Contacts of the strand formed by residues 282 - 291 (chain D) in PDB entry 6C3P
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 GLU 282 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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326C TYR* 4.3 5.7 + - - -
33D ALA 4.9 0.3 - - - +
34D ARG* 4.3 6.2 + - - -
35D PHE* 3.2 42.6 + - - +
36D VAL 3.5 0.9 + - - +
219D VAL* 3.2 4.0 - - - +
220D VAL* 2.5 48.4 + - + +
233D LEU* 5.7 0.5 - - - +
281D LEU* 1.3 81.3 - - - +
283D ILE* 1.3 62.5 + - - +
284D ILE* 3.3 14.3 - - + +
303D SER* 3.1 27.1 + - - -
304D TYR 3.2 21.5 - - - +
305D LEU* 4.2 7.1 - - + +
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Residues in contact with ILE 283 (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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198D PHE* 4.1 28.9 - - + -
217D MET* 4.5 7.0 - - + -
218D GLN 3.3 20.9 - - - +
219D VAL* 3.7 15.7 - - + +
238D ILE* 4.2 11.4 - - + -
267D LEU* 3.7 30.1 - - + -
281D LEU* 5.2 3.8 - - + -
282D GLU* 1.3 79.5 - - - +
284D ILE* 1.3 65.3 + - - +
285D VAL* 3.6 11.0 + - + +
303D SER* 3.8 1.0 - - - -
304D TYR* 2.9 33.4 + - + +
309D ILE* 4.0 23.3 - - + -
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Residues in contact with ILE 284 (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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250C PHE* 4.0 19.5 - - + -
35D PHE* 3.6 19.3 - - + -
36D VAL* 4.6 9.0 - - + +
216D HIS 3.2 5.5 - - - +
217D MET* 3.3 0.2 - - - -
218D GLN* 2.2 66.1 + - + +
220D VAL* 3.6 23.3 - - + -
282D GLU* 3.3 37.2 - - + +
283D ILE* 1.3 65.9 - - - +
285D VAL* 1.3 62.3 + - - +
286D ILE* 3.6 18.6 - - + -
301D ARG* 5.3 2.0 - - + -
302D THR 4.0 5.6 - - - +
303D SER* 3.8 7.2 - - - -
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Residues in contact with VAL 285 (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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183D PHE* 4.7 11.9 - - + -
198D PHE* 5.9 1.1 - - + -
200D LEU* 4.2 27.8 - - + -
215D ILE* 5.0 9.0 - - + -
216D HIS 3.9 1.6 - - - -
217D MET* 4.4 22.4 - - + +
257D ILE* 6.0 1.6 - - + -
283D ILE* 3.8 16.4 - - + +
284D ILE* 1.3 78.2 - - - +
286D ILE* 1.3 69.9 + - - +
300D ALA 4.0 0.5 - - - +
301D ARG* 3.6 6.8 - - - +
302D THR* 2.8 53.2 + - + +
304D TYR* 4.3 7.6 - - + -
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Residues in contact with ILE 286 (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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250C PHE* 3.7 25.6 - - + -
214D THR 3.4 0.3 - - - +
215D ILE* 3.3 10.6 - - - +
216D HIS* 3.0 58.7 + - + +
218D GLN* 4.0 8.5 - - - +
284D ILE* 3.6 30.5 - - + +
285D VAL* 1.3 77.5 - - - +
287D LEU* 1.3 61.8 + - - +
288D GLU* 3.3 24.5 - - + +
299D GLN* 3.3 30.7 - - - +
300D ALA 3.9 2.7 - - - -
301D ARG* 4.3 3.1 - - + -
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Residues in contact with LEU 287 (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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181D LEU* 3.6 37.7 - - + +
183D PHE* 3.9 30.1 - - + -
202D VAL* 4.6 9.0 - - + -
210D ILE* 5.9 5.4 - - + -
213D ALA* 4.2 23.8 - - + -
214D THR 3.4 7.2 - - - +
215D ILE* 3.6 23.6 - - + -
249D ILE* 4.7 5.8 - - + -
251D LEU* 5.3 4.0 - - + -
285D VAL* 4.3 0.4 + - + -
286D ILE* 1.3 75.1 - - - +
288D GLU* 1.3 63.6 + - - +
298D THR 3.9 0.3 - - - +
299D GLN* 3.2 6.9 - - - -
300D ALA* 3.0 35.0 + - + +
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Residues in contact with GLU 288 (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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210C ILE 5.1 0.3 - - - +
211C ILE* 3.7 9.6 - - + -
212C SER* 3.3 40.1 + - - -
249C ILE 5.5 2.4 - - - +
250C PHE* 5.2 2.3 - - - -
210D ILE* 5.2 0.2 - - - -
212D SER 3.1 5.7 - - - +
213D ALA* 4.3 1.3 - - - -
214D THR* 2.8 41.1 + - - +
216D HIS* 4.5 13.3 - - - -
286D ILE* 3.3 17.8 - - + +
287D LEU* 1.3 81.6 - - - +
289D GLY* 1.3 57.7 + - - +
297D THR* 5.0 1.6 - - + -
298D THR 3.5 5.4 - - - +
299D GLN* 3.2 35.3 + - + +
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Residues in contact with GLY 289 (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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210D ILE* 3.4 18.9 - - - +
211D ILE 3.1 13.7 - - - -
212D SER* 4.0 3.4 - - - -
287D LEU* 4.4 0.6 - - - +
288D GLU* 1.3 74.5 - - - +
290D VAL* 1.3 66.2 + - - -
297D THR* 3.1 9.5 - - - +
298D THR 3.0 30.7 + - - +
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Residues in contact with VAL 290 (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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297A THR* 4.2 25.4 - - + +
210D ILE* 3.2 6.3 - - - +
211D ILE* 2.7 55.2 + - + +
212D SER* 5.4 4.3 - - - -
289D GLY* 1.3 74.7 - - - -
291D VAL* 1.3 77.3 + - - +
295D GLY* 3.3 28.3 - - - +
296D ILE 3.5 3.1 - - - +
297D THR* 3.5 19.7 - - - +
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Residues in contact with VAL 291 (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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61A THR* 6.0 5.4 - - + -
297A THR 5.1 0.5 - - - +
174D ALA* 5.3 5.4 - - + -
177D ARG* 4.6 27.4 - - + +
208D SER* 5.9 1.8 - - - +
209D MET 4.4 1.3 - - - -
210D ILE* 3.8 5.1 - - + +
211D ILE* 4.1 0.7 - - - +
289D GLY 4.0 0.4 + - - -
290D VAL* 1.3 82.4 - - - +
292D GLU* 1.3 68.4 + - - +
293D THR* 3.8 17.0 - - + +
294D THR* 2.7 44.2 - - + +
295D GLY* 4.0 0.5 - - - -
296D ILE* 3.0 13.7 + - + +
298D THR* 4.0 28.0 - - + -
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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