Contacts of the helix formed by residues 179 - 188 (chain D) in PDB entry 6Q2J
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 179 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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141D ASP* 4.6 12.1 - - - +
143D VAL* 5.4 7.0 - - + -
144D CYS* 5.4 1.3 - - + -
177D ASN 5.0 0.2 - - - +
178D ILE* 1.3 91.3 - - + +
180D PHE* 1.3 65.7 + - - +
181D ASN* 3.3 17.9 - - - +
182D ILE* 3.4 22.4 + - + +
183D ALA* 3.3 18.9 + - - +
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Residues in contact with PHE 180 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178D ILE 3.8 1.5 + - - -
179D PRO* 1.3 71.3 - - - +
181D ASN* 1.3 61.2 + - - +
183D ALA* 3.5 6.0 + - + +
184D GLN* 2.9 47.6 + - + +
273D ASP* 4.7 12.6 - - + -
276D LYS* 4.5 9.0 - - + -
277D ALA* 4.2 31.2 - - + -
280D ILE* 4.0 29.2 - - + -
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Residues in contact with ASN 181 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179D PRO* 3.4 15.3 - - - +
180D PHE* 1.3 74.5 - - - +
182D ILE* 1.3 85.6 + - - +
184D GLN* 3.3 12.2 + - - +
185D MET* 2.9 44.5 + - + +
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Residues in contact with ILE 182 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134D VAL* 5.1 2.4 - - + +
137D ALA* 4.7 9.6 - - + +
138D CYS* 4.5 11.0 - - + +
141D ASP* 4.5 24.2 - - + +
144D CYS* 3.7 27.4 - - + -
178D ILE* 4.9 4.9 - - + -
179D PRO* 3.4 28.2 + - + +
180D PHE 3.3 0.4 - - - -
181D ASN* 1.3 92.7 + - - +
183D ALA* 1.3 59.6 + - - +
185D MET* 3.4 18.1 + - + +
186D LEU* 2.9 39.5 + - + +
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Residues in contact with ALA 183 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175D TYR* 3.8 25.3 - - + +
178D ILE* 3.7 27.7 - - + +
179D PRO 3.3 10.5 + - - +
180D PHE* 3.9 8.5 - - + +
182D ILE* 1.3 77.8 - - - +
184D GLN* 1.3 57.7 + - - +
186D LEU* 3.8 1.1 - - - -
187D ALA* 2.9 31.4 + - - +
280D ILE* 4.0 16.5 - - + +
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Residues in contact with GLN 184 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180D PHE* 2.9 38.9 + - + +
181D ASN* 3.5 10.9 - - - +
183D ALA* 1.3 79.4 - - - +
185D MET* 1.3 63.3 + - + +
186D LEU 3.5 0.2 + - - -
187D ALA* 3.7 0.3 + - - +
188D PHE* 3.5 29.2 + - + +
273D ASP* 4.9 4.0 + - - -
276D LYS* 3.1 40.1 - - + +
280D ILE* 3.8 15.2 - - + +
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Residues in contact with MET 185 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129D TRP* 3.4 48.3 - - + +
134D VAL* 3.4 20.6 - - + +
137D ALA* 5.2 11.4 - - + -
181D ASN* 2.9 34.2 + - + +
182D ILE* 3.8 23.6 - - + +
184D GLN* 1.3 80.0 - - + +
186D LEU* 1.3 60.2 + - - +
187D ALA 3.4 0.2 - - - -
188D PHE* 3.5 11.4 + - - +
189D CYS* 3.8 8.3 + - - +
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Residues in contact with LEU 186 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134D VAL* 3.7 26.9 - - + -
138D CYS* 4.6 16.8 - - + -
148D LEU* 6.1 1.1 - - + -
174D PHE* 4.4 25.4 - - + -
175D TYR* 3.3 27.4 - - + +
178D ILE* 5.7 0.4 - - + -
182D ILE* 2.9 24.6 + - + +
183D ALA* 4.0 4.9 - - - +
185D MET* 1.3 75.3 - - - +
187D ALA* 1.3 63.6 + - - +
188D PHE 3.3 0.4 - - - -
189D CYS* 4.5 2.7 - - - -
205D LEU* 4.6 34.1 - - + +
206D HIS* 3.3 22.9 + - + +
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Residues in contact with ALA 187 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175D TYR* 4.6 2.0 + - + +
183D ALA 2.9 17.0 + - - +
184D GLN 3.7 4.7 + - - +
186D LEU* 1.3 80.0 - - - +
188D PHE* 1.3 75.3 + - + +
189D CYS 3.8 1.3 - - - -
206D HIS* 4.2 5.2 + - - -
279D TYR* 4.7 3.3 + - + -
280D ILE* 4.2 13.9 - - + -
283D LEU* 3.7 29.9 - - + +
313D ARG* 3.1 20.7 + - - +
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Residues in contact with PHE 188 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129D TRP* 4.3 10.0 - - - +
184D GLN* 3.5 24.0 - - + +
185D MET* 3.5 7.5 + - - +
186D LEU 3.3 1.4 - - - -
187D ALA* 1.3 90.5 - - + +
189D CYS* 1.3 59.7 + - - +
190D ASP* 5.3 1.8 - - - +
276D LYS* 3.5 38.6 - - + -
279D TYR* 3.5 42.8 - + + -
280D ILE* 5.4 4.5 - - + -
313D ARG* 3.7 31.4 - - + +
317D PHE* 4.1 27.8 - + + +
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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