Contacts of the helix formed by residues 155 - 163 (chain A) in PDB entry 5I4E
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 THR 155 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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152A PRO* 4.7 12.8 - - + +
153A ILE 3.7 1.8 - - - -
154A TYR* 1.3 80.3 - - - +
156A GLU* 1.4 58.9 + - - +
157A ALA* 3.7 9.3 + - - +
158A ILE* 3.2 32.4 + - + +
159A VAL* 3.1 31.1 + - - +
213A GLN* 5.5 0.7 - - - -
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Residues in contact with GLU 156 (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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155A THR* 1.4 72.8 - - - +
157A ALA* 1.3 60.3 + - - +
159A VAL* 3.4 9.1 + - - +
160A GLU* 3.2 35.8 + - - +
217A HIS* 3.5 36.1 + - + +
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Residues in contact with ALA 157 (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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155A THR* 3.2 9.2 + - - +
156A GLU* 1.3 76.2 - - - +
158A ILE* 1.3 65.4 + - + +
160A GLU* 3.6 8.0 + - - +
161A MET* 3.3 21.1 + - - +
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Residues in contact with ILE 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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152A PRO 3.4 25.6 - - - +
153A ILE* 3.5 31.4 - - + +
155A THR* 3.2 24.2 + - + +
157A ALA* 1.3 76.1 - - + +
159A VAL* 1.4 65.1 + - - +
161A MET* 3.3 24.5 + - + +
162A TYR* 3.0 45.0 - - + -
173A HIS* 4.1 5.2 - - + +
175A TYR* 4.1 6.3 - - + -
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Residues in contact with VAL 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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155A THR 3.1 19.1 + - - +
156A GLU* 3.6 10.5 - - - +
157A ALA 3.4 0.2 - - - -
158A ILE* 1.4 74.2 - - - +
160A GLU* 1.4 56.0 + - - +
162A TYR 3.1 16.8 + - - -
163A ARG* 3.5 8.8 + - - +
175A TYR* 3.5 32.3 - - + +
213A GLN* 4.8 12.1 - - + +
214A TYR* 3.5 28.3 - - + +
217A HIS* 3.3 35.7 - - + -
218A VAL* 3.8 9.0 - - + -
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Residues in contact with GLU 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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156A GLU* 3.2 24.7 + - - +
157A ALA* 3.8 8.3 - - - +
158A ILE 3.4 0.2 - - - -
159A VAL* 1.4 74.9 - - - +
161A MET* 1.3 59.8 + - - +
162A TYR 3.4 0.5 + - - -
163A ARG* 2.8 55.6 + - - +
165A LYS* 5.1 1.4 + - - -
217A HIS* 2.8 27.7 + - - +
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Residues in contact with MET 161 (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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157A ALA 3.3 10.8 + - - +
158A ILE* 3.3 33.8 + - + +
160A GLU* 1.3 76.9 - - - +
162A TYR* 1.3 91.9 + - + +
165A LYS* 3.0 34.4 + - - +
170A VAL* 3.8 9.5 - - + +
171A PRO* 4.9 10.5 - - + -
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Residues in contact with TYR 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 ILE* 3.0 31.4 - - + -
159A VAL 3.1 7.5 + - - +
161A MET* 1.3 103.6 - - + +
163A ARG* 1.3 65.8 + - - +
164A GLY 3.3 0.7 + - - -
165A LYS* 3.1 19.2 + - - +
170A VAL* 3.2 35.2 - - + -
171A PRO* 2.9 34.8 + - - +
172A PRO 4.1 0.2 + - - -
173A HIS* 3.4 28.1 + + + +
175A TYR* 3.7 15.3 - + + +
176A ALA* 3.7 18.4 - - + -
179A GLU* 3.9 7.3 - - - +
214A TYR* 3.4 22.2 + - + +
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Residues in contact with ARG 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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159A VAL 3.7 6.7 - - - +
160A GLU* 2.8 64.4 + - - +
162A TYR* 1.3 75.1 - - - +
164A GLY* 1.3 63.4 + - - +
165A LYS* 3.2 13.2 + - - +
179A GLU* 3.9 1.8 - - - +
183A ARG* 5.8 1.3 - - - +
214A TYR* 3.3 8.1 + - - +
217A HIS* 4.2 11.9 + - - -
218A VAL* 3.7 52.2 + - + +
225A ARG* 5.6 4.8 - - - +
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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