Contacts of the helix formed by residues 157 - 167 (chain B) in PDB entry 3ISL
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 157 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144B MET* 4.3 21.5 - - + -
146B HIS* 3.2 43.5 - - + +
155B HIS* 3.3 30.7 - - + +
156B PRO* 1.3 76.4 - - - +
158B LYS* 1.3 60.5 + - - +
159B ALA 3.5 2.2 - - - -
160B ILE* 3.5 7.5 + - - +
161B GLY* 2.9 26.3 + - - -
171B PHE* 3.6 18.5 - - + -
173B VAL* 4.1 15.3 - - + -
189B TRP* 4.0 28.4 - - + +
191B ILE* 4.2 7.6 - - + -
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Residues in contact with LYS 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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156B PRO* 3.9 0.8 - - - +
157B LEU* 1.3 76.9 - - - +
159B ALA* 1.3 64.0 + - - +
161B GLY* 3.2 2.8 + - - -
162B GLU* 2.9 52.8 + - - +
188B GLU* 4.1 23.8 - - - +
189B TRP* 3.7 38.1 - - + +
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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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127B PRO* 4.3 16.2 - - + -
131B ILE* 3.9 19.9 - - + +
157B LEU 3.5 0.2 - - - -
158B LYS* 1.3 79.1 - - - +
160B ILE* 1.3 55.8 + - - +
162B GLU* 3.2 14.5 + - - +
163B ALA* 2.8 31.5 + - - +
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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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127B PRO* 4.0 20.6 - - + +
130B ILE* 3.8 47.3 - - + -
131B ILE* 4.3 7.6 - - + +
134B ILE* 4.2 8.0 - - + +
142B VAL* 4.4 2.7 - - + -
144B MET* 3.8 17.3 - - + -
155B HIS* 4.0 4.3 - - - +
156B PRO 3.7 22.0 - - - +
157B LEU* 3.5 8.4 + - - +
158B LYS 3.3 0.2 - - - -
159B ALA* 1.3 74.8 - - - +
161B GLY* 1.3 57.9 + - - +
163B ALA* 3.3 2.9 + - - +
164B CYS* 3.0 29.1 + - - -
171B PHE* 3.7 25.1 - - + -
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Residues in contact with GLY 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 LEU 2.9 12.7 + - - -
158B LYS 3.2 0.4 + - - -
160B ILE* 1.3 72.6 - - - +
162B GLU* 1.3 62.9 + - - +
164B CYS* 3.2 4.0 + - - +
165B ARG* 3.0 24.3 + - - +
171B PHE* 3.4 19.9 - - - -
189B TRP 3.3 20.2 - - - -
190B LYS* 3.8 12.4 - - - +
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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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158B LYS* 2.9 52.7 + - + +
159B ALA* 3.6 15.9 - - - +
161B GLY* 1.3 75.7 - - - +
163B ALA* 1.3 60.9 + - - +
165B ARG* 3.8 1.7 - - - +
166B THR* 2.8 33.2 + - + +
188B GLU 4.9 2.1 - - - +
189B TRP 5.5 0.2 - - - +
190B LYS* 3.7 35.3 - - + +
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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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131B ILE* 3.7 38.6 - - + -
134B ILE* 4.4 10.3 - - + +
159B ALA 2.8 17.8 + - - +
160B ILE 3.7 2.9 - - - +
161B GLY 3.2 0.4 - - - -
162B GLU* 1.3 76.2 - - - +
164B CYS* 1.3 63.9 + - - +
166B THR* 3.3 8.0 + - - +
167B GLU* 3.0 27.3 + - - +
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Residues in contact with CYS 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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134B ILE* 3.9 8.5 - - - -
142B VAL* 3.7 38.1 - - - -
160B ILE 3.0 25.5 + - - -
161B GLY 3.2 6.5 + - - +
163B ALA* 1.3 75.5 - - - +
165B ARG* 1.3 58.0 + - - +
167B GLU* 3.3 1.5 + - - -
168B ASP 2.9 8.8 + - - -
169B ALA* 2.6 50.7 + - + +
171B PHE* 3.7 27.8 - - + -
192B ASP* 4.8 1.1 - - - +
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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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161B GLY 3.0 15.7 + - - +
162B GLU 3.8 4.3 - - - +
164B CYS* 1.3 77.7 - - - +
166B THR* 1.3 62.4 + - - +
168B ASP* 3.3 11.1 + - - +
190B LYS* 3.7 53.7 + - + +
191B ILE 4.3 2.0 + - - -
192B ASP* 3.2 20.4 + - - -
214B ASN* 3.5 14.5 - - - +
216B ARG* 3.5 34.5 + - - +
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Residues in contact with THR 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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162B GLU* 2.8 31.0 + - + +
163B ALA* 3.3 7.7 + - - -
165B ARG* 1.3 76.6 - - - +
167B GLU* 1.3 66.8 + - - +
168B ASP* 3.2 4.4 + - - +
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Residues in contact with GLU 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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134B ILE* 3.8 31.1 - - + +
135B LYS* 4.1 20.8 - - - +
138B LYS* 3.6 39.4 - - + +
139B PRO 5.2 2.1 - - - +
163B ALA 3.0 18.3 + - - +
164B CYS 4.0 2.0 - - - +
166B THR* 1.3 84.2 + - - +
168B ASP* 1.3 69.1 + - - +
169B ALA* 3.2 2.7 + - + +
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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