Contacts of the helix formed by residues 178 - 195 (chain D) in PDB entry 2FYU
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 THR 178 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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167D GLU* 4.0 8.3 - - - +
176D PRO* 3.4 18.5 + - + -
177D ALA* 1.3 77.6 - - - +
179D MET* 1.3 57.9 + - - +
180D SER* 4.3 0.3 - - - -
181D GLN* 3.1 22.7 + - - +
182D VAL* 2.8 33.0 + - - +
15H ASP* 3.5 34.8 - - + +
16H PRO* 3.7 15.8 - - + +
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Residues in contact with MET 179 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131D LEU 4.1 9.9 - - - +
132D THR* 3.9 18.8 - - - +
134D TYR* 5.7 8.7 - - + +
162D PRO* 6.0 1.6 - - + -
164D ILE* 3.5 50.3 - - + +
165D TYR* 3.7 29.8 - - + +
167D GLU* 3.7 5.8 + - - +
178D THR* 1.3 70.8 - - - +
180D SER* 1.3 60.8 + - - +
182D VAL* 3.4 10.6 - - - +
183D ALA* 3.3 24.8 + - - +
15H ASP* 3.5 17.4 + - - +
17H LEU* 4.3 12.8 - - + -
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Residues in contact with SER 180 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128D PHE* 3.4 14.4 - - - -
132D THR* 4.1 7.8 - - - +
179D MET* 1.3 77.4 - - - +
181D GLN* 1.3 56.3 + - - +
183D ALA 3.6 0.5 + - - -
184D LYS* 3.1 23.2 + - - +
15H ASP* 3.4 14.0 + - - -
16H PRO* 4.3 6.1 - - - -
17H LEU* 3.3 26.0 - - - +
73H LEU* 3.4 20.9 - - - +
77H LEU* 3.8 21.5 - - - +
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Residues in contact with GLN 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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28D ARG* 4.2 3.0 - - - +
171D PHE* 5.1 2.0 - - - -
175D THR* 3.6 18.2 + - - -
176D PRO* 3.0 26.1 - - - +
177D ALA* 5.2 0.2 - - - -
178D THR* 3.1 20.7 + - - +
180D SER* 1.3 75.7 - - - +
182D VAL* 1.3 60.1 + - - +
183D ALA 3.3 0.4 - - - -
184D LYS* 3.3 10.4 + - - +
185D ASP* 2.8 72.4 + - - +
77H LEU* 3.9 24.2 - - + -
78H LYS* 2.9 33.8 + - - +
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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
----------------------------------------------------------
32D VAL* 3.7 31.0 - - + +
36D VAL* 5.8 1.1 - - + -
164D ILE* 3.8 33.7 - - + +
166D ASN 5.3 3.6 - - - +
167D GLU* 5.4 0.2 - - - +
168D VAL 6.2 0.4 - - - +
169D LEU* 3.9 21.1 - - + -
171D PHE* 5.6 4.5 - - + -
177D ALA* 4.8 13.1 - - + +
178D THR 2.8 19.7 + - - +
179D MET* 3.4 13.5 - - - +
181D GLN* 1.3 73.2 - - - +
183D ALA* 1.3 57.9 + - - +
185D ASP* 4.5 3.8 - - - -
186D VAL* 3.3 28.6 + - - +
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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
----------------------------------------------------------
128D PHE* 3.7 21.1 - - + -
131D LEU* 4.2 11.2 - - + -
132D THR* 3.8 13.0 - - + -
164D ILE* 4.2 12.3 - - + -
179D MET 3.3 20.0 + - - +
181D GLN 3.3 0.4 - - - -
182D VAL* 1.3 74.7 - - - +
184D LYS* 1.3 65.0 + - - +
186D VAL* 3.5 7.6 - - - +
187D CYS* 3.2 31.5 + - - -
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Residues in contact with LYS 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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12D TRP* 4.1 4.1 - - + -
13D SER* 6.2 5.4 - - - +
22D ASP* 5.7 1.4 - - - +
25D SER* 2.8 35.4 + - - -
28D ARG* 4.7 0.8 - - - +
128D PHE* 3.4 8.4 - - + -
180D SER 3.1 15.2 + - - +
181D GLN* 3.3 12.8 + - - +
183D ALA* 1.3 75.9 - - - +
185D ASP* 1.3 62.0 + - - +
187D CYS* 4.0 1.9 - - - +
188D THR* 2.8 41.9 + - - -
74H PHE* 3.6 38.1 - - + +
77H LEU* 3.8 34.1 - - + -
78H LYS 4.5 8.3 + - - -
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Residues in contact with ASP 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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25D SER* 3.0 40.4 + - - +
28D ARG* 3.4 39.0 + - + +
29D GLY* 3.4 10.8 - - - +
32D VAL* 4.5 3.1 - - + -
171D PHE* 4.4 7.3 - - - -
181D GLN* 2.8 42.1 + - - +
182D VAL* 4.2 4.4 + - - +
184D LYS* 1.3 77.2 + - - +
186D VAL* 1.3 57.9 + - - +
188D THR 3.3 1.4 + - - -
189D PHE 3.0 24.1 + - - -
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Residues in contact with VAL 186 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29D GLY* 3.9 13.2 - - - +
32D VAL* 3.8 28.3 - - + -
33D TYR* 4.6 2.0 - - + +
37D CYS* 4.2 17.5 - - - -
131D LEU* 3.8 25.4 - - + -
182D VAL 3.3 19.2 + - - +
183D ALA* 3.5 9.6 - - - +
185D ASP* 1.3 75.4 - - - +
187D CYS* 1.3 54.6 + - - +
189D PHE* 3.3 5.4 + - + +
190D LEU* 2.8 54.3 + - + +
242D HEM 4.2 8.1 - - + -
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Residues in contact with CYS 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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12D TRP* 3.7 22.2 - - + -
124D GLU* 3.6 21.5 - - + +
127D VAL* 3.8 19.3 - - - -
128D PHE* 3.4 34.8 - - - -
131D LEU* 4.4 3.8 - - - -
183D ALA 3.2 22.7 + - - +
186D VAL* 1.3 73.4 - - - +
188D THR* 1.3 60.8 + - - +
190D LEU* 4.0 6.9 - - - +
191D ARG* 3.1 27.4 + - - +
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Residues in contact with THR 188 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12D TRP* 4.3 7.0 - - - -
14D HIS* 4.2 21.3 - - + +
21D LEU* 3.5 24.8 - - + +
22D ASP* 3.6 25.6 - - + +
25D SER* 3.4 26.9 + - - +
26D ILE* 4.2 2.6 - - + +
184D LYS* 2.8 28.1 + - - -
185D ASP 3.3 3.3 + - - -
187D CYS* 1.3 72.7 - - - +
189D PHE* 1.3 60.8 + - - +
191D ARG* 3.5 1.6 - - - +
192D TRP* 3.4 16.5 + - - +
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Residues in contact with PHE 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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25D SER 4.5 0.6 + - - -
26D ILE* 3.5 25.4 - - + +
29D GLY* 3.6 21.3 - - - -
30D PHE* 3.4 40.4 - + + -
33D TYR* 3.7 19.7 - + + -
43D MET* 3.6 34.5 - - + -
51D LEU* 4.1 6.1 - - + -
91D PHE* 4.4 2.5 - + - -
185D ASP 3.0 13.5 + - - +
186D VAL* 3.5 9.0 - - + +
188D THR* 1.3 77.0 - - - +
190D LEU* 1.3 66.4 + - + +
192D TRP* 3.2 34.0 + + - +
193D ALA* 2.9 24.8 + - + +
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Residues in contact with LEU 190 (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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33D TYR* 5.6 2.2 - - + -
43D MET* 4.8 9.9 - - - -
113D LEU* 3.5 48.0 - - + +
114D SER 4.5 1.0 - - - +
116D ILE* 4.3 8.0 + - + -
117D VAL* 3.7 18.7 + - + +
127D VAL* 4.2 17.5 - - + -
186D VAL* 2.8 45.3 + - + +
187D CYS* 3.5 4.2 + - - +
189D PHE* 1.3 75.1 - - + +
191D ARG* 1.4 58.5 + - - +
193D ALA* 3.8 5.1 - - - +
194D ALA* 3.0 28.6 + - - +
242D HEM 4.0 17.0 - - + -
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Residues in contact with ARG 191 (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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248C ASP* 4.3 5.5 + - - -
14D HIS* 3.7 14.6 - - + +
21D LEU* 3.8 18.6 - - + -
117D VAL* 3.3 26.0 - - - +
118D ARG* 3.9 24.6 - - - +
123D GLY* 5.0 2.2 - - - -
124D GLU* 2.8 48.0 + - + -
187D CYS 3.1 13.8 + - - +
188D THR 3.5 10.3 - - - +
190D LEU* 1.4 74.0 - - - +
192D TRP* 1.3 52.2 + - - +
194D ALA* 3.2 3.1 + - - +
195D GLU* 2.8 68.2 + - + +
198D HIS* 4.2 9.8 - - + -
201D ARG* 5.6 0.4 - - - +
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Residues in contact with TRP 192 (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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21D LEU* 4.2 12.5 - - + +
23D HIS* 5.2 2.5 - + - -
26D ILE* 4.1 21.3 - - + -
46D VAL* 3.8 21.1 - - + -
50D HIS* 3.3 48.5 - - + -
51D LEU* 3.9 9.9 - - + -
54D VAL* 3.5 37.0 - - + +
188D THR 3.4 9.8 + - - +
189D PHE* 3.2 42.0 + + - +
191D ARG* 1.3 77.9 - - - +
193D ALA* 1.3 75.0 + - - +
195D GLU 4.0 4.7 - - - -
196D PRO* 3.1 60.5 + - + +
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Residues in contact with ALA 193 (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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71C ARG* 2.8 35.6 + - - +
43D MET* 3.9 32.8 - - + -
46D VAL* 4.2 8.5 - - + -
113D LEU 4.6 2.2 - - - +
114D SER 3.1 10.0 - - - +
189D PHE* 2.9 19.3 + - + +
190D LEU* 3.8 9.6 - - - +
191D ARG 3.4 0.2 - - - -
192D TRP* 1.3 80.7 - - + +
194D ALA* 1.3 56.3 + - - +
196D PRO* 5.3 0.2 - - - -
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Residues in contact with ALA 194 (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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71C ARG* 5.5 0.2 - - - -
114D SER 3.2 13.2 + - - +
115D TYR* 3.2 27.2 - - + -
117D VAL* 4.2 12.6 - - + -
118D ARG* 3.2 41.0 + - + +
190D LEU 3.0 19.0 + - - +
191D ARG* 3.2 5.4 + - - +
193D ALA* 1.3 74.6 - - - +
195D GLU* 1.3 58.4 + - + +
196D PRO* 3.9 3.9 - - - +
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Residues in contact with GLU 195 (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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247C PRO* 4.4 3.8 - - - +
248C ASP* 4.5 1.9 - - - +
118D ARG* 3.5 18.9 + - - +
191D ARG* 2.8 49.8 + - - +
192D TRP* 3.3 10.2 - - - +
194D ALA* 1.3 77.1 - - - +
196D PRO* 1.4 66.5 - - - +
197D GLU* 3.2 26.3 - - - +
198D HIS* 3.2 41.2 - - + +
201D ARG* 2.7 34.7 + - - -
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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
------------------------------------------------------------
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