Contacts of the strand formed by residues 205 - 217 (chain B) in PDB entry 3HCD
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 LEU 205 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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174B PRO* 4.0 3.2 - - - +
175B ALA 3.6 16.4 - - - +
176B ASP 3.7 20.9 - - - +
177B ALA* 3.8 14.8 - - - +
178B LEU* 4.0 15.9 - - + -
202B THR 2.9 13.2 + - - +
203B THR 4.2 2.3 - - - +
204B LEU* 1.3 79.0 - - - +
206B ARG* 1.3 69.1 + - - +
209B GLY* 4.0 11.0 - - - +
210B HIS 4.0 13.0 - - - +
211B LEU* 4.3 3.4 - - + +
248B TYR* 3.7 33.9 - - + +
279B LYS* 2.9 40.3 + - + +
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Residues in contact with ARG 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71B SER 4.4 9.9 + - - -
72B GLY* 5.8 0.4 - - - -
174B PRO* 3.6 29.1 - - + +
175B ALA 3.1 18.6 + - - +
176B ASP* 3.0 38.4 + - - +
205B LEU* 1.3 82.8 - - - +
207B PRO* 1.3 90.6 + - + +
208B GLY* 3.6 17.2 + - - -
209B GLY* 3.0 29.2 + - - +
210B HIS* 5.4 3.6 - - - -
279B LYS* 3.6 2.6 - - - +
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Residues in contact with PRO 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174B PRO* 5.3 1.8 - - + -
205B LEU 3.8 1.8 - - - +
206B ARG* 1.3 107.7 + - + +
208B GLY* 1.3 57.5 + - - +
279B LYS* 3.9 20.2 - - + +
280B VAL 4.4 2.0 - - - +
281B GLY* 3.6 24.2 - - - -
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Residues in contact with GLY 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B ARG* 3.6 12.3 + - - -
207B PRO* 1.3 71.8 - - - +
209B GLY* 1.3 60.9 + - - +
210B HIS* 3.8 5.7 + - - -
278B GLN* 3.0 28.7 + - - -
279B LYS 2.7 22.6 + - - -
281B GLY* 4.0 5.9 - - - +
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Residues in contact with GLY 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176B ASP 3.5 15.0 - - - -
205B LEU* 4.0 7.4 - - - -
206B ARG* 3.0 27.5 + - - +
207B PRO 3.1 1.6 + - - -
208B GLY* 1.3 78.5 - - - +
210B HIS* 1.3 63.2 + - - -
278B GLN* 3.3 4.0 - - - -
279B LYS* 2.8 31.2 + - - +
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Residues in contact with HIS 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69B GLU* 3.0 27.5 + - + -
70B VAL* 3.7 27.1 - - + +
71B SER 5.2 3.4 - - - -
176B ASP 3.3 9.6 + - - -
177B ALA* 3.2 5.8 - - + +
178B LEU 2.8 31.9 + - - +
205B LEU* 4.0 4.7 - - - +
206B ARG* 5.4 4.0 - - - -
208B GLY 3.8 5.0 + - - -
209B GLY* 1.3 79.5 - - - -
211B LEU* 1.3 54.3 - - - +
212B LEU* 5.3 2.0 - - + +
251B ARG* 3.8 11.0 - - - -
276B TRP* 2.8 35.5 + + + +
277B ALA 3.4 3.1 - - - -
278B GLN* 3.6 36.8 + - - +
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Residues in contact with LEU 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178B LEU* 3.4 27.8 - - + +
180B SER* 4.8 10.3 - - - -
198B LEU* 3.9 21.1 - - + -
201B ILE* 4.9 5.6 - - + -
205B LEU* 4.3 3.5 - - + +
209B GLY 4.2 0.4 + - - -
210B HIS* 1.3 73.0 - - - +
212B LEU* 1.3 81.6 + - - +
213B LEU* 4.3 15.3 - - + +
243B LEU* 3.9 16.6 - - + -
248B TYR* 3.6 40.2 - - + +
275B ALA 3.4 3.5 - - - +
276B TRP* 3.5 2.6 - - - -
277B ALA* 2.7 35.7 + - + +
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Residues in contact with LEU 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61B LEU* 3.9 16.4 - - + -
64B THR* 3.6 29.8 - - + -
65B PHE* 3.3 44.9 - - + -
70B VAL* 5.0 8.7 - - + -
178B LEU 2.8 16.5 + - - +
179B VAL* 3.4 11.8 - - + +
180B SER 3.0 26.2 + - - +
210B HIS* 5.3 1.6 - - + +
211B LEU* 1.3 74.9 - - - +
213B LEU* 1.3 60.4 + - - +
214B ILE* 4.0 1.6 + - - +
274B PHE* 4.1 13.5 - - + -
275B ALA 3.5 2.0 - - - -
276B TRP* 3.6 26.7 - - + -
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Residues in contact with LEU 213 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180B SER* 3.3 31.2 - - - +
182B PHE 5.8 0.2 - - - +
183B CYS 6.1 0.7 - - - +
184B LEU* 4.4 23.1 - - + +
185B GLU* 5.7 2.0 - - - +
194B PHE* 4.9 7.2 - - + -
198B LEU* 4.8 7.9 - - + -
201B ILE* 5.6 0.7 - - + -
211B LEU* 4.3 17.5 - - + -
212B LEU* 1.3 73.7 - - - +
214B ILE* 1.3 64.4 + - - +
239B VAL* 4.6 8.1 - - + -
243B LEU* 4.4 21.1 - - + -
273B PHE* 3.9 25.2 - - + -
274B PHE* 3.4 3.0 - - - -
275B ALA* 2.7 46.4 + - + +
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Residues in contact with ILE 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56B TRP* 5.5 1.1 - - + -
57B LYS* 4.1 23.1 - - + +
60B CYS* 5.7 0.2 - - + -
61B LEU* 3.8 36.1 - - + -
85B TYR* 4.9 2.7 - - + +
86B GLN* 5.3 1.6 - - + -
179B VAL* 6.0 2.2 - - + -
180B SER 2.9 7.5 + - - +
181B ALA* 3.2 19.6 - - + -
182B PHE* 2.8 49.6 + - + -
185B GLU* 4.7 1.0 - - - +
212B LEU 5.4 1.1 - - - +
213B LEU* 1.3 78.9 - - - +
215B GLY* 1.3 61.5 + - - +
272B VAL* 3.8 7.9 - - + -
273B PHE* 3.3 13.9 - - - +
274B PHE* 3.7 24.0 - - + -
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Residues in contact with GLY 215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182B PHE* 3.5 11.7 - - - -
185B GLU* 3.3 11.4 - - - -
214B ILE* 1.3 77.8 - - - +
216B ALA* 1.3 60.9 + - - -
272B VAL* 3.3 6.1 - - - +
273B PHE* 2.8 52.7 + - - -
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Residues in contact with ALA 216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182B PHE* 3.4 14.4 - - + -
185B GLU* 2.9 22.8 + - + +
215B GLY* 1.3 74.0 - - - -
217B LEU* 1.3 60.6 + - - +
218B GLU 4.1 0.5 + - - -
219B GLU* 3.6 31.9 + - + +
231B VAL* 5.9 0.2 - - - +
232B VAL 5.5 0.5 - - - +
234B VAL* 3.7 12.3 + - - +
269B VAL* 3.9 16.4 - - + -
271B GLY 3.7 4.3 - - - -
273B PHE* 3.7 10.2 - - - -
2002B LNR 4.4 1.8 - - - -
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Residues in contact with LEU 217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216B ALA* 1.3 71.8 - - - +
218B GLU* 1.3 74.9 + - + +
219B GLU 3.2 2.1 + - - -
234B VAL 3.6 4.5 - - - +
235B SER* 3.8 8.7 - - - +
236B GLU* 3.7 30.1 - - + +
255B THR* 3.6 39.3 - - + +
269B VAL* 4.1 0.9 - - - +
270B LYS* 3.2 20.2 + - + -
271B GLY* 2.7 22.0 + - - +
272B VAL 3.7 15.3 - - - +
273B PHE* 3.5 33.2 - - + +
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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