1 + + - +
146E LEU 2.9 24.3 + - - -
161E ALA* 3.8 15.5 - - + -
162E ASP 2.7 30.2 + - - -
163E ASN* 4.5 1.7 + - - +
164E THR* 4.3 0.7 - - + -
186E SER* 3.6 5.1 + - - +
187E MET* 3.5 25.8 - - + -
190E PHE* 3.6 37.2 - + + -
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Residues in contact with LEU 143 (chain E).
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* 3.6 17.9 - - + +
119C ALA* 3.4 37.5 - - + +
122C ASN* 3.9 26.5 - - + +
140E SER 5.7 0.4 - - - +
141E SER 3.1 1.6 - - - -
142E TYR* 1.3 78.3 - - - +
144E ALA* 1.3 58.2 - - - +
146E LEU* 3.2 12.3 + - + +
147E ASN* 2.9 39.5 + - - +
186E SER* 3.7 20.0 + - - +
189E ALA* 3.9 12.3 - - + +
190E PHE* 3.7 29.4 - - - +
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Residues in contact with ALA 144 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118C LEU* 3.8 34.5 - - + +
144C ALA* 4.2 6.5 - - + -
147C ASN* 5.0 0.9 + - - -
312C IOD 4.2 3.8 - - + -
118E LEU* 4.0 24.9 - - + +
141E SER* 3.0 10.7 + - - +
143E LEU* 1.3 77.4 - - - +
145E TYR* 1.3 64.1 + - - +
147E ASN* 3.4 7.8 + - - +
148E TRP* 3.1 21.8 + - - +
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Residues in contact with TYR 145 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63E VAL* 4.0 11.9 - - + +
116E GLU* 4.2 4.2 + - - -
117E ALA* 3.5 32.7 - - + +
118E LEU* 4.3 15.4 - - + +
121E LEU* 3.8 18.8 - - + -
133E ILE* 4.4 9.3 - - + +
135E ILE* 3.8 37.9 - - + -
137E ALA* 3.5 21.4 - - - +
138E ASN* 3.3 26.2 + - - +
141E SER* 3.1 33.5 + - - -
142E TYR* 3.6 6.3 - - - +
144E ALA* 1.3 79.5 - - - +
146E LEU* 1.3 61.4 + - - +
148E TRP* 3.3 8.5 + - - +
149E ALA* 3.0 22.2 + - - +
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Residues in contact with LEU 146 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122C ASN* 6.0 0.4 - - - +
135E ILE* 4.5 2.8 - - - +
142E TYR 2.9 13.6 + - - +
143E LEU* 3.2 14.3 + - + +
145E TYR* 1.3 76.8 - - - +
147E ASN* 1.3 59.1 + - - +
149E ALA* 3.0 6.7 + - - +
150E LYS* 2.9 35.9 + - + +
159E ILE* 3.9 25.1 - - + -
190E PHE* 3.9 31.2 - - + +
193E GLU* 3.5 33.9 - - + -
194E LEU* 3.8 24.2 - - + -
200E TYR* 4.5 7.4 - - - +
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Residues in contact with ASN 147 (chain E).
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* 5.3 9.9 + - - +
122C ASN* 4.7 12.7 + - - +
125C LYS* 5.3 1.2 - - - +
144C ALA 5.7 1.4 + - - +
147C ASN* 3.3 15.7 + - + +
148C TRP* 4.1 27.3 - - - +
151C MET* 3.9 21.1 - - + +
152C TYR* 5.3 1.3 - - - -
143E LEU* 2.9 26.5 + - - +
144E ALA* 3.7 8.4 - - - +
145E TYR 3.3 0.2 - - - -
146E LEU* 1.3 79.3 - - - +
148E TRP* 1.3 63.0 + - - +
150E LYS* 3.4 38.6 + - - +
151E MET* 3.6 4.3 + - - +
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Residues in contact with TRP 148 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147C ASN* 3.5 10.2 - - - +
313C IOD 3.9 4.0 - - + -
314C IOD 3.8 19.8 - - + +
61E VAL* 4.0 11.9 - - + -
118E LEU* 6.1 1.3 - - + -
121E LEU* 3.1 64.9 + - + +
124E LEU* 4.2 9.0 - - + -
125E LYS* 4.2 4.6 - - - +
130E PHE* 3.9 20.6 - + - -
133E ILE* 4.1 17.5 - - + -
144E ALA 3.1 12.5 + - - +
145E TYR* 3.5 10.3 - - - +
147E ASN* 1.3 75.4 - - - +
149E ALA* 1.3 65.5 + - - +
151E MET* 3.1 3.8 + - - -
152E TYR* 3.0 71.4 + + + -
153E ILE* 4.3 15.0 - - + -
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Residues in contact with ALA 149 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133E ILE* 4.0 17.3 - - + -
135E ILE* 5.7 0.4 - - + -
145E TYR 3.0 13.8 + - - +
146E LEU* 3.0 11.6 + - - +
148E TRP* 1.3 81.4 - - + +
150E LYS* 1.3 62.8 + - - +
152E TYR 4.3 0.2 - - - +
153E ILE* 3.0 48.0 + - + +
159E ILE* 4.2 14.6 - - + -
216E LYS* 3.4 6.0 - - - -
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Residues in contact with LYS 150 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122C ASN* 5.1 0.6 - - - +
125C LYS* 3.8 13.5 - - - +
151C MET* 4.5 13.5 - - - -
152C TYR* 3.2 25.9 + - - -
146E LEU* 2.9 29.0 + - + +
147E ASN* 3.5 32.7 + - + +
148E TRP 3.2 0.4 - - - -
149E ALA* 1.3 74.5 - - - +
151E MET* 1.3 60.2 + - - +
159E ILE* 5.8 0.4 - - + -
193E GLU* 3.5 25.3 + - - +
199E LYS* 5.6 6.7 - - - +
200E TYR* 3.4 22.0 - - + +
216E LYS* 3.3 25.7 + - - +
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Residues in contact with MET 151 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147C ASN* 3.4 20.9 - - - +
150C LYS* 4.0 14.4 - - + -
151C MET* 3.8 37.2 - - + +
123D THR* 5.0 10.9 - - - +
126D GLU* 3.5 32.6 - - + +
127D MET* 5.2 4.2 - - - +
129E PRO* 5.6 1.6 - - - +
147E ASN 3.6 3.8 + - - +
148E TRP 3.1 8.1 + - - +
149E ALA 3.1 0.4 - - - -
150E LYS* 1.3 80.2 - - - +
152E TYR* 1.3 96.0 + - + +
153E ILE 3.7 4.0 - - - +
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Residues in contact with TYR 152 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147C ASN* 4.4 7.4 - - - -
150C LYS* 4.2 4.5 - - - -
314C IOD 4.6 1.1 - - + -
126D GLU* 3.3 38.0 + - + +
127D MET* 4.1 10.5 - - - -
125E LYS* 3.5 32.7 - - + +
128E ALA* 3.5 25.1 - - + -
129E PRO* 3.2 8.0 - - - +
130E PHE* 2.9 28.1 + - - -
148E TRP* 3.0 69.7 + + + +
151E MET* 1.3 101.9 - - + +
153E ILE* 1.3 64.0 + - - +
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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