Contacts of the helix formed by residues 170 - 181 (chain K) in PDB entry 5GJQ
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 MET 170 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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167K ILE* 5.3 6.1 - - + -
168K GLY 3.4 6.4 - - - +
169K GLY* 1.3 84.9 - - - +
171K ASP* 1.3 56.3 + - - +
172K ILE 3.6 1.1 - - - -
173K GLN* 2.9 54.1 - - - +
174K LYS* 2.2 68.9 + - + +
210K CYS 3.7 24.2 - - - +
211K GLY 5.5 2.2 - - - +
215K LEU* 5.8 2.9 - - + -
333K PHE* 4.7 7.2 - - + -
334K PRO* 3.8 15.9 - - + +
336K PRO* 5.9 3.4 - - + -
340K GLN* 4.2 11.9 - - - +
501K ADP 4.3 9.9 - - - +
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Residues in contact with ASP 171 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169K GLY* 4.1 6.3 + - - -
170K MET* 1.3 78.4 + - - +
172K ILE* 1.3 63.8 + - + +
174K LYS* 4.0 7.2 + - - +
175K GLN* 2.3 47.1 + - + +
339K ARG* 4.8 11.8 + - - -
343K LEU* 5.4 1.0 - - - +
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Residues in contact with ILE 172 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171K ASP* 1.3 83.1 - - + +
173K GLN* 1.3 64.3 + - + +
175K GLN* 3.4 18.6 + - - +
176K GLU* 2.4 45.2 + - + +
339K ARG* 6.4 0.4 - - - +
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Residues in contact with GLN 173 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170K MET* 2.9 37.5 + - + +
171K ASP 3.3 0.2 - - - -
172K ILE* 1.3 86.5 - - + +
174K LYS* 1.3 66.5 + - - +
176K GLU* 2.8 18.6 + - - +
177K VAL* 2.9 18.5 + - - +
215K LEU* 4.6 5.2 - - + -
331K ILE* 3.9 7.3 - - + +
332K GLU 2.2 35.6 + - - +
333K PHE* 3.0 26.6 - - + +
334K PRO* 2.9 31.6 - - - +
340K GLN* 4.3 6.1 + - - -
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Residues in contact with LYS 174 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164K TYR* 3.7 42.9 + - + -
167K ILE* 2.6 33.6 + - + +
168K GLY* 3.4 15.2 - - - -
169K GLY 4.0 2.2 - - - +
170K MET* 2.2 58.3 + - + +
171K ASP* 3.4 5.6 + - - +
173K GLN* 1.3 76.5 - - - +
175K GLN* 1.3 63.6 + - - +
177K VAL* 3.2 3.3 + - - +
178K ARG* 2.9 22.5 + - - +
215K LEU* 4.2 23.3 - - + +
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Residues in contact with GLN 175 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372J ARG* 3.5 15.8 + - - +
389J LYS* 4.5 7.3 - - - +
171K ASP* 2.3 34.7 + - + +
172K ILE* 4.1 20.2 + - - +
174K LYS* 1.3 68.8 - - - +
176K GLU* 1.3 58.3 + - - +
178K ARG* 3.3 21.4 - - - +
179K GLU* 2.3 84.3 + - + +
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Residues in contact with GLU 176 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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389J LYS* 5.6 0.7 + - - -
172K ILE* 2.4 23.8 + - + +
173K GLN* 2.8 18.5 + - - +
175K GLN* 1.3 76.0 + - - +
177K VAL* 1.3 51.0 + - - +
179K GLU* 3.0 14.6 + - - +
180K ALA* 2.4 37.3 + - - +
329K ARG* 2.5 53.3 + - - -
330K LYS 5.2 1.0 - - - +
331K ILE* 2.6 39.3 - - + +
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Residues in contact with VAL 177 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173K GLN 2.9 10.4 + - - +
174K LYS 3.8 4.9 - - - +
176K GLU* 1.3 75.3 - - - +
178K ARG* 1.3 55.6 + - - +
180K ALA* 2.7 10.2 + - + -
181K VAL* 2.6 48.0 + - + -
182K GLU* 3.6 1.5 + - + +
202K VAL* 5.2 3.8 - - + -
204K MET* 4.1 12.1 - - + -
215K LEU* 3.4 35.2 - - + -
219K VAL* 4.0 25.8 - - + -
308K ILE* 4.7 12.3 - - + -
331K ILE* 4.1 13.7 - - + -
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Residues in contact with ARG 178 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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374J ARG* 5.6 5.5 - - - +
164K TYR* 4.4 5.3 + - - +
174K LYS 2.9 14.1 + - - +
175K GLN* 3.3 24.5 - - - +
177K VAL* 1.3 78.5 - - - +
179K GLU* 1.3 59.2 + - - +
182K GLU* 3.2 45.7 + - + +
183K LEU* 2.7 42.3 + - + +
184K PRO* 2.9 6.1 - - - +
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Residues in contact with GLU 179 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368J MET* 4.1 20.5 - - - +
372J ARG* 1.7 44.6 + - + +
389J LYS* 4.2 4.7 + - - -
175K GLN* 2.3 58.1 + - + +
176K GLU* 3.2 14.5 - - - +
178K ARG* 1.3 75.7 - - + +
180K ALA* 1.3 51.2 + - - +
183K LEU* 4.6 12.3 - - + -
184K PRO* 2.3 30.2 - - - +
191K TYR* 2.9 4.5 + - - -
199K PRO* 5.4 0.7 - - - +
329K ARG* 3.6 24.2 + - - +
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Residues in contact with ALA 180 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176K GLU* 2.4 30.5 + - + +
177K VAL* 2.7 14.0 + - + +
179K GLU* 1.3 68.7 - - - +
181K VAL* 1.3 65.5 + - + +
184K PRO* 3.1 17.1 - - - +
199K PRO* 3.5 25.2 - - + +
202K VAL* 3.7 30.7 - - + -
306K LYS* 4.2 4.3 - - - +
329K ARG* 5.2 7.6 - - + +
331K ILE* 5.1 0.7 - - + -
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Residues in contact with VAL 181 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177K VAL* 2.6 20.4 + - + +
180K ALA* 1.3 87.6 - - + +
182K GLU* 1.3 59.2 + - - +
183K LEU 3.1 1.8 - - - -
184K PRO* 3.6 0.7 - - - -
185K LEU* 2.4 66.7 + - + +
202K VAL* 5.3 5.2 - - + -
219K VAL* 5.3 1.8 - - + -
261K ILE* 3.7 22.2 - - + -
306K LYS* 3.8 27.1 - - + -
307K VAL 5.7 0.2 - - - +
308K ILE* 4.4 19.1 - - + -
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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