Contacts of the helix formed by residues 143 - 162 (chain A) in PDB entry 3M62
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 THR 143 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99A VAL* 4.7 2.7 - - + -
103A GLN* 2.9 36.4 + - - +
138A ALA* 3.0 23.6 + - + +
141A GLU* 4.5 15.5 - - + +
142A GLY* 1.3 78.8 - - - +
144A ALA* 1.3 66.2 + - - +
145A LEU 3.3 3.9 + - - +
146A ASP* 2.9 30.7 + - - -
147A LEU 3.5 1.0 + - - -
52B GLN* 5.1 9.6 - - - +
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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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135A ILE 5.5 0.2 - - - +
138A ALA* 3.4 13.5 + - + -
139A ILE* 4.0 21.5 - - + -
142A GLY* 3.8 1.8 - - - -
143A THR* 1.3 77.2 - - - +
145A LEU* 1.3 61.3 + - - +
147A LEU* 3.0 7.9 + - - +
148A LEU* 3.0 24.1 + - - +
189A PRO* 5.5 3.1 - - + +
190A ILE* 3.9 24.0 - - + +
193A ILE* 4.4 10.3 - - + -
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Residues in contact with LEU 145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A THR 3.3 1.0 - - - -
144A ALA* 1.3 73.6 - - - +
146A ASP* 1.3 67.8 + - - +
148A LEU* 3.1 5.9 + - + +
149A ASN* 2.8 45.1 + - - +
193A ILE* 3.8 29.1 - - + +
196A LYS* 4.0 33.9 - - + +
197A ILE* 4.2 14.1 - - + +
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Residues in contact with ASP 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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102A LEU 4.2 1.2 - - - +
103A GLN* 3.6 24.6 + - + +
143A THR* 2.9 28.1 + - - +
144A ALA 3.3 0.6 - - - -
145A LEU* 1.3 78.7 - - - +
147A LEU* 1.3 63.7 + - - +
149A ASN* 3.5 7.3 + - - +
150A ALA* 3.4 18.0 + - - +
50B VAL* 6.1 0.5 - - - +
52B GLN* 6.2 0.2 - - - +
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Residues in contact with LEU 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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99A VAL* 5.1 1.3 - - + +
102A LEU* 3.5 40.8 - - + +
103A GLN* 3.8 10.0 + - + +
134A ILE* 4.1 13.7 - - + -
135A ILE* 3.8 40.8 - - + +
138A ALA* 4.0 15.5 - - + -
143A THR 3.5 6.0 + - - +
144A ALA* 3.0 14.0 + - - +
146A ASP* 1.3 78.5 - - - +
148A LEU* 1.3 62.8 + - + +
150A ALA* 3.1 5.7 + - - +
151A VAL* 3.0 33.6 + - + +
184A PHE* 4.0 13.5 - - + -
190A ILE* 5.5 2.5 - - + -
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Residues in contact with LEU 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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144A ALA 3.0 14.1 + - - +
145A LEU* 3.6 7.6 - - + +
147A LEU* 1.3 75.9 - - + +
149A ASN* 1.3 58.3 + - - +
151A VAL* 4.6 0.4 - - - -
152A PHE* 2.9 46.6 + - + +
153A PRO* 3.3 4.9 - - - +
184A PHE* 3.6 32.8 - - + -
190A ILE* 4.0 34.1 - - + +
193A ILE* 4.0 26.9 - - + -
194A PHE* 4.6 3.1 - - + -
197A ILE* 3.7 28.2 - - + +
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Residues in contact with ASN 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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145A LEU* 2.8 40.0 + - - +
146A ASP* 4.0 7.4 + - - +
147A LEU 3.2 0.2 - - - -
148A LEU* 1.3 77.1 - - - +
150A ALA* 1.3 58.6 + - - +
153A PRO* 3.2 22.4 - - - +
154A THR* 5.2 0.3 + - - -
196A LYS 4.7 0.8 + - - -
197A ILE* 3.3 8.7 - - - +
198A ASP* 2.8 56.1 + - - +
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Residues in contact with ALA 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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102A LEU* 3.3 28.9 - - + +
103A GLN* 4.5 1.6 - - - +
113A PHE* 3.7 40.8 - - + +
117A ILE* 4.5 1.2 - - - +
146A ASP 3.4 8.7 + - - +
147A LEU 3.1 3.0 + - - +
149A ASN* 1.3 78.3 - - - +
151A VAL* 1.3 60.3 + - + +
154A THR* 2.7 32.1 + - - +
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Residues in contact with VAL 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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102A LEU* 4.3 16.8 - - + -
117A ILE* 4.3 19.8 - - + +
120A ILE* 6.4 1.3 - - + -
131A LEU* 6.1 0.2 - - + -
147A LEU* 3.0 39.1 + - + +
148A LEU* 3.2 0.4 + - - -
150A ALA* 1.3 81.1 - - - +
152A PHE* 1.3 86.3 + - + +
154A THR* 3.3 2.3 + - - -
155A LEU* 2.9 28.8 + - + +
180A ILE* 4.5 9.2 - - + -
184A PHE* 3.9 23.1 - - + -
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Residues in contact with PHE 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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148A LEU* 2.9 35.4 + - + +
151A VAL* 1.3 84.5 - - + +
153A PRO* 1.3 70.1 - - + +
155A LEU* 3.1 22.7 + - + +
156A LEU* 3.1 17.3 + - - +
180A ILE* 4.1 6.5 - - + -
181A PHE* 3.7 51.8 - + - -
184A PHE* 3.6 42.4 - + + -
194A PHE* 3.8 16.8 - + - -
197A ILE* 4.0 11.2 - - + -
216A ILE* 3.7 17.7 - - + +
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Residues in contact with PRO 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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148A LEU 3.3 8.3 - - - +
149A ASN* 3.2 31.4 - - - +
152A PHE* 1.3 90.1 - - + +
154A THR* 1.3 57.8 + - - +
156A LEU* 3.0 27.2 + - + +
157A GLU* 3.2 7.8 + - - +
197A ILE* 3.7 9.4 - - + -
198A ASP* 3.8 25.6 - - + +
216A ILE* 3.8 9.2 - - + -
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Residues in contact with THR 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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113A PHE* 3.4 43.3 - - - +
114A ILE* 3.7 12.9 - - + +
117A ILE* 3.7 21.3 - - + -
149A ASN 5.2 0.2 + - - -
150A ALA* 2.7 25.6 + - - -
151A VAL 3.3 3.3 + - - -
152A PHE 3.2 0.6 - - - -
153A PRO* 1.3 75.2 - - - +
155A LEU* 1.3 60.3 + - - +
157A GLU* 3.6 9.2 + - - +
158A TYR* 3.0 26.3 + - - +
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Residues in contact with LEU 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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117A ILE* 3.7 23.1 - - + -
121A VAL* 3.8 19.3 - - + -
151A VAL* 2.9 19.0 + - + +
152A PHE* 3.1 28.2 + - + +
154A THR* 1.3 74.4 - - - +
156A LEU* 1.3 67.5 + - - +
158A TYR* 3.7 5.7 - - + +
159A CYS* 3.1 28.1 + - - -
177A VAL* 4.2 19.5 - - + -
180A ILE* 3.8 36.3 - - + -
181A PHE* 4.2 13.2 - - + -
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Residues in contact with LEU 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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152A PHE 3.1 7.4 + - - +
153A PRO* 3.0 17.1 + - + +
155A LEU* 1.3 74.6 - - - +
157A GLU* 1.3 57.3 + - - +
159A CYS* 2.9 21.5 + - - +
160A ASN* 2.9 20.6 + - - +
199A GLY* 4.8 3.4 - - - +
213A ARG 3.8 12.6 - - - +
214A LYS* 3.5 29.4 - - - +
215A THR 3.3 26.7 - - - +
216A ILE* 4.0 22.2 - - + +
219A PRO* 3.6 23.8 - - + -
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Residues in contact with GLU 157 (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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114A ILE* 4.2 25.4 - - + +
153A PRO 3.2 6.9 + - - +
154A THR* 3.8 10.3 - - - +
156A LEU* 1.3 73.6 - - - +
158A TYR* 1.3 62.3 + - - +
160A ASN* 4.0 7.6 - - - +
161A LYS* 2.8 51.2 + - + +
162A HIS* 3.9 15.4 + - - -
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Residues in contact with TYR 158 (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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114A ILE* 3.8 13.1 - - + +
117A ILE* 4.3 5.4 - - + -
118A THR* 3.5 42.2 + - + +
121A VAL* 3.7 36.7 - - + +
122A SER* 5.3 2.9 + - - -
154A THR 3.0 19.2 + - - +
155A LEU* 3.7 9.6 - - + +
157A GLU* 1.3 74.9 - - - +
159A CYS* 1.3 69.6 - - - +
162A HIS* 3.2 40.9 + + + -
163A VAL* 3.3 28.3 - - + +
173A ILE* 3.7 34.4 - - + +
177A VAL* 4.6 2.5 - - + -
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Residues in contact with CYS 159 (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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155A LEU* 3.1 23.9 + - - -
156A LEU* 2.9 9.6 + - - +
158A TYR* 1.3 88.0 - - - +
160A ASN* 1.3 59.5 + - - +
163A VAL* 4.3 11.6 - - - +
166A PHE* 3.4 61.4 + - + +
177A VAL* 4.5 11.9 - - - -
219A PRO* 4.0 20.6 - - + -
220A ILE* 6.0 0.4 - - - -
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Residues in contact with ASN 160 (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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156A LEU* 2.9 32.6 + - - +
157A GLU* 4.0 4.5 - - - +
159A CYS* 1.3 80.5 - - - +
161A LYS* 1.3 74.0 + - + +
162A HIS 3.9 0.2 - - - -
163A VAL 4.2 7.8 - - - +
164A SER 5.6 0.9 - - - +
213A ARG* 3.1 62.2 + - - +
214A LYS* 5.2 1.2 - - - +
219A PRO* 4.5 5.2 - - - +
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Residues in contact with LYS 161 (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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157A GLU* 2.8 37.7 + - + +
160A ASN* 1.3 89.7 - - + +
162A HIS* 1.3 72.3 + - + +
163A VAL 3.5 4.6 - - - +
213A ARG* 6.0 2.2 - - - +
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Residues in contact with HIS 162 (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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114A ILE* 3.5 43.1 - - + +
115A ASN* 5.8 2.7 - - - -
118A THR* 4.2 9.4 + - + +
157A GLU* 3.9 13.0 + - - -
158A TYR* 3.2 29.8 + - + +
161A LYS* 1.3 95.3 - - + +
163A VAL* 1.3 61.8 + - - +
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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