Contacts of the strand formed by residues 288 - 295 (chain A) in PDB entry 1SDW
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 288 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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226A SER* 4.2 4.9 - - - -
227A CYS 3.3 12.6 - - - +
228A GLN* 4.2 22.2 - - + +
254A ARG* 3.6 2.6 - - - -
255A VAL* 2.7 44.3 + - + +
286A GLY 4.4 3.1 - - - +
287A ASP* 1.3 79.0 - - - +
289A LEU* 1.3 73.9 + - - +
290A ALA* 4.8 0.2 - - + -
338A VAL* 5.1 5.2 - - + -
339A ALA* 4.6 11.7 - - + -
342A MET* 3.6 38.1 - - + -
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Residues in contact with LEU 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205A TYR* 3.4 50.0 - - + +
207A MET* 3.5 15.6 - - + +
226A SER* 3.1 25.8 - - - -
227A CYS 2.9 14.9 + - - +
229A TYR* 4.3 8.5 - - + -
234A MET* 3.9 13.2 - - + -
253A TYR 3.4 3.1 - - - +
254A ARG* 4.4 3.6 - - - -
263A ILE* 3.6 31.4 - - + -
283A VAL* 3.9 26.0 - - + -
287A ASP 4.2 0.2 - - - -
288A ILE* 1.3 72.9 - - - +
290A ALA* 1.3 59.4 + - - +
319A ILE* 4.4 5.6 - - + -
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Residues in contact with ALA 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207A MET* 3.9 1.7 - - - +
225A ILE 3.3 4.5 - - - -
252A GLY* 3.3 1.4 - - - -
253A TYR* 2.6 42.6 + - - +
255A VAL* 4.2 7.2 - - + -
260A TRP* 3.7 26.9 - - + -
288A ILE 3.9 0.2 + - - -
289A LEU* 1.3 77.3 - - - +
291A ALA* 1.3 60.8 + - - +
342A MET* 4.0 15.5 - - + -
343A PHE* 3.8 15.3 - - + -
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Residues in contact with ALA 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207A MET* 3.7 26.9 - - + +
223A ALA 3.8 0.7 - - - +
224A ASP* 3.4 2.8 - - - -
225A ILE* 2.8 44.5 + - + +
250A VAL* 5.8 1.6 - - + -
251A SER 3.1 12.6 - - - +
253A TYR* 5.5 0.9 - - - -
290A ALA* 1.3 75.8 - - - +
292A ARG* 1.3 63.1 + - - +
293A CYS* 6.4 0.2 - - - -
315A CYS* 6.1 0.9 - - - -
317A LEU* 4.0 15.3 - - + -
343A PHE* 3.6 4.5 - - - -
346A ILE* 5.5 0.4 - - - -
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Residues in contact with ARG 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222A ASN* 3.6 28.0 + - - +
223A ALA 3.2 4.7 - - - -
224A ASP* 2.8 39.6 + - - +
249A VAL 3.9 1.0 - - - +
250A VAL* 3.4 3.1 - - - +
251A SER* 2.9 33.6 + - - +
291A ALA* 1.3 75.0 - - - +
293A CYS* 1.3 75.4 + - - +
294A VAL* 4.0 4.8 - - + +
315A CYS* 4.9 0.2 - - - -
343A PHE* 3.8 18.6 + - + +
346A ILE* 3.8 35.3 - - + +
350A ALA* 4.1 11.3 - - + +
351A ASN* 2.7 44.3 + - - +
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Residues in contact with CYS 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221A VAL 3.8 0.9 - - - +
222A ASN* 3.5 3.6 - - - -
223A ALA* 2.8 31.5 + - + +
243A THR* 4.3 2.5 - - + -
249A VAL 3.4 6.1 - - - +
250A VAL* 3.7 31.6 - - + -
291A ALA* 6.4 0.7 - - - -
292A ARG* 1.3 75.4 - - - +
294A VAL* 1.3 62.5 + - - +
295A PHE* 3.7 19.5 + - + -
315A CYS* 2.0 54.5 - - - -
316A ASN 4.2 0.2 - - - -
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Residues in contact with VAL 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220A VAL* 4.0 18.6 - - + -
221A VAL 3.7 2.2 - - - -
222A ASN* 3.7 22.7 - - - +
247A GLY* 3.8 2.1 - - - -
248A LYS* 2.8 38.1 + - + +
249A VAL* 2.8 39.1 + - + +
292A ARG* 4.0 7.0 - - + -
293A CYS* 1.3 76.0 - - - +
295A PHE* 1.3 64.2 + - - +
350A ALA 3.3 15.5 - - - +
351A ASN* 4.3 12.8 - - + +
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Residues in contact with PHE 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212A THR* 4.4 10.1 - - + -
214A ILE* 3.5 33.7 - - + -
219A LYS 3.9 0.3 - - - +
220A VAL* 3.5 5.7 - - - +
221A VAL* 2.8 40.9 + - + +
223A ALA* 3.7 18.6 - - + -
243A THR* 4.1 9.6 - - + -
246A LEU 3.4 8.7 - - - +
247A GLY* 3.8 17.7 - - - -
248A LYS* 4.8 2.2 - - - -
293A CYS* 3.7 24.0 - - + -
294A VAL* 1.3 78.6 - - - +
296A THR* 1.3 61.8 + - - +
306A ILE* 5.5 1.3 - - + -
313A GLU* 3.2 31.6 - - + -
314A MET 3.5 19.7 - - - -
315A CYS* 3.8 11.4 - - + -
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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