Contacts of the helix formed by residues 180 - 187 (chain D) in PDB entry 5GQQ
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 TYR 180 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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124C TYR* 3.6 16.4 - + - -
125C ARG 5.0 7.2 - - - -
126C LEU* 3.6 26.2 - - + +
158C LEU* 3.6 5.0 - - - +
162C THR* 2.4 50.4 + - + +
165C PHE* 3.6 39.2 - + + -
174C GLY* 3.2 14.7 + - - +
179D SER* 1.3 74.6 - - - +
181D GLU* 1.3 67.6 + - + +
183D TYR* 3.3 3.3 + + - +
184D LEU* 3.1 45.7 + - + +
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Residues in contact with GLU 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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125C ARG 4.5 2.0 - - - +
126C LEU* 3.4 20.6 - - + -
127C SER* 2.7 49.3 + - - -
130C PHE* 3.7 22.4 - - + +
179D SER* 3.3 6.0 + - - +
180D TYR* 1.3 79.4 - - + +
182D GLN* 1.3 65.7 + - - +
184D LEU* 3.5 9.9 + - - +
185D SER* 3.1 22.0 + - - -
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Residues in contact with GLN 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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175C TRP* 4.0 12.4 - - - -
168D TYR* 4.2 13.4 + - + -
177D GLN 4.2 0.9 - - - +
178D VAL* 3.3 26.0 - - + +
179D SER* 3.2 33.9 + - - +
181D GLU* 1.3 74.7 - - - +
183D TYR* 1.3 60.7 - - - +
185D SER* 3.1 8.9 + - - -
186D MET* 2.8 32.5 + - - +
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Residues in contact with TYR 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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161C LEU* 2.9 63.3 + - + +
164C ILE* 3.8 15.1 - - - +
165C PHE* 3.3 37.2 - + + -
176C ILE* 4.6 7.4 - - + -
183C TYR* 4.9 1.6 - + - -
186C MET* 4.2 24.1 + - + +
187C VAL* 5.6 1.9 - - + +
178D VAL* 4.4 5.1 - - + +
179D SER 3.0 17.4 + - - +
180D TYR* 3.4 6.5 - + - +
182D GLN* 1.3 77.5 - - - +
184D LEU* 1.3 69.4 + - + +
186D MET* 3.2 41.1 + - + +
187D VAL* 3.3 16.9 + - + +
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Residues in contact with LEU 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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126C LEU* 4.2 3.6 - - + -
130C PHE* 3.4 35.9 - - + -
158C LEU* 3.7 20.6 - - + -
161C LEU* 3.8 35.2 - - + -
162C THR* 4.6 0.7 - - - +
180D TYR* 3.1 48.2 + - + +
181D GLU* 3.7 4.0 - - - +
183D TYR* 1.3 87.3 - - + +
185D SER* 1.3 61.8 + - - +
186D MET 3.2 0.9 + - - -
187D VAL 3.3 10.9 + - - +
188D PHE* 3.3 26.1 + - + -
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Residues in contact with SER 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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130C PHE* 4.1 4.4 - - - -
133C ILE* 4.8 24.1 - - - +
137C LYS* 5.9 0.9 - - - -
168D TYR* 3.4 14.3 + - - -
181D GLU 3.1 14.5 + - - -
182D GLN* 3.1 12.3 + - - -
184D LEU* 1.3 76.4 - - - +
186D MET* 1.3 63.4 + - - +
187D VAL 3.6 0.2 + - - -
188D PHE* 3.8 16.5 + - - +
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Residues in contact with MET 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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183C TYR* 3.6 37.7 - - + +
186C MET* 5.9 0.4 - - + -
164D ILE* 3.5 33.4 - - + +
165D PHE* 5.5 1.1 - - - -
168D TYR* 3.3 51.1 - - + -
176D ILE* 3.8 28.3 - - + -
178D VAL* 4.0 10.3 - - + -
182D GLN 2.8 8.6 + - - +
183D TYR* 3.2 29.4 - - + +
184D LEU 3.1 0.2 - - - -
185D SER* 1.3 79.3 + - - +
187D VAL* 1.3 59.6 + - - +
188D PHE 3.3 6.5 + - - +
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Residues in contact with VAL 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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157C VAL* 4.9 1.2 - - - +
161C LEU* 3.8 16.7 - - + +
183C TYR* 3.2 26.7 - - + +
187C VAL* 3.4 25.1 - - + -
191C VAL* 3.3 34.7 - - + +
161D LEU* 4.7 8.7 - - + -
164D ILE* 5.2 4.0 - - + -
183D TYR* 3.3 24.4 + - + +
184D LEU 3.3 5.2 + - - -
186D MET* 1.3 74.1 - - + +
188D PHE* 1.3 72.1 + - - +
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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