Contacts of the helix formed by residues 175 - 186 (chain A) in PDB entry 6J95
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 175 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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173A SER* 3.1 11.2 + - - -
174A LYS* 1.3 74.6 - - - +
176A ILE* 1.3 64.6 + - - -
178A ALA* 3.1 19.8 + - - +
179A GLU* 3.9 2.4 + - - +
446A ARG 4.6 0.4 - - - -
447A ARG* 3.7 44.3 + - - -
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Residues in contact with ILE 176 (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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152A PHE* 5.2 8.7 - - + -
174A LYS 3.2 1.2 + - - -
175A GLY* 1.3 69.2 - - - -
177A LEU* 1.3 66.3 + - - +
179A GLU* 3.0 39.5 + - - +
180A ILE* 3.1 32.6 + - + +
291A PRO* 4.6 12.6 - - + -
292A ILE* 6.2 0.2 - - + -
445A ILE* 4.0 22.0 - - + +
446A ARG 5.3 0.2 + - - -
447A ARG* 3.2 16.4 - - - +
464A ASP* 3.2 41.2 + - + +
466A PHE* 4.8 10.3 - - + -
602A RET 6.1 0.2 - - + -
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Residues in contact with LEU 177 (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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174A LYS* 3.0 50.6 + - + +
176A ILE* 1.3 80.4 - - - +
178A ALA* 1.3 60.8 + - - +
180A ILE* 3.2 7.5 + - + +
181A LEU* 3.1 33.1 + - + +
190A ILE* 3.8 19.5 - - + +
191A PRO* 4.7 1.1 - - + -
445A ILE* 3.7 26.4 - - + +
601A HEM 4.0 10.1 - - - +
602A RET 3.6 44.4 - - + -
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Residues in contact with ALA 178 (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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174A LYS* 4.1 4.1 + - + +
175A GLY 3.1 12.0 + - - +
176A ILE 3.1 0.6 - - - -
177A LEU* 1.3 77.1 - - - +
179A GLU* 1.3 61.0 + - - +
182A ASP* 2.9 38.6 + - + +
191A PRO* 3.7 32.5 - - + +
193A ASP* 6.1 0.2 - - - +
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Residues in contact with GLU 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 GLY 3.9 1.9 + - - +
176A ILE* 3.0 36.5 + - - +
178A ALA* 1.3 78.3 - - - +
180A ILE* 1.3 69.3 + - + +
182A ASP* 4.5 5.7 + - - +
183A PHE 5.5 0.3 + - - -
287A ARG* 4.6 13.3 + - - -
291A PRO* 3.6 26.0 - - - +
447A ARG* 5.1 2.8 + - - -
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Residues in contact with ILE 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A ILE* 3.1 32.6 + - + +
177A LEU* 3.5 8.5 - - - +
178A ALA 3.1 0.2 - - - -
179A GLU* 1.3 84.4 - - + +
181A LEU* 1.3 71.6 + - + +
183A PHE* 3.4 23.9 - - - -
284A ALA 4.2 2.2 - - - +
287A ARG* 3.6 24.6 - - + +
288A SER* 3.4 49.6 - - - +
291A PRO* 4.4 5.6 - - + -
445A ILE* 4.4 14.8 - - + -
602A RET 4.1 11.0 - - + -
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Residues in contact with LEU 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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177A LEU* 3.1 31.7 + - + +
180A ILE* 1.3 84.1 - - + +
182A ASP* 1.3 64.9 + - - +
183A PHE* 3.1 7.1 + - - -
184A VAL* 3.1 8.3 + - + +
185A MET* 2.9 56.1 + - + +
190A ILE* 3.7 29.8 - - + -
191A PRO* 4.5 7.2 - - + -
284A ALA* 4.8 16.2 - - + -
288A SER* 5.4 0.4 - - - +
376A ILE* 5.6 2.2 - - + -
554A ALA* 5.9 1.3 - - + -
602A RET 4.1 26.0 - - + -
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Residues in contact with ASP 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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178A ALA* 2.9 23.6 + - + +
179A GLU* 4.5 5.1 - - - +
180A ILE 3.6 1.0 - - - -
181A LEU* 1.3 75.5 - - - +
183A PHE* 1.3 66.2 + - - +
186A GLY* 3.0 40.3 + - - +
191A PRO* 5.0 3.3 - - + +
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Residues in contact with PHE 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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179A GLU 5.5 0.2 + - - -
180A ILE 3.4 23.1 - - - -
181A LEU* 3.1 2.1 + - - -
182A ASP* 1.3 83.9 + - - +
184A VAL* 1.3 84.8 + - + +
280A VAL* 3.8 12.8 - - + -
283A GLU* 3.5 28.5 - - + -
284A ALA* 3.6 26.0 - - + -
287A ARG* 3.6 41.8 - - - +
310A VAL* 4.4 10.3 - - + -
314A LEU* 3.7 27.2 - - + +
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Residues in contact with VAL 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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181A LEU* 3.4 12.8 - - + +
183A PHE* 1.3 109.9 - - + +
185A MET* 1.3 73.6 + - + +
186A GLY 3.4 1.3 - - - -
280A VAL* 3.4 24.9 - - + -
284A ALA* 5.0 6.1 - - + -
314A LEU* 4.1 11.8 - - + +
369A ASP* 4.6 5.4 - - - +
372A MET* 3.4 37.1 - - + +
376A ILE* 4.4 12.6 - - + -
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Residues in contact with MET 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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181A LEU* 2.9 48.3 + - + +
184A VAL* 1.3 85.4 - - + +
186A GLY* 1.3 65.9 + - - +
187A LYS 3.1 0.9 + - - -
188A GLY* 2.8 16.8 + - - -
190A ILE* 4.0 20.0 - - + -
191A PRO* 3.9 18.8 - - + -
369A ASP* 3.3 15.1 - - - +
373A THR* 3.4 38.4 + - - +
376A ILE* 3.6 37.7 - - + -
377A ALA 4.7 0.2 - - - +
602A RET 4.2 4.9 - - + -
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Residues in contact with GLY 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182A ASP* 3.0 35.1 + - - +
184A VAL 3.4 1.8 - - - -
185A MET* 1.3 76.5 - - - +
187A LYS* 1.3 57.5 + - - -
188A GLY 3.3 2.6 + - - -
191A PRO* 3.6 15.8 - - - +
192A ALA* 5.5 0.3 + - - -
369A ASP* 3.5 11.4 + - - -
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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