Contacts of the helix formed by residues 174 - 189 (chain D) in PDB entry 6QXT
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 SER 174 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25C VAL* 4.9 12.2 - - - +
172D TYR 3.8 2.0 + - - -
173D PHE* 1.3 76.6 - - - +
175D LYS* 1.3 62.6 + - - +
176D ASP* 3.2 7.9 - - - -
177D GLU* 3.0 12.2 + - - +
178D ILE* 2.8 27.1 + - - +
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Residues in contact with LYS 175 (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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173D PHE 4.0 0.2 + - - -
174D SER* 1.3 73.9 - - - +
176D ASP* 1.3 58.2 + - - +
178D ILE* 3.2 9.4 + - - +
179D TYR* 2.9 27.0 + - - +
201D GLU 4.7 14.1 - - - +
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Residues in contact with ASP 176 (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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174D SER* 3.2 5.6 - - - -
175D LYS* 1.3 78.3 - - - +
177D GLU* 1.3 58.3 + - - +
179D TYR* 3.1 10.2 + - - +
180D GLN* 2.9 26.9 + - - +
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Residues in contact with GLU 177 (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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145D PHE* 5.1 14.1 - - + -
173D PHE* 3.9 11.7 - - + -
174D SER* 3.0 24.9 + - - +
176D ASP* 1.3 77.4 - - - +
178D ILE* 1.3 59.0 + - - +
180D GLN* 3.2 8.8 + - - +
181D ILE* 2.9 27.5 + - - +
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Residues in contact with ILE 178 (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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170D LEU* 6.1 5.8 - - + +
173D PHE* 4.5 9.8 - - + +
174D SER 2.8 12.6 + - - +
175D LYS* 3.2 11.9 + - - +
177D GLU* 1.3 73.4 - - - +
179D TYR* 1.3 60.8 + - - +
181D ILE* 3.2 7.9 + - - +
182D LEU* 2.9 30.7 + - - +
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Residues in contact with TYR 179 (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 LYS 2.9 13.5 + - - +
176D ASP* 3.4 12.1 - - - +
178D ILE* 1.3 76.3 - - - +
180D GLN* 1.3 57.8 + - - +
182D LEU* 3.9 4.9 - - - +
183D GLU* 2.9 31.9 + - - +
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Residues in contact with GLN 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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176D ASP 2.9 12.9 + - - +
177D GLU* 3.6 11.2 - - - +
178D ILE 3.2 0.2 - - - -
179D TYR* 1.3 75.7 - - - +
181D ILE* 1.3 58.2 + - - +
183D GLU* 4.1 3.9 - - - +
184D TYR* 2.9 32.2 + - - +
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Residues in contact with ILE 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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177D GLU 2.9 16.1 + - - +
178D ILE* 3.6 8.7 - - - +
180D GLN* 1.3 78.2 - - - +
182D LEU* 1.3 57.5 + - - +
184D TYR* 3.8 4.6 - - - +
185D THR* 2.9 28.8 + - - -
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Residues in contact with LEU 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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17D GLY* 5.6 6.4 + - - -
178D ILE 2.9 15.7 + - - +
179D TYR* 4.0 4.9 - - - +
181D ILE* 1.3 74.3 - - - +
183D GLU* 1.3 59.2 + - - +
185D THR* 3.0 8.6 + - - -
186D LYS* 2.9 28.9 + - - +
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Residues in contact with GLU 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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179D TYR 2.9 19.5 + - - +
180D GLN* 4.1 4.7 - - - +
182D LEU* 1.3 76.2 - - - +
184D TYR* 1.3 61.1 - - - +
186D LYS* 3.6 8.4 + - - +
187D LEU* 3.5 17.3 + - - +
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Residues in contact with TYR 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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152D LEU* 6.3 2.9 - - + -
180D GLN 2.9 20.1 + - - +
181D ILE* 3.9 4.9 - - - +
183D GLU* 1.3 74.3 - - - +
185D THR* 1.3 60.9 + - - +
187D LEU* 3.2 8.1 + - - +
188D SER* 2.9 28.8 + - - -
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Residues in contact with THR 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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16D LEU* 4.4 5.1 - - - +
17D GLY* 4.2 21.8 - - - -
152D LEU* 6.3 2.2 - - - -
181D ILE 2.9 18.7 + - - -
182D LEU* 3.0 8.9 + - - -
184D TYR* 1.3 76.7 - - - +
186D LYS* 1.3 62.0 + - - +
188D SER* 3.8 6.2 - - - +
189D GLN* 3.0 22.9 + - - -
190D ALA* 4.0 10.4 + - - +
192D VAL* 5.4 7.0 - - - -
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Residues in contact with LYS 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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16D LEU* 4.4 15.1 - - + +
182D LEU 2.9 11.8 + - - +
183D GLU* 3.8 12.1 - - - +
184D TYR 3.2 0.4 - - - -
185D THR* 1.3 78.5 - - - +
187D LEU* 1.3 58.7 + - - +
189D GLN* 3.8 8.0 + - - +
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Residues in contact with LEU 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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183D GLU 3.5 9.6 + - - +
184D TYR* 3.2 10.1 + - - +
186D LYS* 1.3 79.3 - - - +
188D SER* 1.3 61.5 + - - +
189D GLN* 3.2 3.4 + - - +
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Residues in contact with SER 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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152D LEU* 4.8 15.3 - - - -
156D LYS* 5.9 3.7 - - - +
184D TYR 2.9 16.6 + - - -
185D THR* 3.3 7.6 + - - -
187D LEU* 1.3 75.2 - - - +
189D GLN* 1.3 63.1 + - - +
190D ALA* 2.9 20.0 + - - +
49H SER* 4.7 8.7 - - - +
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Residues in contact with GLN 189 (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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16D LEU* 4.9 8.0 + - - +
185D THR 3.0 9.9 + - - -
186D LYS 4.3 6.7 - - - +
187D LEU 3.2 6.1 - - - +
188D SER* 1.3 76.1 - - - +
190D ALA* 1.3 64.0 + - - +
191D ASP* 3.8 1.0 + - - +
49H SER* 4.4 19.6 - - - -
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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