Contacts of the helix formed by residues 156 - 171 (chain B) in PDB entry 4I6J
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 156 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121B LYS* 5.6 3.6 - - + +
125B GLU* 5.3 5.2 - - - +
154B ASP 4.1 3.6 - - - +
155B LEU* 1.3 92.5 - - + +
157B LYS* 1.3 67.7 + - - +
158B SER* 4.7 5.4 - - - +
159B HIS* 3.1 32.8 + - + +
160B PHE* 3.4 7.4 + - - +
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Residues in contact with LYS 157 (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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155B LEU 3.5 4.5 + - - -
156B PRO* 1.3 69.7 - - - +
158B SER* 1.3 59.1 + - - +
160B PHE* 3.0 9.2 + - - +
161B ILE* 2.9 35.9 + - - +
183B PRO* 3.8 24.5 - - + +
185B ASP* 2.9 42.2 + - - +
187B PRO* 5.9 0.4 - - - +
210B HIS* 3.5 34.8 - - + +
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Residues in contact with SER 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156B PRO* 3.3 5.6 - - - +
157B LYS* 1.3 78.0 - - - +
159B HIS* 1.3 67.9 + - - +
161B ILE* 3.8 9.6 - - - +
162B SER* 3.0 26.5 + - - -
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Residues in contact with HIS 159 (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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125B GLU* 4.4 20.7 + - + +
128B CYS* 4.1 23.3 + - + +
129B ASP* 4.3 13.1 + - - -
132B SER* 5.7 2.6 + - - -
155B LEU* 4.6 13.2 - - + +
156B PRO* 3.1 28.5 + - + +
158B SER* 1.3 81.1 + - - +
160B PHE* 1.3 66.2 + - - +
162B SER* 3.8 6.1 - - - -
163B ALA* 3.3 18.3 + - + +
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Residues in contact with PHE 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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128B CYS* 4.1 13.2 - - - -
131B LEU* 5.4 3.4 - - + -
144B LEU* 3.6 23.3 - - + -
152B PHE* 3.6 33.9 - + - -
155B LEU* 4.0 14.7 - - + +
156B PRO 3.4 4.4 + - - +
157B LYS 3.0 8.1 + - - +
159B HIS* 1.3 77.1 - - - +
161B ILE* 1.3 77.4 + - + +
163B ALA* 3.0 5.7 + - - +
164B LEU* 3.0 35.5 + - + +
182B THR* 3.4 38.4 - - + -
183B PRO* 3.5 25.8 - - + -
184B VAL* 3.5 14.4 - - + -
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Residues in contact with ILE 161 (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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157B LYS* 2.9 26.9 + - - +
158B SER* 4.1 7.4 - - - +
160B PHE* 1.3 83.6 - - + +
162B SER* 1.3 56.5 + - - +
164B LEU* 3.2 5.9 + - + +
165B THR* 2.6 47.9 + - - +
183B PRO 4.1 4.3 - - - +
184B VAL* 3.6 33.2 - - + -
185B ASP* 3.7 19.3 - - - +
188B SER* 3.7 27.1 - - - +
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Residues in contact with SER 162 (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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132B SER* 5.0 2.6 + - - -
158B SER 3.0 20.3 + - - -
159B HIS* 3.8 8.5 + - - -
160B PHE 3.2 0.2 - - - -
161B ILE* 1.3 78.2 - - - +
163B ALA* 1.3 64.5 + - - +
165B THR* 3.4 17.1 + - - -
166B VAL* 3.6 12.3 + - - +
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Residues in contact with ALA 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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128B CYS* 3.6 31.2 - - + +
131B LEU* 3.7 18.9 - - + +
132B SER* 3.3 25.4 - - - +
159B HIS* 3.3 10.8 + - + +
160B PHE 3.0 8.3 + - - +
162B SER* 1.3 76.4 + - - +
164B LEU* 1.3 65.6 + - - +
165B THR 3.1 1.1 - - - -
166B VAL* 3.2 19.4 + - - +
167B VAL* 4.1 1.2 + - - +
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Residues in contact with LEU 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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131B LEU* 4.5 8.8 - - + +
142B LEU* 4.1 24.0 - - + -
144B LEU* 4.8 5.8 - - + -
160B PHE* 3.0 29.8 + - + +
161B ILE* 3.5 11.2 - - + +
163B ALA* 1.3 77.8 - - - +
165B THR* 1.3 58.1 + - - +
167B VAL* 2.9 19.7 + - + +
168B PHE* 3.2 50.9 + - + -
179B ILE* 4.6 12.8 - - + -
184B VAL* 3.4 31.0 - - + -
188B SER* 5.4 0.9 - - - +
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Residues in contact with THR 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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161B ILE* 2.6 36.8 + - - +
162B SER* 3.4 10.2 - - - -
163B ALA 3.1 0.4 - - - -
164B LEU* 1.3 77.2 - - - +
166B VAL* 1.3 63.4 + - - +
167B VAL 2.9 0.7 + - - -
168B PHE* 3.0 11.9 + - - -
169B VAL* 2.9 43.4 + - + +
188B SER* 5.2 2.6 - - - -
191B VAL* 4.4 16.2 - - + +
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Residues in contact with VAL 166 (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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131B LEU 3.8 10.3 - - - +
132B SER* 3.8 20.6 - - - +
134B LEU 3.6 25.3 - - - +
135B VAL* 4.1 12.8 - - + -
162B SER* 3.6 11.4 - - - +
163B ALA* 3.5 13.2 - - - +
164B LEU 3.2 0.6 - - - -
165B THR* 1.3 77.3 - - - +
167B VAL* 1.3 58.2 + - - +
169B VAL* 4.9 0.9 - - - -
170B ASN* 2.7 48.9 + - - +
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Residues in contact with VAL 167 (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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131B LEU* 4.2 18.8 - - + +
134B LEU* 4.6 14.4 - - + +
137B CYS* 6.0 0.4 - - + -
139B LEU* 4.2 16.4 - - + -
142B LEU* 3.7 33.4 - - + -
163B ALA 5.1 1.3 - - - +
164B LEU 2.9 10.4 + - - +
166B VAL* 1.3 77.8 - - - +
168B PHE* 1.3 77.3 + - + +
169B VAL 3.2 0.4 - - - -
171B SER* 2.9 36.3 + - - +
174B LEU* 4.3 17.0 - - + +
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Residues in contact with PHE 168 (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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164B LEU* 3.2 47.5 + - + -
165B THR* 3.0 13.1 + - - +
167B VAL* 1.3 82.6 - - + +
169B VAL* 1.3 62.2 + - - +
171B SER 3.6 3.1 - - - +
174B LEU* 4.4 3.8 - - + -
177B LEU* 3.4 35.4 - - + -
179B ILE* 5.6 0.4 - - + -
184B VAL* 5.3 1.3 - - + -
188B SER* 3.6 36.8 - - - -
189B LEU* 5.1 4.0 - - + -
191B VAL* 4.2 16.8 - - + -
192B LEU* 3.6 31.2 - - + -
195B ASN* 3.1 22.7 - - - +
196B ASN* 3.2 12.2 - - - +
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Residues in contact with VAL 169 (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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165B THR* 2.9 34.2 + - + +
166B VAL* 4.9 0.2 - - - -
168B PHE* 1.3 77.6 - - - +
170B ASN* 1.3 78.0 + - - +
172B LYS* 3.2 34.9 + - - +
191B VAL* 4.3 5.2 - - + -
195B ASN* 3.6 19.9 - - - +
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Residues in contact with ASN 170 (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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134B LEU 4.2 6.1 - - - +
135B VAL* 3.5 41.6 - - - +
137B CYS 3.3 12.0 - - - +
138B SER* 4.1 4.0 + - - -
166B VAL* 2.7 46.4 + - - +
169B VAL* 1.3 90.0 - - - +
171B SER* 1.3 61.6 + - - +
172B LYS* 3.6 12.4 + - - +
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Residues in contact with SER 171 (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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134B LEU 5.6 0.5 + - - -
137B CYS* 3.5 10.8 + - - +
138B SER* 4.1 2.9 - - - -
139B LEU* 2.8 49.1 + - - +
167B VAL* 2.9 26.8 + - - +
168B PHE 3.6 5.4 - - - +
170B ASN* 1.3 75.8 - - - +
172B LYS* 1.3 55.6 + - - +
173B SER 3.3 0.9 - - - -
174B LEU* 4.6 4.0 - - - -
196B ASN* 2.3 32.2 + - - +
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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