Contacts of the helix formed by residues 166 - 184 (chain D) in PDB entry 1F5Q
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 ASP 166 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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162D ALA* 5.2 0.2 - - + -
163D PRO* 3.1 20.5 + - - +
165D GLU* 1.3 95.6 - - - +
167D TYR* 1.3 67.0 + - + +
168D LEU 3.4 0.4 + - - -
169D ASN* 3.4 5.9 + - - +
170D ILE* 3.1 32.6 + - + +
208D TYR* 3.0 23.8 - - + -
210D TYR* 2.8 34.6 + - - +
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Residues in contact with TYR 167 (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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9D PHE* 4.7 13.2 - - + -
153D ILE* 5.7 0.2 - - - +
154D CYS* 3.6 38.1 - - + -
157D LEU* 3.4 28.6 + - + +
158D HIS* 3.1 37.2 + - - +
162D ALA* 3.5 23.8 + - + -
163D PRO 3.2 28.7 - - - -
164D ARG* 3.2 18.6 + - + +
166D ASP* 1.3 76.8 - - - +
168D LEU* 1.3 59.0 + - - +
170D ILE* 3.2 2.8 + - - +
171D TYR* 2.8 30.5 + - - +
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Residues in contact with LEU 168 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6D PHE* 6.1 5.4 - - + -
164D ARG 4.6 1.2 + - - -
165D GLU 4.6 5.5 + - - +
166D ASP 3.5 0.8 - - - -
167D TYR* 1.3 78.1 - - - +
169D ASN* 1.3 63.7 + - - +
171D TYR* 3.2 8.9 + - + +
172D ASN* 3.0 50.0 + - - +
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Residues in contact with ASN 169 (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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165D GLU 4.9 4.6 + - - +
166D ASP* 3.4 9.9 + - - +
167D TYR 3.4 0.4 - - - -
168D LEU* 1.3 81.1 - - - +
170D ILE* 1.3 63.2 + - + +
172D ASN* 3.5 6.1 + - - +
173D LEU* 3.2 43.8 + - - +
208D TYR* 3.8 16.4 + - - +
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Residues in contact with ILE 170 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153D ILE* 4.3 8.2 - - + +
157D LEU* 3.9 20.0 - - + -
166D ASP 3.1 20.6 - - - +
167D TYR 3.2 3.5 + - - +
169D ASN* 1.3 74.1 - - - +
171D TYR* 1.3 65.5 + - - +
173D LEU* 3.6 6.8 + - + +
174D CYS* 3.2 36.1 + - - -
200D MET* 4.9 0.9 - - + -
203D THR* 4.3 3.4 - - - +
204D MET* 3.9 37.9 - - + -
208D TYR* 3.9 25.1 - - + +
210D TYR* 3.8 22.2 - - - +
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Residues in contact with TYR 171 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5D GLU* 4.3 20.6 - - + +
67D ASN* 4.5 12.9 + - + +
68D ASN* 3.8 25.3 + - - -
150D THR* 3.7 38.0 - - + +
153D ILE* 4.5 15.9 - - + +
154D CYS* 4.7 17.0 - - - -
167D TYR 2.8 16.5 + - - +
168D LEU* 3.4 12.6 - - + +
170D ILE* 1.3 76.8 - - - +
172D ASN* 1.3 73.3 + - - +
174D CYS* 3.3 2.4 + - - +
175D ARG* 3.0 48.7 + - + +
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Residues in contact with ASN 172 (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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67D ASN* 5.7 1.2 - - - +
168D LEU* 3.0 43.8 + - - +
169D ASN* 4.1 6.6 - - - +
171D TYR* 1.3 92.6 - - - +
173D LEU* 1.3 59.3 + - + +
174D CYS 3.3 0.2 - - - -
175D ARG* 4.3 6.8 - - - +
176D PRO* 3.0 24.6 - - - +
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Residues in contact with LEU 173 (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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169D ASN* 3.2 44.1 + - - +
170D ILE* 4.1 4.9 - - + +
171D TYR 3.3 0.2 - - - -
172D ASN* 1.3 79.4 - - + +
174D CYS* 1.3 58.7 + - - +
176D PRO* 3.4 11.2 - - - +
177D LYS* 3.7 20.2 - - - +
203D THR* 3.9 29.8 - - + +
208D TYR* 5.7 1.6 - - - +
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Residues in contact with CYS 174 (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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153D ILE* 3.4 23.6 - - + -
170D ILE* 3.2 28.4 + - - +
171D TYR 3.9 0.4 - - - +
173D LEU* 1.3 78.0 - - - +
175D ARG* 1.3 64.9 + - - +
176D PRO* 3.3 0.9 - - - -
177D LYS* 3.2 4.7 + - - +
178D ILE* 3.0 26.2 + - + +
199D CYS* 3.7 31.4 - - + -
200D MET* 3.9 13.0 - - - -
203D THR* 3.6 22.0 - - - -
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Residues in contact with ARG 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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65D GLN 4.9 1.4 + - - -
66D ASP 4.7 0.4 + - - -
67D ASN* 2.7 68.0 + - - +
150D THR* 4.6 4.7 - - + -
153D ILE* 4.8 0.2 - - - +
171D TYR* 3.0 37.2 + - + +
172D ASN* 4.3 7.9 - - - +
174D CYS* 1.3 76.3 - - - +
176D PRO* 1.3 67.3 - - + +
178D ILE* 3.4 7.7 + - - +
179D PHE* 3.0 72.8 + - + -
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Residues in contact with PRO 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 ASN 3.0 23.6 - - - +
173D LEU* 3.4 9.2 - - - +
174D CYS 3.4 4.3 - - - -
175D ARG* 1.3 91.0 - - + +
177D LYS* 1.3 66.1 + - + +
179D PHE* 3.5 5.4 + - + +
180D CYS* 3.1 33.8 + - - -
240D ILE* 5.5 0.4 - - - -
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Residues in contact with LYS 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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173D LEU* 3.7 15.9 - - - +
174D CYS* 3.2 3.8 + - - +
176D PRO* 1.3 79.9 - - + +
178D ILE* 1.3 57.9 + - - +
180D CYS* 3.3 2.9 + - - +
181D ALA* 2.9 28.1 + - - +
199D CYS* 3.5 29.4 - - + +
202D LEU* 4.2 26.5 - - + +
203D THR* 3.6 28.0 - - + -
236D VAL* 3.9 10.4 - - + +
237D ASP* 4.9 2.6 + - - -
240D ILE* 3.7 31.3 - - + +
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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
----------------------------------------------------------
71D PRO* 5.8 1.1 - - + -
149D SER* 3.7 39.9 - - - +
150D THR* 3.8 17.7 - - + -
153D ILE* 3.5 32.8 - - + -
174D CYS* 3.0 16.4 + - + +
175D ARG 3.7 4.0 - - - +
177D LYS* 1.3 75.9 - - - +
179D PHE* 1.3 65.4 + - + +
181D ALA* 2.9 18.7 + - - +
182D LEU* 3.0 33.2 + - + +
195D ILE* 4.7 6.3 - - + -
196D THR* 5.0 4.0 - - - -
199D CYS* 3.7 17.9 - - + -
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Residues in contact with PHE 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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57D PHE* 3.9 23.1 - + + -
67D ASN 2.9 26.2 - - - -
70D PHE* 3.3 31.6 - + + -
71D PRO* 3.3 29.2 - - + -
150D THR* 4.3 5.8 - - + -
175D ARG* 3.0 62.8 + - + +
176D PRO* 3.8 7.2 - - + +
178D ILE* 1.3 79.9 - - + +
180D CYS* 1.3 63.8 + - - +
182D LEU* 3.3 18.4 + - + +
183D CYS* 3.5 17.0 + - - -
243D PHE* 6.0 0.4 - - - -
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Residues in contact with CYS 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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57D PHE* 6.5 0.4 - - - -
176D PRO* 3.1 24.7 + - - +
177D LYS 3.7 3.8 - - - +
179D PHE* 1.3 77.5 - - - +
181D ALA* 1.3 66.1 + - - +
183D CYS* 3.2 12.8 + - - +
184D ASP* 3.4 8.0 + - - +
239D ALA* 3.5 29.4 - - - +
240D ILE* 4.1 20.2 - - + -
243D PHE* 3.8 39.2 - - + -
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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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177D LYS 2.9 12.9 + - - +
178D ILE* 2.9 16.9 + - - +
180D CYS* 1.3 79.3 - - - +
182D LEU* 1.3 55.3 + - + +
184D ASP 3.1 14.9 + - - +
187D SER* 2.9 35.7 + - - +
188D ALA* 3.4 6.4 + - - -
195D ILE* 4.2 19.5 - - + -
236D VAL* 4.5 11.2 - - + -
239D ALA* 3.7 6.0 - - + +
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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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49D ARG* 2.8 32.7 + - - -
53D THR* 4.2 3.1 - - - +
70D PHE* 4.6 7.0 - - + -
71D PRO* 4.1 32.1 - - + +
74D VAL* 4.2 26.0 - - + -
149D SER* 5.8 2.7 - - - +
178D ILE* 3.0 31.6 + - + +
179D PHE* 3.6 13.5 - - - +
180D CYS 3.1 0.4 - - - -
181D ALA* 1.3 74.5 - - + +
183D CYS* 1.3 56.2 + - - +
184D ASP 3.1 5.7 + - - -
188D ALA* 3.3 17.3 - - + +
195D ILE* 5.1 11.0 - - + -
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Residues in contact with CYS 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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49D ARG* 3.9 5.8 + - - -
50D LYS* 4.4 15.9 - - - +
53D THR* 3.8 33.5 + - - +
54D THR* 4.4 8.6 - - + +
57D PHE* 4.9 1.1 - - - -
70D PHE* 3.8 22.7 - - - -
179D PHE 3.5 11.4 + - - -
180D CYS 3.2 9.4 + - - +
182D LEU* 1.3 77.1 - - - +
184D ASP* 1.3 57.9 + - - +
185D GLY 3.8 1.6 + - - -
243D PHE* 3.8 34.1 - - + -
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Residues in contact with ASP 184 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49D ARG* 4.1 0.4 - - - -
50D LYS* 6.2 0.2 - - - -
180D CYS 3.4 2.1 + - - +
181D ALA 3.1 0.8 + - - +
182D LEU 3.1 0.6 - - - -
183D CYS* 1.3 78.4 - - - +
185D GLY* 1.3 61.9 + - - +
186D ARG* 3.5 28.3 + - - +
187D SER* 3.3 19.3 + - - +
188D ALA* 2.8 32.4 + - - +
235D LEU 4.9 0.9 - - - +
238D ILE* 4.6 10.4 - - - +
239D ALA* 3.7 22.7 + - + +
242D SER* 3.5 20.3 + - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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