Contacts of the helix formed by residues 157 - 167 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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144A MET* 4.2 17.7 - - + -
145A VAL 4.6 0.9 - - - +
146A HIS* 3.4 38.8 - - + +
155A HIS* 3.4 24.0 + - + +
156A PRO* 1.3 77.2 - - - +
158A LYS* 1.3 65.9 + - - +
159A ALA 3.4 2.7 - - - -
160A ILE* 3.3 4.9 + - - +
161A GLY* 3.0 19.8 + - - -
171A PHE* 3.6 25.8 - - + -
173A VAL* 3.8 23.3 - - + -
189A TRP* 4.0 21.9 - - + +
191A ILE* 4.0 14.6 - - + -
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Residues in contact with LYS 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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156A PRO* 3.9 1.2 - - - +
157A LEU* 1.3 77.9 - - - +
159A ALA* 1.3 65.1 + - - +
161A GLY* 3.3 1.0 + - - -
162A GLU* 2.9 55.0 + - - +
188A GLU* 3.4 26.9 + - - +
189A TRP* 3.7 39.6 - - + +
190A LYS* 5.4 0.8 - - - +
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Residues in contact with ALA 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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127A PRO* 4.1 18.4 - - + -
131A ILE* 3.6 26.4 - - + +
156A PRO* 5.5 1.6 - - + +
157A LEU 3.4 0.4 - - - -
158A LYS* 1.3 79.8 - - - +
160A ILE* 1.3 62.8 + - - +
162A GLU* 3.5 11.8 + - - +
163A ALA 3.1 17.5 + - - -
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Residues in contact with ILE 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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127A PRO* 4.2 18.6 - - + -
130A ILE* 3.6 43.1 - - + -
131A ILE* 4.3 7.6 - - + -
134A ILE* 4.2 9.8 - - + +
142A VAL* 4.4 3.8 - - + -
144A MET* 3.9 15.5 - - + -
155A HIS* 4.1 3.4 - - - +
156A PRO 3.6 22.0 - - - +
157A LEU* 3.3 8.2 + - - +
158A LYS 3.1 0.6 - - - -
159A ALA* 1.3 76.8 - - - +
161A GLY* 1.3 63.6 + - - +
163A ALA* 3.1 5.4 + - - +
164A CYS* 3.0 27.6 + - - -
171A PHE* 3.5 28.7 - - + -
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Residues in contact with GLY 161 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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157A LEU 3.0 11.5 + - - -
160A ILE* 1.3 75.7 - - - +
162A GLU* 1.3 62.2 + - - +
164A CYS* 3.1 3.4 + - - +
165A ARG* 3.0 20.3 + - - +
171A PHE* 3.3 27.9 - - - -
189A TRP 3.4 12.6 - - - -
190A LYS* 3.6 16.9 - - - +
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Residues in contact with GLU 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 LYS* 2.9 56.1 + - + +
159A ALA* 3.7 9.3 - - - +
161A GLY* 1.3 75.0 - - - +
163A ALA* 1.3 61.5 + - - +
165A ARG* 3.6 3.0 + - - +
166A THR* 3.2 29.5 + - + +
188A GLU 4.6 0.2 - - - +
190A LYS* 3.6 34.9 + - + +
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Residues in contact with ALA 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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131A ILE* 3.7 40.4 - - + -
134A ILE* 4.3 11.9 - - + -
135A LYS* 6.2 0.7 - - + -
159A ALA 3.1 8.1 + - - +
160A ILE 3.1 7.6 + - - +
162A GLU* 1.3 76.0 - - - +
164A CYS* 1.3 57.5 + - - +
166A THR* 3.4 7.4 + - - -
167A GLU* 2.9 36.4 + - + +
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Residues in contact with CYS 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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134A ILE* 3.8 11.4 - - - -
142A VAL* 3.3 34.8 - - - -
160A ILE 3.0 21.7 + - - -
161A GLY 3.1 7.8 + - - +
163A ALA* 1.3 73.8 - - - +
165A ARG* 1.3 59.6 + - - +
167A GLU 3.3 1.0 + - - -
168A ASP 2.8 25.1 + - - -
169A ALA* 2.8 31.5 + - + +
171A PHE* 3.8 31.6 - - + -
192A ASP* 4.7 0.7 - - - +
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Residues in contact with ARG 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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161A GLY 3.0 14.0 + - - +
162A GLU* 3.8 6.1 - - - +
164A CYS* 1.3 77.1 - - - +
166A THR* 1.3 63.6 + - + +
168A ASP* 3.2 13.2 + - - +
190A LYS* 3.5 59.6 + - + +
191A ILE 4.2 2.0 + - - -
192A ASP* 3.0 20.5 + - - -
214A ASN* 3.5 14.6 - - - +
216A ARG* 3.4 36.1 + - - +
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Residues in contact with THR 166 (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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162A GLU* 3.2 18.2 + - + +
163A ALA* 3.4 9.6 + - - -
165A ARG* 1.3 78.6 - - + +
167A GLU* 1.3 74.0 + - - +
168A ASP* 3.2 2.8 + - - +
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Residues in contact with GLU 167 (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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134A ILE* 3.8 27.6 - - + +
135A LYS* 3.5 37.0 - - + +
138A LYS* 4.5 25.1 - - + +
139A PRO* 5.1 2.1 - - + +
163A ALA* 2.9 23.5 + - + +
164A CYS 4.1 1.8 - - - +
166A THR* 1.3 84.4 + - - +
168A ASP* 1.3 71.5 + - - +
169A ALA* 3.2 3.1 + - + +
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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