Contacts of the helix formed by residues 178 - 186 (chain A) in PDB entry 4N7X
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 PHE 178 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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174A ILE* 2.8 46.2 + - + +
177A THR* 1.3 98.0 - - + +
179A THR* 1.3 58.2 + - - +
180A LYS 3.4 2.2 - - - -
181A THR* 3.3 20.5 + - + +
182A VAL* 3.0 28.3 + - + +
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Residues in contact with THR 179 (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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175A HIS* 2.7 38.4 + - + +
176A HIS* 3.5 14.7 + - - -
177A THR 3.6 2.5 + - - -
178A PHE* 1.3 69.8 - - - +
180A LYS* 1.3 66.9 + - - +
182A VAL* 3.3 2.9 + - - +
183A LYS* 3.0 39.4 + - + +
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Residues in contact with LYS 180 (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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178A PHE 3.4 0.2 - - - -
179A THR* 1.3 79.4 - - - +
181A THR* 1.3 62.8 + - - +
183A LYS* 3.6 7.2 + - - +
184A ARG* 3.3 54.1 + - - +
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Residues in contact with THR 181 (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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178A PHE* 3.3 23.1 + - + +
179A THR 3.3 0.2 - - - -
180A LYS* 1.3 79.5 - - - +
182A VAL* 1.3 58.3 + - + +
184A ARG* 3.3 15.1 + - + +
185A ILE* 3.0 44.9 + - + +
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Residues in contact with VAL 182 (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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47A VAL* 3.4 47.3 - - + +
48A THR* 4.9 3.8 - - - -
174A ILE* 3.8 12.1 - - + +
175A HIS* 3.5 32.1 - - + +
178A PHE* 3.0 21.9 + - + +
179A THR 3.3 4.5 + - - +
181A THR* 1.3 74.4 - - + +
183A LYS* 1.3 69.5 + - - +
185A ILE* 3.3 11.7 + - + +
186A GLU* 3.0 27.8 + - + +
189A LEU* 5.4 1.1 - - + -
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Residues in contact with LYS 183 (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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48A THR* 6.1 0.4 - - - +
50A ARG* 5.8 1.0 - - - +
175A HIS* 2.9 35.4 + - - -
179A THR* 3.0 28.7 + - + +
180A LYS* 3.8 7.9 - - - +
181A THR 3.4 0.2 - - - -
182A VAL* 1.3 77.5 - - - +
184A ARG* 1.3 62.5 + - + +
186A GLU* 3.5 39.0 - - - +
187A PRO* 3.9 6.1 - - - +
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Residues in contact with ARG 184 (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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180A LYS* 3.3 47.0 + - - +
181A THR* 3.3 15.4 + - - +
182A VAL 3.1 0.6 - - - -
183A LYS* 1.3 78.0 - - + +
185A ILE* 1.3 60.9 + - + +
186A GLU 3.2 4.0 - - - -
187A PRO* 3.4 12.2 - - - +
188A TYR* 4.1 10.4 - - - -
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Residues in contact with ILE 185 (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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47A VAL* 4.8 9.0 - - + -
174A ILE* 6.2 1.3 - - + -
181A THR* 3.0 34.5 + - + +
182A VAL* 3.4 22.4 - - + +
184A ARG* 1.3 78.4 - - + +
186A GLU* 1.3 66.1 + - - +
187A PRO* 3.4 1.6 - - - -
188A TYR* 3.1 29.4 + - + +
189A LEU* 3.6 20.9 + - + +
192A MET* 6.6 0.2 - - + -
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Residues in contact with GLU 186 (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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48A THR* 3.6 33.4 - - + +
113A TYR* 3.1 27.3 + - - +
182A VAL* 3.0 16.5 + - + +
183A LYS* 3.5 35.2 - - - +
185A ILE* 1.3 78.1 - - - +
187A PRO* 1.3 68.6 - - + +
188A TYR 3.1 1.2 + - - -
189A LEU* 3.2 20.1 + - + +
190A PRO* 3.4 9.0 - - - +
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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