Contacts of the helix formed by residues 151 - 165 (chain B) in PDB entry 3SI5
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 LEU 151 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116B TYR 5.2 0.2 - - - +
117B SER 3.9 28.9 - - - +
118B ASP 4.2 1.6 - - - +
119B PRO* 4.0 29.4 - - + -
122B LEU* 3.7 34.1 - - + -
148B GLY* 3.0 18.0 + - - +
149B VAL 3.3 1.4 - - - -
150B SER* 1.3 89.5 - - - +
152B ALA* 1.3 65.1 + - - +
153B GLN* 3.3 2.7 - - + +
154B PHE* 3.1 18.2 + - - +
155B TYR* 3.3 7.4 - - - -
183B ALA* 3.6 3.4 - - - -
184B GLU* 3.9 9.0 - - + +
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Residues in contact with ALA 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151B LEU* 1.3 71.0 - - - +
153B GLN* 1.3 58.0 + - - +
155B TYR* 3.1 8.0 + - - +
156B ILE* 2.9 37.6 + - + +
183B ALA* 3.6 13.2 - - - +
184B GLU 2.8 31.7 + - - +
185B PRO* 3.7 19.5 - - + +
189B LEU* 3.9 18.1 - - + +
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Residues in contact with GLN 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122B LEU* 4.1 10.5 - - + -
126B LEU* 3.9 20.6 - - + +
151B LEU* 3.3 2.2 - - + +
152B ALA* 1.3 78.0 - - - +
154B PHE* 1.3 63.6 + - - +
156B ILE* 4.2 20.0 - - - +
157B SER* 2.8 60.0 + - - +
184B GLU 4.6 0.4 + - - -
185B PRO* 5.5 1.4 - - - +
188B ARG* 5.1 8.8 + - - -
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Residues in contact with PHE 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B LEU* 3.7 21.9 - - + +
126B LEU* 5.1 1.3 - - - -
139B TYR* 3.5 39.3 - + - -
142B LEU* 3.5 42.0 - - + -
143B HIS* 3.9 10.8 - + + -
147B ILE 4.4 4.5 - - - -
148B GLY 3.3 23.3 - - - +
149B VAL* 4.5 4.3 - - + -
151B LEU 3.1 12.6 + - - +
153B GLN* 1.3 79.3 - - - +
155B TYR* 1.3 82.1 + + - +
157B SER* 4.1 2.9 - - - -
158B TRP* 3.2 53.0 + + - +
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Residues in contact with TYR 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B HIS* 5.3 2.4 - + - -
149B VAL* 2.7 46.5 + - - +
151B LEU 3.3 14.8 - - - -
152B ALA* 3.1 5.8 + - - +
154B PHE* 1.3 95.9 - + - +
156B ILE* 1.3 60.1 - - - +
158B TRP* 4.4 4.7 - + - -
159B ALA* 2.9 34.2 + - - +
174B ILE* 3.5 35.0 - - + +
175B PHE* 5.2 0.7 - - - -
177B GLU* 3.8 19.6 + - + +
178B GLY* 3.6 22.4 - - - -
181B GLN* 3.8 12.4 - - + +
183B ALA* 3.7 17.9 - - + -
189B LEU* 4.2 14.4 - - + -
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Residues in contact with ILE 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152B ALA* 2.9 35.2 + - + +
153B GLN* 4.0 21.3 - - - +
154B PHE 3.4 0.2 - - - -
155B TYR* 1.3 75.8 - - - +
157B SER* 1.3 58.6 + - - +
159B ALA* 3.9 1.4 - - - +
160B GLU* 2.9 45.8 + - - +
175B PHE* 4.4 9.8 - - + -
188B ARG* 4.7 20.2 - - + +
189B LEU* 3.9 19.5 - - + -
192B GLN* 3.9 38.4 - - + +
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Residues in contact with SER 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B LEU* 4.2 13.1 - - - +
139B TYR* 3.3 30.4 + - - -
153B GLN* 2.8 40.5 + - - +
154B PHE 4.1 0.7 - - - -
156B ILE* 1.3 76.1 - - - +
158B TRP* 1.3 58.1 + - - +
160B GLU* 3.4 6.1 + - - +
161B GLU* 3.0 24.3 + - - +
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Residues in contact with TRP 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136B LEU* 3.9 12.7 + - + +
139B TYR* 3.2 51.7 - + + +
140B SER* 4.4 11.3 + - - +
143B HIS* 3.7 36.1 - + + -
154B PHE* 3.2 46.4 + + - +
155B TYR* 3.8 9.0 - + - +
157B SER* 1.3 76.2 - - - +
159B ALA* 1.3 67.4 + - - +
161B GLU* 3.0 13.5 + - - +
162B TYR* 3.1 31.0 + + - -
174B ILE* 3.7 35.2 - - + -
177B GLU* 5.8 2.5 - - + -
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Residues in contact with ALA 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155B TYR 2.9 20.2 + - - +
156B ILE 3.9 2.2 - - - +
158B TRP* 1.3 74.8 - - - +
160B GLU* 1.3 57.4 + - - +
162B TYR 3.2 1.7 + - - -
163B GLU* 2.8 25.9 + - - +
171B ALA* 3.3 25.8 - - - +
174B ILE* 3.7 11.7 - - + +
175B PHE* 3.4 38.4 - - + -
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Residues in contact with GLU 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156B ILE* 2.9 35.4 + - - +
157B SER* 3.6 7.6 - - - +
158B TRP 3.2 0.2 - - - -
159B ALA* 1.3 73.2 - - - +
161B GLU* 1.3 61.7 + - - +
163B GLU* 3.7 15.8 - - + +
164B ALA* 2.9 30.3 + - - +
175B PHE* 5.3 4.7 - - - -
192B GLN* 4.6 7.3 - - - +
199B ARG* 4.4 13.0 + - - +
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Residues in contact with GLU 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B PRO* 3.8 22.8 - - + +
136B LEU* 3.5 25.8 - - + -
139B TYR* 4.1 17.2 + - + -
157B SER 3.0 12.2 + - - +
158B TRP 3.0 10.6 + - - +
160B GLU* 1.3 77.8 - - - +
162B TYR* 1.3 60.9 + - - +
164B ALA* 3.4 7.7 + - - +
165B ARG* 2.6 59.8 + - - +
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Residues in contact with TYR 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B LEU* 3.8 32.2 - - + +
140B SER* 5.2 4.5 + - - -
158B TRP* 3.1 29.5 + + - -
159B ALA 3.6 6.7 - - - +
161B GLU* 1.3 76.8 - - - +
163B GLU* 1.3 59.5 + - - +
165B ARG* 3.2 8.7 + - + +
166B GLU 3.2 3.8 + - - -
167B ASN* 3.0 50.7 + - + +
170B LYS* 3.6 43.9 + - + +
171B ALA* 3.8 6.5 - - + +
174B ILE* 3.0 35.7 - - + -
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Residues in contact with GLU 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159B ALA 2.8 15.6 + - - +
160B GLU* 3.7 16.3 - - - +
162B TYR* 1.3 74.4 - - - +
164B ALA* 1.3 61.6 + - - +
166B GLU* 2.8 22.6 + - - +
168B PHE* 3.7 21.1 - - + -
171B ALA* 3.9 10.9 - - + +
175B PHE* 5.3 1.9 - - - -
196B PHE* 3.4 25.8 - - + -
199B ARG* 2.8 50.8 + - - +
200B VAL* 4.7 2.6 - - - +
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Residues in contact with ALA 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160B GLU 2.9 18.3 + - - +
161B GLU* 3.4 9.2 + - - +
163B GLU* 1.3 75.7 - - - +
165B ARG* 1.3 61.3 + - + +
166B GLU* 3.3 10.2 + - - +
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Residues in contact with ARG 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134A GLU* 5.3 6.0 + - - +
136A LEU* 5.5 1.7 - - - +
165A ARG* 3.5 21.1 + - - +
133B ASN 5.0 1.4 + - - -
134B GLU* 2.6 42.8 + - - -
135B PRO* 3.7 8.5 - - - +
136B LEU* 3.5 20.5 - - + +
161B GLU* 2.6 45.0 + - - +
162B TYR* 3.5 10.8 - - + +
163B GLU 3.2 0.2 - - - -
164B ALA* 1.3 74.8 - - - +
166B GLU* 1.3 70.1 + - - +
167B ASN* 3.3 4.6 + - + +
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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