Contacts of the helix formed by residues 175 - 184 (chain D) in PDB entry 3LOC
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 PHE 175 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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114C PHE* 4.0 7.9 - + - -
115C CYS* 3.8 34.8 - - + -
118C MSE 3.6 24.7 - - + -
170C GLN* 3.7 19.1 - - + -
174C ASP* 4.1 7.4 - - - -
175C PHE* 6.5 0.4 - + - -
212C URA 3.7 15.0 - - - -
115D CYS* 5.8 0.2 - - - -
171D HIS* 2.8 53.9 + + + +
174D ASP* 1.3 85.6 - - + +
176D ALA* 1.3 63.5 - - - +
177D PRO* 3.2 6.3 - - - -
178D GLN* 3.0 35.0 + - + +
179D VAL* 3.0 12.0 + - - +
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Residues in contact with ALA 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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172D TYR 3.4 17.7 + - - +
173D ALA* 3.2 19.0 + - - +
175D PHE* 1.3 74.8 - - - +
177D PRO* 1.4 61.0 - - + +
179D VAL* 3.3 5.9 + - - +
180D GLU* 2.7 41.5 + - - +
185D ALA 5.0 0.5 - - - +
186D THR* 5.8 6.9 - - + +
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Residues in contact with PRO 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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118C MSE 3.2 38.1 - - + +
121C GLY* 3.9 27.6 - - - +
122C ALA* 4.1 5.2 - - + -
126C MSE 4.1 14.8 - - + +
129C LEU* 4.4 2.2 - - - -
173D ALA 4.7 0.2 - - - +
174D ASP 4.3 1.8 - - - +
175D PHE* 3.2 6.3 - - - -
176D ALA* 1.4 96.8 - - + +
178D GLN* 1.3 51.1 + - - +
180D GLU* 3.6 7.8 + - + +
181D ALA* 2.7 34.7 + - - +
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Residues in contact with GLN 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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114C PHE* 3.3 19.2 - - - -
118C MSE 3.2 14.3 - - + +
129C LEU* 3.9 12.0 - - + +
133C LEU* 3.6 20.2 - - + +
163C PHE* 5.5 1.5 - - + -
166C TRP* 3.5 21.8 - - + -
212C URA 2.7 44.0 + - - -
171D HIS* 4.4 4.4 + - - -
175D PHE* 3.0 25.1 + - + +
177D PRO* 1.3 76.4 - - - +
179D VAL* 1.3 65.2 + - - +
181D ALA* 3.1 2.2 + - - +
182D VAL* 2.8 34.3 + - + +
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Residues in contact with VAL 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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163C PHE* 3.9 29.6 - - + -
171D HIS* 4.2 24.7 - - + +
172D TYR* 4.1 17.3 - - + +
175D PHE* 3.0 18.2 + - + +
176D ALA* 3.6 9.6 - - - +
178D GLN* 1.3 75.5 - - + +
180D GLU* 1.3 54.7 + - - +
182D VAL* 3.1 1.0 + - - +
183D THR* 2.7 40.8 + - - +
185D ALA 4.2 4.9 - - - +
186D THR* 5.9 0.9 - - - -
192D PHE* 3.9 29.6 - - + -
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Residues in contact with GLU 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 ALA* 2.7 24.6 + - - +
177D PRO* 3.7 8.4 - - + +
179D VAL* 1.3 73.3 - - - +
181D ALA* 1.3 63.1 + - - +
184D GLY* 2.9 28.0 + - - +
185D ALA 3.5 24.2 + - - +
186D THR* 3.4 23.8 - - + +
188D ARG* 5.3 0.5 + - - -
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Residues in contact with ALA 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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126C MSE 4.5 3.6 - - - -
129C LEU* 3.6 39.6 - - + +
130C THR* 3.9 19.2 - - + +
134C LYS* 3.6 22.0 + - - +
177D PRO 2.7 22.7 + - - +
178D GLN 3.1 5.8 + - - +
180D GLU* 1.3 74.2 - - - +
182D VAL* 1.3 59.2 + - + +
184D GLY 4.9 0.3 + - - -
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Residues in contact with VAL 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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129C LEU 5.2 1.3 - - - +
133C LEU* 4.8 13.9 - - + -
134C LYS* 3.9 28.7 - - + -
137C ILE* 4.0 23.6 - - + -
138C ASP* 4.5 3.4 - - - +
159C GLN* 3.5 24.3 + - - +
163C PHE* 3.6 31.0 - - + -
166C TRP* 5.6 0.7 - - + -
178D GLN* 2.8 30.6 + - + +
179D VAL 4.1 0.4 - - - +
181D ALA* 1.3 78.9 - - + +
183D THR* 1.3 60.1 + - - +
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Residues in contact with THR 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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134C LYS* 5.8 1.8 - - - -
159C GLN* 4.1 16.8 + - - +
163C PHE* 4.2 13.9 - - - -
179D VAL* 2.7 21.9 + - - -
182D VAL* 1.3 75.0 - - - +
184D GLY* 1.3 56.6 + - - +
185D ALA* 2.9 42.4 - - + +
192D PHE* 3.4 26.4 - - + -
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Residues in contact with GLY 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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134C LYS* 5.7 2.8 - - - +
180D GLU* 2.9 25.3 + - - +
181D ALA 4.9 0.4 + - - -
182D VAL 3.8 0.6 - - - -
183D THR* 1.3 75.9 - - - +
185D ALA* 1.3 58.0 + - - +
189D ASP* 4.7 1.2 - - - +
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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