Contacts of the helix formed by residues 163 - 173 (chain A) in PDB entry 5LSW
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 ILE 163 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120A TYR* 3.5 33.0 - - + +
123A LEU* 4.3 20.4 - - + -
143A ILE* 4.5 13.7 - - + -
158A LEU* 3.3 40.4 - - + +
159A LEU* 5.3 0.7 - - + -
161A THR* 3.3 2.9 + - - +
162A GLU* 1.3 77.7 - - - +
164A ILE* 1.3 64.5 + - + +
166A LEU* 3.2 5.7 + - + +
167A CYS* 2.8 46.9 + - - -
185A ILE* 4.3 11.4 - - + -
189A ILE* 3.9 14.8 - - + -
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Residues in contact with ILE 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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159A LEU* 4.0 24.7 - - + -
161A THR 5.1 0.4 + - - -
163A ILE* 1.3 79.7 - - + +
165A PRO* 1.3 72.6 - - + +
167A CYS* 3.2 7.5 + - - +
168A LEU* 2.9 40.5 + - + +
186A LEU* 4.5 13.4 - - + +
189A ILE* 4.2 21.8 - - + -
198A TYR* 4.0 15.0 - - + -
199A ILE* 3.9 32.5 - - + -
209A VAL* 5.0 4.5 - - + -
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Residues in contact with PRO 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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162A GLU* 3.3 40.8 - - + +
164A ILE* 1.3 98.0 - - + +
166A LEU* 1.3 55.4 - - + +
168A LEU* 3.7 10.7 - - + +
169A ARG* 2.9 36.4 + - + +
208A HIS* 5.6 7.0 - - + +
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Residues in contact with LEU 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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120A TYR* 3.7 40.4 - - + +
123A LEU* 4.2 31.1 - - + +
124A HIS* 3.4 48.2 - - + +
162A GLU* 3.4 14.7 + - + +
163A ILE* 3.2 9.6 + - + +
164A ILE 3.2 0.8 - - - -
165A PRO* 1.3 80.4 - - + +
167A CYS* 1.3 62.5 + - - +
169A ARG* 3.4 10.0 + - + +
170A ILE* 3.2 29.1 + - - +
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Residues in contact with CYS 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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123A LEU* 5.9 1.1 - - - -
140A LEU* 5.5 2.5 - - - -
163A ILE* 2.8 36.4 + - - +
164A ILE* 3.7 6.7 - - - +
166A LEU* 1.3 72.1 - - - +
168A LEU* 1.3 59.1 + - + +
170A ILE* 3.1 6.1 + - - +
171A MET* 2.8 37.9 + - - +
182A ALA* 3.7 22.6 - - + +
185A ILE* 3.6 41.3 - - - -
186A LEU* 4.7 7.4 - - + -
189A ILE* 5.5 1.3 - - - -
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Residues in contact with LEU 168 (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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164A ILE* 2.9 30.9 + - + +
165A PRO* 3.7 7.4 - - + +
167A CYS* 1.3 76.1 - - - +
169A ARG* 1.3 63.3 + - - +
171A MET* 3.2 21.5 + - + +
172A GLU* 3.0 25.1 + - - +
186A LEU* 4.2 16.4 - - + -
208A HIS* 3.6 37.7 - - + +
209A VAL* 4.0 28.9 - - + +
212A ILE* 3.9 27.2 - - + +
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Residues in contact with ARG 169 (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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123A LEU 6.0 1.3 - - - +
165A PRO* 2.9 23.1 + - + +
166A LEU* 3.6 13.0 - - + +
168A LEU* 1.3 74.9 - - - +
170A ILE* 1.3 63.1 + - + +
172A GLU* 2.7 33.6 + - - +
173A SER* 3.1 33.6 + - - +
208A HIS* 5.2 15.0 + - - -
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Residues in contact with ILE 170 (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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123A LEU* 4.0 35.9 - - + +
136A ARG* 4.6 11.2 - - + -
140A LEU* 4.2 25.8 - - + -
166A LEU 3.2 14.3 + - - +
167A CYS* 3.1 7.9 + - - +
169A ARG* 1.3 75.2 - - + +
171A MET* 1.3 62.2 + - - +
173A SER 5.1 0.2 - - - -
174A GLY* 2.8 31.7 + - - +
178A SER* 3.5 41.5 - - - +
179A LYS* 3.6 4.2 - - - +
182A ALA* 3.6 8.7 - - + -
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Residues in contact with MET 171 (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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167A CYS 2.8 26.5 + - - +
168A LEU* 3.2 15.2 + - + +
170A ILE* 1.3 72.5 - - - +
172A GLU* 1.3 53.7 + - - +
179A LYS* 2.6 34.4 + - - +
182A ALA* 3.8 16.4 - - + +
183A THR* 3.4 35.7 - - + +
186A LEU* 3.7 34.8 - - + -
212A ILE* 4.0 9.0 - - + -
213A LEU* 3.7 15.3 - - + -
216A MET* 3.6 37.1 - - + +
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Residues in contact with GLU 172 (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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168A LEU 3.0 16.0 + - - +
169A ARG* 2.7 35.5 + - - +
170A ILE 3.1 0.2 - - - -
171A MET* 1.3 75.0 - - - +
173A SER* 1.3 62.8 + - - +
179A LYS* 3.0 15.2 + - - -
208A HIS* 5.6 0.2 - - - -
212A ILE* 3.7 31.0 - - + +
215A LYS* 4.2 23.4 - - + +
216A MET* 5.3 1.8 - - - -
219A GLN* 4.1 13.2 + - - +
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Residues in contact with SER 173 (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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126A VAL* 5.7 9.3 - - - +
128A LYS* 5.8 3.5 - - - +
169A ARG* 3.1 20.1 + - - +
170A ILE* 5.1 0.2 - - - -
172A GLU* 1.3 84.6 + - - +
174A GLY* 1.3 62.8 + - - +
179A LYS* 4.0 1.6 - - - +
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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