Contacts of the strand formed by residues 180 - 192 (chain E) in PDB entry 1DU3
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 GLY 180 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178E GLU 3.8 1.6 + - - -
179E LYS* 1.3 76.1 - - - +
181E PHE* 1.3 69.1 + - - -
182E TYR* 3.3 8.1 - - - -
249E GLU* 3.5 10.4 - - - +
250E LEU 3.1 29.7 + - - +
279E LEU* 4.2 6.1 - - - -
281E GLY 4.2 12.3 - - - -
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Residues in contact with PHE 181 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180E GLY* 1.3 74.6 - - - -
182E TYR* 1.3 59.7 + - - +
247E ILE* 3.8 9.9 - - + -
248E PHE 3.6 3.1 - - - -
249E GLU* 4.1 31.6 - - + -
279E LEU* 2.9 20.3 - - - +
280E VAL* 3.1 27.3 + - + +
281E GLY* 3.2 35.0 - - - -
121F ARG* 3.7 17.3 - - + -
123F ALA* 4.3 5.6 - - + -
163F PHE* 3.6 47.3 - + + -
165F SER* 3.9 15.5 - - - -
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Residues in contact with TYR 182 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122E VAL* 3.5 31.7 - - + +
167E LEU* 4.4 7.8 - - + +
176E ILE* 3.7 26.1 - - + +
177E HIS 4.7 1.0 + - - -
178E GLU* 2.8 36.5 + - - +
180E GLY 3.3 26.0 - - - -
181E PHE* 1.3 73.4 - - - +
183E TYR* 1.3 61.8 + - - +
184E ILE* 3.5 11.3 + - + +
246E GLY 3.4 1.0 - - - +
247E ILE* 3.0 23.9 - - - +
248E PHE 3.0 12.2 + - - +
250E LEU* 3.8 26.5 - - + -
277E ALA* 4.5 7.4 - - + -
278E PHE 3.1 22.7 - - - -
279E LEU* 3.3 20.4 - - + +
280E VAL* 3.9 0.2 - - - -
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Residues in contact with TYR 183 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183D TYR* 4.2 9.0 - + - -
182E TYR* 1.3 71.0 - - - +
184E ILE* 1.3 57.2 + - - +
185E TYR* 3.9 18.6 - + + -
243E TYR* 3.0 24.4 + - - -
245E GLY* 3.3 10.2 - - - -
246E GLY* 3.3 27.6 - - - -
247E ILE* 4.2 6.7 - - + +
277E ALA* 2.9 6.4 - - - +
278E PHE* 2.8 74.3 + + + -
280E VAL* 3.9 5.3 - - + +
183F TYR* 3.7 15.3 + + - -
185F TYR* 4.2 5.4 - + - -
243F TYR* 2.3 36.0 + - - -
278F PHE* 3.9 17.5 - + + -
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Residues in contact with ILE 184 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182E TYR* 3.8 13.9 - - + +
183E TYR* 1.3 79.4 - - - +
185E TYR* 1.3 62.9 + - - +
210E ILE* 4.0 25.8 - - + -
222E LEU* 4.2 22.9 - - + -
223E MET* 3.3 8.3 - - + +
245E GLY* 3.0 21.8 - - - -
246E GLY 2.8 12.7 + - - +
248E PHE* 4.4 11.0 - - + -
250E LEU* 4.0 24.5 - - + -
256E ILE* 4.3 12.8 - - + -
275E PHE* 4.0 18.2 - - + -
276E GLY 3.6 5.8 - - - +
277E ALA* 3.8 10.5 - - + -
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Residues in contact with TYR 185 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183D TYR* 4.4 6.1 - + - -
245D GLY 3.7 13.2 - - - -
246D GLY* 3.7 8.3 - - - -
247D ILE* 3.1 39.3 + - + +
125E HIS* 2.8 24.8 + - - +
183E TYR* 3.9 19.3 - + + -
184E ILE* 1.3 74.2 - - - +
186E SER* 1.3 69.8 + - - +
210E ILE* 4.1 4.5 - - - -
243E TYR* 3.2 37.0 - + + +
244E GLN 3.0 12.3 - - - +
245E GLY* 3.9 1.8 - - - -
274E PHE* 3.7 17.9 - + - -
275E PHE* 3.3 4.2 - - - -
276E GLY* 3.0 55.1 + - - +
277E ALA* 3.9 2.2 - - - -
278E PHE* 4.7 0.9 - + - -
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Residues in contact with SER 186 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154E TRP* 4.7 0.3 - - - -
185E TYR* 1.3 85.2 - - - +
187E GLN* 1.3 62.0 + - - +
188E THR* 3.7 12.1 - - - +
208E GLN* 3.2 34.7 + - - +
210E ILE* 3.9 2.6 - - - +
242E ILE 3.3 3.3 - - - +
243E TYR* 3.4 15.4 - - - -
244E GLN 3.1 6.2 + - - -
258E VAL* 3.6 27.4 - - - +
274E PHE 3.1 16.7 + - - -
275E PHE* 3.8 2.0 - - - -
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Residues in contact with GLN 187 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224D LYS 3.8 6.3 + - - -
225D SER* 3.6 15.4 + - - -
243D TYR 3.8 0.3 - - - +
244D GLN* 3.2 42.2 + - - +
154E TRP* 4.5 0.2 - - - -
186E SER* 1.3 75.5 + - - +
188E THR* 1.3 66.3 + - - +
241E SER* 4.4 5.6 - - - +
242E ILE 3.0 13.2 - - - +
243E TYR* 3.5 18.9 + - + +
272E ALA 3.7 10.5 - - - +
273E SER* 3.0 6.3 - - - -
274E PHE* 2.7 81.9 + - + +
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Residues in contact with THR 188 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151E ILE* 4.3 8.5 - - + -
154E TRP* 5.1 1.8 - - + -
186E SER* 3.7 14.4 - - - +
187E GLN* 1.3 80.6 - - - +
189E TYR* 1.3 60.9 + - - +
190E PHE* 3.2 25.1 + - - -
208E GLN* 3.5 28.6 + - + +
241E SER* 3.7 0.3 - - - -
242E ILE* 2.8 28.3 + - - +
258E VAL* 4.2 5.2 - - + -
260E VAL* 4.0 18.2 - - + -
266E ILE* 4.4 6.7 - - - -
272E ALA 4.4 0.7 - - - -
273E SER* 3.8 5.6 - - - -
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Residues in contact with TYR 189 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98B GLU* 2.9 32.2 - - - +
224D LYS* 3.9 7.9 - - + -
226D ALA* 3.8 11.1 - - + +
188E THR* 1.3 72.5 - - - +
190E PHE* 1.3 70.6 + - - +
191E ARG* 3.4 18.7 + - + -
239E LEU* 2.7 38.7 - - + +
240E TYR 4.2 1.3 - - - -
241E SER* 3.3 24.2 - - - +
266E ILE* 3.3 5.1 - - - +
267E ASP* 2.9 51.8 + - + +
272E ALA* 3.3 39.7 + - + +
273E SER* 3.2 10.0 + - - +
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Residues in contact with PHE 190 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188E THR* 3.2 27.4 - - - -
189E TYR* 1.3 73.7 - - - +
191E ARG* 1.3 58.6 + - - +
192E PHE* 4.4 4.5 - - + -
206E MET* 3.3 46.0 - - + -
207E VAL 3.9 22.0 - - - -
238E GLY 3.7 1.6 - - - +
239E LEU* 3.5 2.4 - - - -
240E TYR* 2.8 50.1 + - - +
242E ILE* 4.0 16.4 - - + -
260E VAL* 4.0 4.3 - - + -
261E THR 3.1 27.8 - - - -
262E ASN* 4.0 8.5 - - + -
265E LEU* 3.6 10.5 - - + +
266E ILE* 3.3 25.4 - - + -
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Residues in contact with ARG 191 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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67B ASP* 2.6 42.0 + - - +
70B GLU* 4.9 1.8 + - - -
92B ARG* 6.1 0.2 - - - +
98B GLU* 3.5 20.9 + - - -
99B MET* 3.2 26.3 - - - +
100B CYS* 5.9 0.6 - - - +
130E ARG* 6.2 1.6 - - - +
189E TYR* 3.4 32.5 + - + -
190E PHE* 1.3 74.3 - - - +
192E PHE* 1.3 64.0 + - - +
238E GLY 3.4 3.4 - - - -
239E LEU* 3.4 19.3 - - + -
265E LEU* 3.0 19.3 + - - +
267E ASP* 3.2 31.9 + - + +
269E ASP* 5.4 2.2 + - - -
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Residues in contact with PHE 192 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99B MET* 3.2 10.8 - - - +
190E PHE 4.4 1.6 - - - -
191E ARG* 1.3 83.3 - - - +
193E GLN* 1.3 58.5 + - - +
194E GLU* 3.2 44.2 + - + +
204E LYS* 3.7 23.6 - - + -
206E MET* 3.7 28.0 - - + -
229E SER* 4.3 3.8 - - - -
237E TYR* 3.3 2.2 - - - -
238E GLY* 2.9 41.1 + - - -
240E TYR* 3.6 28.3 - + - -
265E LEU* 3.7 36.3 - - + -
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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
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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