Contacts of the helix formed by residues 158 - 167 (chain A) in PDB entry 5H1Y
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 GLU 158 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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157A GLU* 1.3 98.3 + - + +
159A ARG* 1.3 67.3 + - - +
160A HIS* 3.3 2.1 + - - +
161A GLU* 3.7 12.2 + - - +
162A ARG* 3.8 29.3 + - - +
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Residues in contact with ARG 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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158A GLU* 1.3 76.7 + - - +
160A HIS* 1.3 69.3 + - + +
162A ARG* 2.9 62.2 + - - +
163A VAL* 3.0 20.8 + - + +
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Residues in contact with HIS 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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157A GLU* 4.1 36.5 + - - -
158A GLU 3.3 0.6 - - - -
159A ARG* 1.3 85.3 - - + +
161A GLU* 1.3 57.7 + - - +
163A VAL* 3.5 11.1 + - + +
164A ARG* 3.1 46.2 + - - +
176A ILE 5.9 0.4 + - - -
178A PRO* 3.5 31.3 - - + +
179A PRO* 3.7 29.0 - - + +
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Residues in contact with GLU 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 GLU 4.8 7.0 + - - +
158A GLU 3.7 10.8 + - - +
159A ARG 3.2 0.6 - - - -
160A HIS* 1.3 76.3 - - - +
162A ARG* 1.3 61.2 + - - +
164A ARG* 3.3 32.7 + - - +
165A LYS* 2.8 47.5 + - + +
169A ILE 4.9 3.0 - - - +
171A VAL* 5.0 3.8 - - - +
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Residues in contact with ARG 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 GLU* 3.8 27.8 + - - +
159A ARG* 2.9 62.1 + - - +
161A GLU* 1.3 76.0 - - + +
163A VAL* 1.3 65.1 + - - +
165A LYS* 3.4 5.9 + - - +
166A LYS* 3.0 27.5 + - - +
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Residues in contact with VAL 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 ARG* 3.0 23.6 + - + +
160A HIS* 3.5 12.1 - - + +
162A ARG* 1.3 75.9 - - - +
164A ARG* 1.3 64.7 + - - +
166A LYS* 3.3 8.9 + - - +
167A TYR* 3.1 44.8 + - + -
179A PRO* 3.8 29.8 - - + +
181A LYS* 4.0 35.7 - - + +
209A ILE* 4.4 5.4 - - + -
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Residues in contact with ARG 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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157A GLU 5.7 1.4 + - - -
160A HIS* 3.1 42.4 + - - +
161A GLU* 3.6 30.8 + - - +
162A ARG 3.2 0.2 - - - -
163A VAL* 1.3 73.5 - - - +
165A LYS* 1.3 59.2 + - - +
167A TYR 3.4 1.2 + - - -
168A HIS 2.9 9.0 + - - -
169A ILE* 2.6 57.2 + - + +
171A VAL* 3.8 33.2 - - - +
176A ILE* 3.4 31.8 + - - +
177A PRO 3.7 7.1 + - - -
178A PRO* 4.7 0.4 - - - +
179A PRO* 4.1 4.6 - - + +
210A GLN* 2.9 26.3 + - - +
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Residues in contact with LYS 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 GLU* 2.8 36.7 + - - +
162A ARG* 4.0 5.4 - - - +
164A ARG* 1.3 71.8 - - - +
166A LYS* 1.3 65.0 + - - +
168A HIS* 3.2 21.7 + - - +
169A ILE 5.3 0.7 - - - -
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Residues in contact with LYS 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 ARG 3.0 14.8 + - - +
163A VAL* 3.5 11.2 - - - +
164A ARG 3.3 0.2 - - - -
165A LYS* 1.3 78.9 - - - +
167A TYR* 1.3 96.6 + - + +
168A HIS* 3.4 15.1 + - - -
181A LYS* 3.0 30.7 - - - +
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Residues in contact with TYR 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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163A VAL* 3.1 28.9 + - + +
166A LYS* 1.3 115.2 + - + +
168A HIS* 1.3 74.6 + - - +
169A ILE* 3.3 16.3 + - + -
181A LYS* 4.1 16.8 - - + +
204A PRO 5.9 0.7 - - - -
206A PRO* 3.6 32.4 - - + +
209A ILE* 3.7 29.2 - - + -
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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