Contacts of the helix formed by residues 141 - 152 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118A LEU* 4.4 2.5 - - - +
138A ASN* 3.1 17.2 + - - -
139A LYS 3.1 1.2 - - - -
140A SER* 1.3 80.9 + - - +
142A TYR* 1.3 64.1 + - - +
143A LEU 3.2 3.1 - - - -
144A ALA* 3.1 7.0 + - - +
145A TYR* 3.0 52.3 + - - -
182D ASN* 2.7 35.8 + - - -
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Residues in contact with TYR 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A ILE* 3.4 32.7 + - + -
136A ASP* 3.8 9.0 + - - -
137A ALA 3.4 25.0 + - - -
138A ASN 3.5 10.5 - - - -
139A LYS* 3.2 26.4 + - + +
141A SER* 1.3 77.2 - - - +
143A LEU* 1.3 57.9 + - - +
145A TYR* 3.1 8.5 + + - +
146A LEU 2.9 25.5 + - - -
161A ALA* 3.8 15.5 - - + -
162A ASP 2.6 30.3 + - - -
163A ASN* 4.4 0.7 - - - +
164A THR* 4.3 0.4 - - + -
186A SER* 3.4 4.2 + - - +
187A MET* 3.4 31.9 - - + -
190A PHE* 3.5 35.3 - + + -
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Residues in contact with LEU 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A SER 5.7 0.2 - - - +
141A SER 3.2 0.6 - - - -
142A TYR* 1.3 78.3 - - - +
144A ALA* 1.3 56.7 + - - +
146A LEU* 3.3 7.0 + - + +
147A ASN* 2.9 37.8 + - - +
186A SER* 3.3 17.7 + - - +
189A ALA* 4.0 32.8 - - + +
190A PHE* 4.0 14.8 - - - +
318A IOD 3.7 27.8 - - + -
185D ALA* 3.6 34.1 - - + +
189D ALA* 4.1 11.2 - - + -
316D IOD 4.2 16.4 - - + -
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Residues in contact with ALA 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118A LEU* 3.8 21.6 - - + +
141A SER* 3.1 10.0 + - - +
143A LEU* 1.3 78.4 - - - +
145A TYR* 1.3 62.1 + - - +
147A ASN* 3.3 5.9 + - - +
148A TRP* 3.0 21.8 + - - +
181D SER* 4.2 18.5 - - - +
182D ASN* 3.6 23.3 - - - +
185D ALA* 4.0 11.1 - - + +
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Residues in contact with TYR 145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A VAL* 3.9 15.2 - - + +
117A ALA* 3.5 33.3 - - + +
118A LEU* 3.8 23.4 - - + +
121A LEU* 3.8 17.7 - - + -
133A ILE* 4.4 8.9 - - + +
135A ILE* 3.8 39.9 - - + -
137A ALA* 5.0 0.4 - - + -
138A ASN* 2.5 39.3 + - - -
141A SER* 3.0 33.8 + - - -
142A TYR* 3.1 6.9 + + - +
144A ALA* 1.3 72.4 - - - +
146A LEU* 1.3 62.4 + - - +
148A TRP* 3.2 7.1 + - - +
149A ALA* 2.9 27.2 + - - +
301A SAH 3.7 4.2 + - - -
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Residues in contact with LEU 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A ILE* 4.4 2.8 - - - +
142A TYR 2.9 13.4 + - - +
143A LEU* 3.5 13.7 - - + +
145A TYR* 1.3 78.0 - - - +
147A ASN* 1.3 57.8 + - - +
149A ALA* 3.0 5.2 + - - +
150A LYS* 2.9 41.3 + - + +
159A ILE* 3.9 24.9 - - + -
190A PHE* 3.7 32.3 - - + +
193A GLU* 3.5 34.1 - - + -
194A LEU* 3.8 26.2 - - + -
200A TYR* 4.5 1.6 - - - +
318A IOD 4.6 0.4 - - + -
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Residues in contact with ASN 147 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143A LEU* 2.9 21.4 + - - +
144A ALA* 3.7 8.1 - - - +
145A TYR 3.3 0.2 - - - -
146A LEU* 1.3 77.2 - - - +
148A TRP* 1.3 63.4 + - - +
150A LYS* 3.4 19.3 + - + +
151A MET 3.7 0.7 + - - -
318A IOD 2.8 40.1 - - - +
173D GLU* 5.2 7.3 - - - +
174D HIS* 3.5 29.7 + - + -
175D PRO* 5.5 7.6 - - + -
184D HIS* 5.2 4.4 + - - +
185D ALA* 3.6 27.4 - - + +
188D ARG* 5.5 3.6 - - - +
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Residues in contact with TRP 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A VAL* 4.1 8.1 - - + -
118A LEU* 5.9 2.9 - - + -
121A LEU* 3.2 70.8 + - + +
122A ASN* 5.4 0.2 - - - -
124A LEU* 4.3 8.7 - - + -
125A LYS* 4.0 8.8 - - - +
130A PHE* 3.9 22.2 - + - -
133A ILE* 4.0 17.5 - - + -
144A ALA 3.0 13.7 + - - +
145A TYR* 3.5 9.9 - - - +
147A ASN* 1.3 76.5 - - - +
149A ALA* 1.3 64.9 + - - +
151A MET 3.0 3.5 + - - -
152A TYR* 3.0 76.5 + + + -
153A ILE* 4.3 15.7 - - + -
311A IOD 4.1 19.7 - - + -
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Residues in contact with ALA 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133A ILE* 4.0 19.5 - - + -
135A ILE* 5.6 0.2 - - + -
145A TYR 2.9 13.2 + - - +
146A LEU* 3.0 12.3 + - - +
148A TRP* 1.3 79.3 - - - +
150A LYS* 1.3 64.3 + - - +
153A ILE* 3.0 47.9 + - + +
159A ILE* 4.2 13.9 - - + -
216A LYS* 3.4 5.3 - - - -
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Residues in contact with LYS 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146A LEU* 2.9 27.9 + - + +
147A ASN* 3.4 23.2 - - - +
148A TRP 3.3 0.2 - - - -
149A ALA* 1.3 76.4 - - - +
151A MET* 1.3 59.6 + - - +
159A ILE* 5.4 0.9 - - + +
193A GLU* 3.4 17.4 + - - +
199A LYS* 3.9 8.2 - - - +
200A TYR* 3.3 22.7 - - + +
216A LYS* 3.3 26.2 + - - +
318A IOD 2.9 32.5 - - - +
173D GLU* 3.5 29.8 + - - +
174D HIS* 4.1 9.9 - - + +
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Residues in contact with MET 151 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129A PRO* 5.6 1.7 - - - +
147A ASN 3.7 1.3 + - - +
148A TRP* 3.0 4.2 + - - +
150A LYS* 1.3 80.7 - - - +
152A TYR* 1.3 102.9 + - + +
153A ILE 3.8 3.9 + - - +
174D HIS* 3.1 53.6 - - + +
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Residues in contact with TYR 152 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125A LYS* 3.4 43.5 + - + +
128A ALA* 3.5 23.6 - - + -
129A PRO* 3.2 8.2 - - - +
130A PHE* 2.9 27.9 + - - -
148A TRP* 3.0 70.7 + + + +
151A MET* 1.3 113.6 - - + +
153A ILE* 1.3 63.7 + - - +
154A ARG 4.1 0.2 - - - -
311A IOD 4.2 7.0 - - + -
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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