Contacts of the helix formed by residues 143 - 156 (chain A) in PDB entry 3O21
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 PHE 143 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79A GLN* 4.2 18.8 - - + -
104A ASP* 3.1 17.2 + - - +
139A THR* 3.6 34.1 - - + -
142A GLY* 1.3 77.9 - - - -
144A SER* 1.3 58.3 + - - +
145A VAL 3.5 2.2 - - - -
146A LEU* 3.5 28.1 + - + +
147A GLN* 3.0 51.7 + - - +
83B ASN* 5.6 7.9 - - - -
104B ASP* 6.0 4.0 - - + -
105B ALA* 3.8 31.2 - - + -
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Residues in contact with SER 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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104A ASP* 3.1 21.6 + - - -
118A LYS* 3.8 24.7 + - - +
141A ARG 5.7 2.0 - - - -
142A GLY 3.5 1.2 - - - -
143A PHE* 1.3 75.5 - - - +
145A VAL* 1.3 69.9 + - - +
147A GLN* 3.6 5.9 + - - +
148A ALA* 3.2 23.9 + - - +
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Residues in contact with VAL 145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A LEU* 4.8 6.3 - - + +
118A LYS* 4.2 29.2 - - + +
121A ILE* 3.7 28.0 - - + -
135A TYR* 3.7 13.5 - - + +
142A GLY 5.3 1.2 + - - -
143A PHE 3.5 0.2 - - - -
144A SER* 1.3 75.5 - - - +
146A LEU* 1.3 67.7 + - - +
148A ALA* 3.2 6.3 + - - +
149A ILE* 2.9 38.9 + - + +
190A LEU* 5.4 0.2 - - + -
192A ASP* 3.7 21.3 - - - +
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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 TYR* 3.2 36.3 + - + +
137A TYR* 3.8 35.9 - - + +
142A GLY 5.5 2.2 + - - +
143A PHE* 3.5 36.7 + - + +
144A SER 3.4 0.4 - - - -
145A VAL* 1.3 78.7 - - - +
147A GLN* 1.3 68.5 + - + +
149A ILE* 3.3 1.7 + - - +
150A MET* 3.1 59.1 + - + +
192A ASP* 4.4 2.3 + - - +
147B GLN* 5.1 3.1 - - - +
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Residues in contact with GLN 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 PHE* 3.0 41.3 + - + +
144A SER* 4.2 4.1 - - - +
146A LEU* 1.3 83.7 - - + +
148A ALA* 1.3 61.6 + - - +
150A MET* 3.5 3.6 + - - +
151A GLU* 3.0 31.6 + - - +
79B GLN* 4.6 6.0 + - - +
104B ASP* 4.7 5.3 + - - +
143B PHE* 3.2 56.3 - - + -
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Residues in contact with ALA 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A LYS* 3.3 44.6 - - + +
122A LEU* 4.4 15.4 - - + +
144A SER 3.2 9.6 + - - +
145A VAL 3.8 2.9 - - - +
147A GLN* 1.3 74.7 - - - +
149A ILE* 1.3 65.9 + - + +
151A GLU* 4.1 4.8 - - - +
152A ALA* 2.9 26.9 + - - +
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Residues in contact with ILE 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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121A ILE* 4.3 5.4 - - + -
122A LEU* 4.2 10.5 - - + -
125A LEU* 3.5 31.9 - - + -
133A PHE* 4.5 7.2 - - + -
135A TYR* 4.2 27.4 - - + -
145A VAL* 2.9 33.6 + - + +
146A LEU 3.6 4.5 - - - +
148A ALA* 1.3 77.4 - - + +
150A MET* 1.3 54.7 + - + +
152A ALA* 3.2 5.6 + - - +
153A ALA* 2.8 33.4 + - - +
158A TRP* 4.6 2.0 - - + -
160A VAL* 4.3 18.2 - - + -
190A LEU* 3.6 18.6 - - + -
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Residues in contact with MET 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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135A TYR* 5.8 0.4 - - + -
146A LEU* 3.1 41.6 + - + +
147A GLN* 4.0 5.2 - - - +
149A ILE* 1.3 83.2 - - + +
151A GLU* 1.3 62.6 + - + +
154A VAL* 3.1 15.1 + - - +
162A ALA* 4.1 15.3 - - + -
143B PHE* 5.1 11.9 - - + +
146B LEU* 3.8 13.1 - - + +
147B GLN* 2.7 66.0 - - + +
150B MET* 2.9 39.0 - - + +
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Residues in contact with GLU 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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147A GLN* 3.0 22.0 + - - +
148A ALA* 4.1 4.1 - - - +
150A MET* 1.3 75.9 - - - +
152A ALA* 1.3 66.1 + - - +
154A VAL* 3.4 6.5 + - - +
155A GLN* 3.0 43.0 + - - +
137B TYR* 2.8 31.1 + - - +
139B THR* 4.1 8.2 - - - +
143B PHE* 3.5 32.6 - - + -
146B LEU* 4.2 5.4 - - + -
164B SER* 4.3 5.5 + - - -
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Residues in contact with ALA 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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122A LEU* 4.1 14.1 - - + -
148A ALA 2.9 19.0 + - - +
149A ILE 3.5 3.6 - - - +
151A GLU* 1.3 74.6 - - - +
153A ALA* 1.3 58.5 + - - +
155A GLN* 3.7 4.9 - - - -
156A ASN* 2.8 48.9 + - - +
158A TRP* 3.6 22.9 - - + -
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Residues in contact with ALA 153 (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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149A ILE 2.8 14.8 + - - +
151A GLU 3.2 0.2 - - - -
152A ALA* 1.3 73.6 - - - +
154A VAL* 1.3 59.6 + - - +
157A ASN* 3.2 3.8 + - - -
158A TRP* 2.9 45.6 + - + +
160A VAL* 3.4 27.8 - - + -
150B MET* 3.0 32.5 - - + -
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Residues in contact with VAL 154 (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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150A MET 3.1 15.2 + - - +
151A GLU* 3.6 6.1 - - - +
153A ALA* 1.3 77.7 - - - +
155A GLN* 1.3 64.7 + - - +
156A ASN 3.7 0.2 + - - -
157A ASN* 3.8 8.4 + - - +
135B TYR* 5.1 6.1 - - + -
137B TYR* 4.1 10.1 - - + +
146B LEU* 4.1 29.6 - - + +
149B ILE* 5.4 2.9 - - + -
150B MET* 3.8 36.3 - - + +
160B VAL* 4.6 8.2 - - + +
162B ALA* 3.3 35.8 + - + +
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Residues in contact with GLN 155 (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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151A GLU* 3.0 31.9 + - - +
152A ALA* 3.9 4.9 - - - +
154A VAL* 1.3 80.6 - - + +
156A ASN* 1.3 65.7 + - - +
157A ASN* 3.7 7.8 + - - +
137B TYR* 2.8 28.6 + - + +
162B ALA 3.9 15.7 - - - +
163B ARG* 4.2 14.0 + - - +
164B SER* 3.6 22.0 - - - +
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Residues in contact with ASN 156 (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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131A GLU* 5.6 1.9 - - - +
152A ALA* 2.8 42.2 + - - +
155A GLN* 1.3 79.0 + - - +
157A ASN* 1.3 72.8 + - - +
158A TRP* 3.4 35.6 + - + +
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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