Contacts of the helix formed by residues 185 - 195 (chain A) in PDB entry 4Q44
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 GLY 185 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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179A ALA* 6.0 0.7 - - - -
184A VAL* 1.3 73.1 - - - +
186A LYS* 1.3 66.2 + - - -
189A ALA* 3.0 26.9 + - - +
871C C 2.9 32.1 + - - -
872C C 4.0 12.8 - - - -
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Residues in contact with LYS 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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185A GLY* 1.3 72.0 - - - +
187A VAL* 1.3 78.6 + - + +
189A ALA* 3.8 3.5 - - - +
190A ALA* 2.9 32.3 + - - +
870C A 5.6 2.8 + - - -
871C C 3.6 7.3 + - - +
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Residues in contact with VAL 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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186A LYS* 1.3 93.1 - - + +
188A SER* 1.3 59.7 + - - +
190A ALA* 3.2 6.8 + - - +
191A LYS* 2.9 49.3 + - + +
870C A 3.9 38.6 - - - +
871C C 3.3 17.5 + - - +
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Residues in contact with SER 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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183A GLY 4.2 1.7 + - - -
184A VAL* 3.9 9.9 - - - -
185A GLY 4.1 1.1 + - - -
187A VAL* 1.3 76.3 - - - +
189A ALA* 1.3 58.7 + - - +
191A LYS* 3.0 17.2 + - - +
192A LEU* 2.9 34.2 + - - +
215A PHE* 5.5 0.2 - - - -
218A PHE* 3.6 37.2 - - - -
870C A 3.6 6.1 + - - -
871C C 2.4 26.8 + - - -
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Residues in contact with ALA 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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178A LEU* 5.9 1.3 - - + -
179A ALA* 4.1 26.2 - - + +
184A VAL* 3.9 5.6 - - + +
185A GLY 3.0 20.0 + - - +
186A LYS* 3.9 4.0 - - - +
188A SER* 1.3 76.8 - - - +
190A ALA* 1.3 55.8 + - - +
192A LEU* 3.8 11.3 - - - +
193A GLU* 2.9 29.1 + - - +
197A LEU 4.8 0.3 - - - +
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Residues in contact with ALA 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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186A LYS 2.9 18.6 + - - +
187A VAL* 3.6 7.0 - - - +
188A SER 3.2 0.2 - - - -
189A ALA* 1.3 75.1 - - - +
191A LYS* 1.3 60.1 + - - +
193A GLU* 3.6 6.8 - - - +
194A ALA* 2.9 30.0 + - - +
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Residues in contact with LYS 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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187A VAL* 2.9 34.7 + - + +
188A SER* 3.0 13.6 + - - +
190A ALA* 1.3 73.0 - - - +
192A LEU* 1.3 66.7 + - - +
194A ALA* 3.1 7.8 + - - +
195A MET* 2.9 31.1 + - + +
214A ARG 5.7 1.1 - - - +
215A PHE* 3.5 36.4 - - + -
870C A 5.7 3.4 - - - -
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Residues in contact with LEU 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 LEU* 3.6 27.1 - - + -
184A VAL* 4.2 13.7 - - + -
188A SER 2.9 29.0 + - - +
189A ALA* 3.8 8.3 - - - +
191A LYS* 1.3 75.5 - - - +
193A GLU* 1.3 54.4 + - - +
195A MET* 2.9 24.8 + - + +
197A LEU* 2.7 46.4 + - + +
211A LEU* 6.3 0.2 - - + -
215A PHE* 3.4 31.4 - - + -
218A PHE* 4.5 5.6 - - + -
222A LEU* 4.0 25.1 - - + -
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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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189A ALA 2.9 20.3 + - - +
190A ALA* 3.6 9.2 - - - +
192A LEU* 1.3 75.7 - - - +
194A ALA* 1.3 57.8 + - - +
196A GLY* 2.9 19.7 + - - -
197A LEU 3.3 7.2 + - - +
198A ARG* 3.9 30.7 - - - +
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Residues in contact with ALA 194 (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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190A ALA 2.9 18.6 + - - +
191A LYS* 3.1 8.5 + - - +
193A GLU* 1.3 77.3 - - - +
195A MET* 1.3 60.1 + - + +
196A GLY 3.2 0.8 + - - -
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Residues in contact with MET 195 (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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191A LYS* 2.9 17.9 + - + +
192A LEU* 2.9 12.7 + - + +
194A ALA* 1.3 77.5 - - + +
196A GLY* 1.3 59.7 + - - +
197A LEU* 3.3 34.2 + - + +
210A MET* 4.5 11.4 - - - +
211A LEU* 4.9 1.3 - - + -
214A ARG* 3.2 48.0 - - - +
215A PHE* 3.5 33.7 - - + -
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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