Contacts of the strand formed by residues 279 - 288 (chain D) in PDB entry 1S9C
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 ILE 279 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82B ILE 6.3 1.3 - - - +
247D ALA* 3.1 21.5 - - + +
248D LYS* 3.2 19.1 + - - +
270D GLN* 3.2 29.8 - - + +
271D THR 3.6 4.7 - - - +
272D LYS* 3.9 22.7 - - + -
277D GLY 3.6 2.7 + - - +
278D ASP* 1.3 73.5 - - - +
280D VAL* 1.3 60.3 + - - +
281D ILE 3.7 21.1 - - - +
282D SER* 4.0 17.0 - - - -
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Residues in contact with VAL 280 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219D THR* 3.9 10.1 - - + -
246D PHE* 3.8 4.3 - - - +
247D ALA* 2.9 22.4 + - - -
248D LYS* 3.3 23.5 - - + +
249D PRO 3.6 4.9 - - - +
250D VAL* 3.3 33.2 - - + -
256D LEU* 4.7 0.4 - - + -
271D THR* 2.8 42.5 + - + +
272D LYS* 4.2 3.4 - - - +
273D VAL* 3.5 18.6 - - + -
278D ASP* 3.6 6.3 + - + +
279D ILE* 1.3 76.4 - - - +
281D ILE* 1.3 61.7 + - + +
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Residues in contact with ILE 281 (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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219D THR* 3.8 17.0 - - + +
220D PHE* 3.7 35.4 - - + +
223D SER* 4.8 1.1 - - - +
244D ALA* 3.8 22.2 - - + -
245D ARG 3.3 10.5 - - - +
246D PHE* 4.3 16.2 - - + -
269D PHE* 4.0 17.7 - - + -
270D GLN* 3.5 9.4 - - - +
271D THR* 2.9 41.7 + - - +
279D ILE* 3.6 1.8 - - - +
280D VAL* 1.3 91.7 - - + +
282D SER* 1.3 62.6 + - - +
284D ALA* 4.1 4.0 - - + -
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Residues in contact with SER 282 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245D ARG* 2.8 45.9 + - - +
247D ALA* 4.8 7.9 - - - +
269D PHE 4.7 0.4 - - - -
270D GLN* 4.4 8.5 - - - -
279D ILE* 4.0 16.8 - - - -
280D VAL 4.4 0.2 - - - -
281D ILE* 1.3 75.3 - - - +
283D ASN* 1.3 89.2 + - - +
284D ALA* 2.9 5.3 + - - +
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Residues in contact with ASN 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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164D ALA* 3.7 17.0 - - + +
165D VAL 2.8 44.7 + - - +
166D ALA* 3.2 24.1 + - - +
167D ILE* 4.3 16.3 + - - +
243D LYS* 4.3 2.3 - - - +
244D ALA* 4.8 0.7 - - - -
245D ARG* 3.9 20.6 - - + +
269D PHE 4.4 0.6 + - - -
270D GLN* 5.1 0.6 + - - +
282D SER* 1.3 97.7 + - - +
284D ALA* 1.3 57.1 + - - +
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Residues in contact with ALA 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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165D VAL 4.4 1.4 - - - +
167D ILE* 5.1 1.0 - - - +
243D LYS 2.9 18.4 - - - +
244D ALA* 3.5 14.6 - - + -
268D HIS* 3.5 6.8 + - - +
269D PHE* 3.0 58.6 + - + +
281D ILE* 4.1 3.6 - - + -
282D SER 3.1 4.0 - - - +
283D ASN* 1.3 80.5 - - - +
285D TYR* 1.3 64.1 + - - +
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Residues in contact with TYR 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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93D TYR* 3.9 21.0 - + - -
162D LYS* 5.7 1.0 - - - +
163D VAL 4.1 5.8 + - - -
165D VAL* 3.5 38.4 - - + -
241D ALA 4.8 3.8 - - - -
242D VAL* 3.2 5.6 - - - +
243D LYS* 2.8 59.3 + - + +
266D ARG* 3.2 48.7 + - + -
267D ILE 3.2 14.4 - - - +
268D HIS* 4.1 6.1 - - - +
269D PHE* 3.5 6.2 - - - -
284D ALA* 1.3 77.6 - - - +
286D VAL* 1.3 70.7 + - - +
287D ASP* 3.3 15.6 + - - -
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Residues in contact with VAL 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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224D ALA* 6.0 1.3 - - - -
227D VAL* 3.1 37.2 - - + -
239D PHE* 3.7 28.3 - - + -
241D ALA 3.0 13.7 - - - +
242D VAL* 3.9 8.3 - - + -
265D ASN 3.8 0.5 - - - +
266D ARG* 3.6 0.5 - - - -
267D ILE* 2.9 37.8 + - + +
269D PHE* 4.3 5.2 - - + -
285D TYR* 1.3 79.1 - - - +
287D ASP* 1.3 66.9 + - - +
288D LEU* 3.8 20.3 + - + -
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Residues in contact with ASP 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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238D ARG 3.8 0.2 - - - +
240D LYS* 3.0 34.5 + - + +
241D ALA* 2.7 24.8 + - + +
265D ASN* 3.6 4.3 - - + +
266D ARG* 2.8 53.2 + - - +
285D TYR* 3.3 10.8 + - - -
286D VAL* 1.3 72.5 - - - +
288D LEU* 1.3 64.9 + - - +
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Residues in contact with LEU 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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227D VAL* 5.2 4.3 - - + -
228D LEU* 5.7 0.4 - - - -
231D PHE* 3.2 35.9 - - + +
232D ALA* 3.9 15.5 - - + -
238D ARG* 3.1 28.7 - - + +
239D PHE* 4.2 8.3 - - + -
240D LYS* 4.4 9.3 + - - +
265D ASN* 2.8 36.6 + - + +
267D ILE* 3.8 26.2 - - + -
286D VAL* 3.9 22.0 - - + +
287D ASP* 1.3 76.4 - - - +
289D ALA* 1.3 62.3 + - - +
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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