Contacts of the helix formed by residues 154 - 164 (chain B) in PDB entry 5ICN
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 ASN 154 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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67B TYR* 4.5 2.5 - - + -
68B HIS* 3.4 16.2 - - + +
139B LEU 3.6 8.9 + - - -
140B HIS* 3.5 32.9 + - - +
142B ALA* 3.5 25.7 + - + +
153B VAL* 1.3 73.3 - - - +
155B ASP* 1.3 60.9 + - - +
156B ILE* 3.0 14.2 + - - +
157B VAL* 2.7 52.2 + - + +
158B LEU* 3.5 14.4 + - - +
182B GLY 3.8 10.3 - - - -
183B VAL* 3.9 1.8 - - - +
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Residues in contact with ASP 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B SER* 3.9 5.2 - - - +
114B THR* 3.8 25.6 - - - +
117B SER* 2.5 31.4 + - - +
118B VAL* 5.2 0.5 - - - +
137B GLY* 3.2 6.0 - - - -
138B GLY 2.9 22.0 + - - -
139B LEU* 3.0 30.7 + - - +
153B VAL 3.2 5.3 + - - +
154B ASN* 1.3 73.6 - - - +
156B ILE* 1.3 60.0 + - - +
158B LEU* 3.5 13.0 + - - +
159B ALA* 2.9 30.5 + - - +
298B LEU* 3.6 4.5 - - - +
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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
----------------------------------------------------------
138B GLY* 3.4 18.8 - - - +
139B LEU 4.6 0.2 - - - -
140B HIS* 3.3 37.7 - - + -
154B ASN* 3.0 6.7 - - - +
155B ASP* 1.3 86.9 - - - +
157B VAL* 1.3 61.7 + - - +
159B ALA* 3.2 6.8 + - - +
160B ILE* 2.8 49.1 + - + +
172B TYR* 3.5 31.4 - - + +
183B VAL* 3.6 9.9 - - + -
258B VAL* 4.4 9.0 - - + -
260B GLN* 4.4 2.9 - - + -
298B LEU* 3.8 15.9 - - + -
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Residues in contact with VAL 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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175A ALA* 4.3 1.3 - - + -
67B TYR* 3.7 33.2 - - + -
154B ASN* 2.7 40.0 + - + +
156B ILE* 1.3 72.4 - - - +
158B LEU* 1.3 52.0 + - - +
160B ILE* 2.8 6.2 + - - +
161B LEU* 2.7 47.9 + - + +
182B GLY 4.3 0.4 - - - +
183B VAL* 4.2 8.7 - - + -
186B ALA* 3.5 25.8 - - + -
187B PHE* 3.7 26.2 - - + -
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Residues in contact with LEU 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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63B GLU 3.2 25.4 - - - +
64B MET* 3.9 11.9 - - - +
66B LYS* 4.4 5.4 - - + -
67B TYR* 3.8 31.4 - - + +
68B HIS* 4.6 2.5 - - + +
114B THR* 3.4 28.0 - - + -
118B VAL* 4.4 15.6 - - + +
153B VAL* 3.7 22.0 - - + -
154B ASN 3.5 10.3 + - - +
155B ASP* 3.7 4.3 - - - +
156B ILE 3.3 0.2 - - - -
157B VAL* 1.3 75.3 - - - +
159B ALA* 1.3 63.6 + - - +
161B LEU* 3.3 9.6 + - + +
162B GLU* 3.2 23.9 + - - +
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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
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117B SER* 4.0 28.0 - - - +
118B VAL* 4.7 4.4 - - - +
121B ALA* 3.6 8.6 - - + +
155B ASP 2.9 18.6 + - - +
156B ILE* 3.3 8.1 - - + +
158B LEU* 1.3 76.2 - - - +
160B ILE* 1.3 64.6 + - + +
162B GLU* 3.2 7.8 + - - +
163B LEU* 3.2 23.7 + - - +
258B VAL* 5.9 0.9 - - + -
296B LEU* 4.2 16.4 - - + -
298B LEU* 5.5 2.0 - - + -
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Residues in contact with ILE 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* 2.8 40.3 + - + +
157B VAL 3.3 5.6 - - - +
159B ALA* 1.3 73.6 - - + +
161B LEU* 1.3 57.2 + - - +
163B LEU* 3.0 9.6 + - - +
164B LEU* 2.9 29.4 + - + +
170B VAL* 3.9 22.0 - - + -
172B TYR* 4.3 17.3 - - + -
183B VAL* 3.7 18.4 - - + -
187B PHE* 3.5 28.9 - - + -
193B VAL* 3.9 20.0 - - + -
258B VAL* 4.3 12.3 - - + -
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Residues in contact with LEU 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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175A ALA* 4.3 8.1 - - + -
176A ASP 3.7 17.5 - - - +
177A ILE* 4.5 2.0 - - - -
178A THR* 3.1 41.0 + - - +
66B LYS* 4.1 15.7 - - + +
67B TYR* 3.8 18.8 - - + -
157B VAL* 2.7 38.3 + - + +
158B LEU* 3.6 15.7 - - + +
159B ALA 3.2 0.2 - - - -
160B ILE* 1.3 72.9 - - - +
162B GLU* 1.3 61.7 + - - +
164B LEU* 3.6 16.3 + - + +
165B LYS* 3.8 3.7 - - - +
187B PHE* 4.1 19.1 - - + -
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Residues in contact with GLU 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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187A ASP* 4.6 4.9 - - - +
189A ARG* 2.8 45.2 + - - +
66B LYS* 4.6 2.7 + - + -
118B VAL* 4.5 12.3 - - + -
121B ALA* 4.2 11.9 - - + -
122B VAL* 3.6 12.0 - - + +
125B ASN* 2.8 27.0 + - - +
158B LEU 3.2 9.1 + - - +
159B ALA* 3.2 11.2 + - - +
161B LEU* 1.3 77.8 - - - +
163B LEU* 1.3 62.7 + - - +
165B LYS* 2.7 55.4 + - + +
166B TYR* 5.8 0.2 - - - -
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Residues in contact with LEU 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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121B ALA* 3.8 21.8 - - + +
124B LEU* 4.1 18.4 - - + -
125B ASN* 3.4 18.2 - - - +
159B ALA 3.2 15.6 + - - +
160B ILE* 3.0 13.1 + - - +
162B GLU* 1.3 71.4 - - - +
164B LEU* 1.3 51.5 + - - +
165B LYS 3.0 4.5 - - - -
166B TYR 2.9 6.1 + - - -
167B HIS* 2.7 52.8 + - + +
170B VAL* 4.1 14.6 - - + -
256B ALA* 4.7 9.4 - - + -
257B VAL 5.5 0.7 - - - +
258B VAL* 3.8 29.2 - - + -
296B LEU* 4.6 10.3 - - + -
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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
----------------------------------------------------------
177A ILE* 4.3 17.3 - - + -
178A THR 3.6 16.8 - - - +
180A LEU* 3.7 9.0 - - - +
160B ILE* 2.9 22.4 + - + +
161B LEU* 3.7 23.1 - - + +
162B GLU 3.3 0.2 - - - -
163B LEU* 1.3 76.1 - - - +
165B LYS* 1.3 61.3 + - - +
166B TYR 3.2 0.7 + - - -
167B HIS 3.4 11.0 + - - +
168B GLN 4.3 1.1 - - - +
170B VAL* 3.8 11.0 - - + -
187B PHE* 4.2 9.2 - - + -
192B ARG* 2.7 50.1 + - + +
193B VAL* 3.8 30.7 - - + -
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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