Contacts of the helix formed by residues 149 - 165 (chain A) in PDB entry 3E6D
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 PRO 149 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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150A THR* 1.3 73.9 + - - +
151A ILE* 3.0 14.0 - - + -
152A ARG* 3.0 34.1 + - + +
153A ILE 3.8 1.0 + - - -
189A VAL* 3.3 35.5 - - + +
193A THR* 5.5 3.4 - - + -
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Residues in contact with THR 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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149A PRO* 1.3 82.2 - - - +
151A ILE* 1.3 63.6 + - + +
153A ILE* 3.2 17.5 + - - +
154A LEU* 3.2 28.9 + - + +
193A THR* 4.1 12.3 - - - +
197A VAL* 3.8 32.1 - - + +
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Residues in contact with ILE 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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149A PRO* 3.0 9.7 - - + +
150A THR* 1.3 80.9 - - + +
152A ARG* 1.3 58.6 + - + +
154A LEU* 3.2 9.4 + - + +
155A ARG* 2.8 44.9 + - + +
225A LEU 4.2 18.4 - - - +
226A SER 4.2 11.2 - - - -
185B GLU* 5.4 3.8 - - + +
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Residues in contact with ARG 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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149A PRO* 3.0 29.5 + - + +
151A ILE* 1.3 79.2 - - + +
153A ILE* 1.3 57.8 + - - +
155A ARG* 3.4 2.7 + - - +
156A LEU* 3.1 27.0 + - - +
187A THR* 2.8 46.5 + - - +
188A GLY* 4.1 14.1 + - - -
189A VAL* 4.3 4.9 - - - +
152B ARG* 4.5 7.5 - - - +
185B GLU 3.3 23.1 - - - +
186B ILE* 3.4 18.6 - - - +
188B GLY* 3.5 29.4 + - - +
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Residues in contact with ILE 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 PRO 4.9 0.9 - - - +
150A THR* 3.2 9.3 + - - +
152A ARG* 1.3 73.8 - - - +
154A LEU* 1.3 66.2 + - + +
156A LEU* 3.4 6.0 + - + +
157A PHE* 3.2 44.6 + - + -
183A ILE* 4.1 21.5 - - + -
187A THR* 4.1 15.7 - - - +
189A VAL* 4.0 16.2 - - + -
193A THR* 4.9 0.2 - - + -
194A VAL* 3.8 39.3 - - + -
197A VAL* 4.0 31.0 - - + -
198A LEU* 4.4 3.4 - - + -
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Residues in contact with LEU 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 THR* 3.2 26.6 + - + +
151A ILE* 3.2 11.3 + - + +
153A ILE* 1.3 78.6 - - - +
155A ARG* 1.3 56.9 + - - +
157A PHE* 3.4 3.7 + - + +
158A TYR* 3.0 29.1 + - - +
197A VAL* 4.5 7.9 - - + -
201A LEU* 3.9 36.1 - - + -
222A LEU* 4.0 19.3 - - + +
225A LEU* 3.6 42.0 - - + +
226A SER* 3.8 15.5 - - - +
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Residues in contact with ARG 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 ILE* 2.8 34.8 + - + +
152A ARG* 3.7 7.2 - - - +
154A LEU* 1.3 73.6 - - - +
156A LEU* 1.3 65.1 + - - +
158A TYR* 3.5 22.2 - - - +
159A GLU* 2.4 66.5 + - - +
226A SER* 4.1 24.0 + - - -
181B LYS* 5.3 0.4 - - - +
182B SER* 3.3 23.6 + - - +
185B GLU* 2.9 40.9 + - + +
186B ILE* 4.0 10.8 - - + -
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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 ARG 3.1 14.4 + - - +
153A ILE* 3.6 9.6 - - + +
155A ARG* 1.3 77.4 - - - +
157A PHE* 1.3 66.2 + - + +
159A GLU* 3.9 1.2 - - - +
160A LEU* 3.0 44.5 + - + +
178A LEU* 4.4 10.8 - - + -
183A ILE* 4.2 28.7 - - + -
186A ILE* 4.5 20.4 - - + -
187A THR* 4.5 8.3 - - + -
156B LEU* 4.1 20.0 - - + -
186B ILE* 3.8 29.8 - - + +
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Residues in contact with PHE 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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153A ILE* 3.2 38.5 + - + -
154A LEU* 3.4 7.4 + - - +
156A LEU* 1.3 80.9 - - + +
158A TYR* 1.3 57.9 + - - +
160A LEU* 3.4 6.2 + - + +
161A CYS* 2.8 31.7 + - - +
174A ILE* 4.6 2.3 - - + +
178A LEU* 3.9 15.5 - - + -
183A ILE* 3.8 20.9 - - + -
198A LEU* 3.9 27.1 - - + -
201A LEU* 4.1 13.7 - - + -
207A LEU* 3.6 34.3 - - + -
209A LYS* 5.4 3.8 - - + -
214A ILE* 3.9 29.8 - - + -
216A VAL* 5.6 0.5 - - - +
222A LEU* 4.1 9.0 - - + -
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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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154A LEU 3.0 18.1 + - - +
155A ARG* 3.5 30.1 - - - +
156A LEU 3.2 0.2 - - - -
157A PHE* 1.3 76.6 - - - +
159A GLU* 1.3 65.7 - - - +
161A CYS* 3.3 1.2 + - - +
162A SER* 3.0 42.2 + - - -
219A LEU* 3.9 27.6 - - + -
222A LEU* 3.9 12.3 - - + +
223A LYS* 2.9 61.8 + - + -
226A SER* 4.5 9.4 - - - +
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Residues in contact with GLU 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 ARG* 2.4 49.8 + - - +
156A LEU 3.9 2.7 - - - +
158A TYR* 1.3 81.7 - - - +
160A LEU* 1.3 60.4 + - + +
162A SER* 3.5 8.9 + - - -
163A SER* 2.9 29.3 + - - -
176B MET* 3.8 16.3 - - + +
177B PRO 4.0 16.3 - - - +
178B LEU* 4.3 5.7 - - + +
182B SER* 3.2 20.9 + - - -
186B ILE* 3.9 20.9 - - + -
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Residues in contact with LEU 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* 3.0 37.8 + - + +
157A PHE* 3.6 10.3 - - + +
159A GLU* 1.3 79.4 - - + +
161A CYS* 1.3 57.0 - - - +
163A SER* 4.2 2.2 - - - -
164A GLN* 2.8 40.6 + - + +
165A GLY 3.6 0.2 + - - -
174A ILE* 4.0 10.3 - - + +
176A MET* 3.7 31.0 - - + -
178A LEU* 3.8 24.9 - - + -
214A ILE* 4.9 2.5 - - + -
156B LEU* 5.9 0.2 - - + -
160B LEU* 3.8 29.8 - - + -
176B MET* 4.3 9.4 - - + -
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Residues in contact with CYS 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 PHE 2.8 17.9 + - - +
158A TYR* 3.3 4.5 + - - +
160A LEU* 1.3 78.9 - - - +
162A SER* 1.3 58.6 + - - +
165A GLY* 3.0 27.0 + - - +
172A TYR* 3.5 37.9 - - - -
174A ILE* 3.5 16.8 - - + -
216A VAL* 3.6 21.5 - - + -
219A LEU* 3.9 24.5 - - + -
222A LEU* 4.9 0.4 - - + -
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Residues in contact with SER 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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158A TYR* 3.0 38.0 + - - -
159A GLU* 3.5 15.4 + - - -
161A CYS* 1.3 76.9 - - - +
163A SER* 1.3 61.4 + - - +
165A GLY 4.7 1.9 - - - +
172A TYR* 6.0 2.2 - - - -
219A LEU* 5.5 6.9 - - - +
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Residues in contact with SER 163 (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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159A GLU* 2.9 20.8 + - - -
160A LEU 3.8 0.7 + - - -
161A CYS 3.3 0.2 - - - -
162A SER* 1.3 83.7 + - - +
164A GLN* 1.3 89.1 + - - +
165A GLY 3.6 0.9 - - - -
175B THR 4.6 3.1 - - - +
176B MET* 3.5 24.9 - - - +
177B PRO* 4.2 17.3 - - - -
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Residues in contact with GLN 164 (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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160A LEU* 2.8 22.5 + - + +
163A SER* 1.3 114.9 + - - +
165A GLY* 1.3 63.9 + - - +
166A LYS* 3.9 10.0 + - - +
173A GLU 4.2 3.5 - - - +
174A ILE* 3.9 19.0 - - + +
175A THR 5.4 0.5 + - - -
176A MET* 5.4 1.8 - - - -
164B GLN* 3.0 49.8 - - + +
166B LYS* 5.6 3.3 + - - -
174B ILE* 5.3 0.8 - - - +
175B THR* 3.8 17.6 + - - +
176B MET* 4.0 12.9 - - - +
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Residues in contact with GLY 165 (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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160A LEU 3.6 1.0 + - - -
161A CYS* 3.0 20.5 + - - +
162A SER 5.4 1.0 - - - +
163A SER 3.6 1.4 - - - -
164A GLN* 1.3 80.0 - - - +
166A LYS* 1.3 64.3 + - - +
167A ARG 4.1 0.3 + - - -
172A TYR* 4.0 16.3 - - - -
173A GLU 3.4 9.0 - - - -
174A ILE* 3.8 11.4 - - - -
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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