Contacts of the helix formed by residues 184 - 193 (chain A) in PDB entry 6I4X
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 PRO 184 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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182A PRO 4.6 0.2 - - - +
183A LEU* 1.3 89.1 - - + +
185A THR* 1.3 58.6 + - + +
186A ARG* 3.0 27.4 - - + +
187A LEU* 2.8 38.0 + - + +
188A LYS 3.2 6.9 + - - -
105C MET* 4.3 16.2 - - + -
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Residues in contact with THR 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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183A LEU 3.6 1.7 + - - +
184A PRO* 1.3 71.3 - - - +
186A ARG* 1.3 57.5 + - - +
187A LEU 3.3 0.2 - - - -
188A LYS* 3.7 22.9 - - + +
189A ASP* 3.0 28.1 + - - +
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Residues in contact with ARG 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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184A PRO* 3.0 21.1 + - + +
185A THR* 1.3 82.2 + - - +
187A LEU* 1.3 68.7 + - + +
189A ASP* 3.6 7.5 + - - +
190A TYR* 3.4 17.2 + - - +
108C ASN* 3.4 31.7 + - - +
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Residues in contact with LEU 187 (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 GLN* 5.0 2.2 - - - +
183A LEU* 4.2 11.4 - - + -
184A PRO* 2.8 21.4 + - + +
186A ARG* 1.3 85.4 - - + +
188A LYS* 1.3 61.0 + - - +
189A ASP 3.2 1.8 - - - -
190A TYR* 2.9 13.7 + - + +
191A LEU* 2.9 31.9 + - - +
104C LEU* 4.1 27.8 - - + -
105C MET* 3.6 39.7 - - + -
108C ASN* 3.6 37.9 - - + +
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Residues in contact with LYS 188 (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 ILE* 3.3 44.0 - - + +
179A TRP* 3.4 23.2 + - - +
181A LEU 3.3 18.9 + - - -
183A LEU* 3.4 22.7 + - + +
184A PRO 3.2 9.5 + - - +
185A THR* 3.4 22.2 + - + +
187A LEU* 1.3 75.7 - - - +
189A ASP* 1.3 61.5 + - - +
191A LEU* 3.3 4.4 + - - +
192A GLU* 3.3 25.1 + - - +
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Residues in contact with ASP 189 (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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185A THR 3.0 18.0 + - - +
186A ARG* 3.6 8.3 - - - +
188A LYS* 1.3 77.6 - - - +
190A TYR* 1.3 61.3 + - - +
192A GLU* 3.4 14.9 + - - +
193A GLU* 3.6 30.2 + - - +
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Residues in contact with TYR 190 (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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45A GLN* 4.7 4.8 + - - -
162A SER* 4.2 2.4 + - - -
164A GLN* 3.6 40.8 - - + +
165A HIS* 3.3 21.7 + - - +
168A ARG* 2.6 71.8 + - + -
186A ARG 3.4 8.4 + - - +
187A LEU* 2.9 21.3 + - + +
189A ASP* 1.3 79.2 - - - +
191A LEU* 1.3 63.2 + - + +
192A GLU 3.3 0.5 + - - -
193A GLU* 3.4 19.2 + - - +
104C LEU* 4.3 14.8 - - + -
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Residues in contact with LEU 191 (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 ARG* 3.6 37.5 - - + +
171A ILE* 4.1 15.9 - - + -
172A ASN* 4.6 6.6 - - - +
178A ILE* 3.7 23.5 - - + +
181A LEU* 3.7 30.1 - - + -
183A LEU* 3.8 15.7 - - + -
187A LEU 2.9 16.7 + - - +
188A LYS 3.8 7.0 - - - +
189A ASP 3.3 0.4 - - - -
190A TYR* 1.3 79.3 - - + +
192A GLU* 1.3 59.3 + - - +
194A TYR 3.1 23.5 - - - +
195A LYS* 3.7 6.6 - - - +
104C LEU* 4.1 15.9 - - + -
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Residues in contact with GLU 192 (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 ILE* 3.6 20.1 - - + +
188A LYS 3.3 9.5 + - - +
189A ASP* 3.4 13.4 + - - +
190A TYR 3.2 1.0 - - - -
191A LEU* 1.3 73.6 - - - +
193A GLU* 1.3 61.7 - - + +
194A TYR 3.1 6.0 + - - -
195A LYS* 3.5 49.0 + - - +
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Residues in contact with GLU 193 (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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42A GLU* 4.5 16.5 - - - +
45A GLN* 5.6 5.1 - - + +
168A ARG* 4.2 4.7 - - - +
189A ASP* 3.6 34.9 + - - +
190A TYR* 3.4 23.3 + - - +
192A GLU* 1.3 77.0 - - - +
194A TYR* 1.3 64.7 + - - +
196A PHE* 5.4 0.5 - - - -
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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