Contacts of the strand formed by residues 353 - 362 (chain I) in PDB entry 5DST
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 353 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273D CYS* 3.1 32.0 - - - +
274D LEU* 4.7 3.4 - - - +
293D ALA 4.8 1.0 - - - +
295D CYS* 4.3 4.6 - - - +
295I CYS* 4.1 10.9 - - - -
296I LEU 3.3 10.5 - - - +
297I GLN* 3.5 24.0 - - - +
298I ILE* 4.1 1.6 - - - -
351I GLY 3.9 8.5 - - - +
352I GLU* 1.3 86.5 - - - +
354I ILE* 1.3 60.5 + - - +
355I TYR* 2.9 41.7 + - + -
377I ASP 4.3 1.9 - - - +
378I PHE* 3.2 21.8 - - - -
379I LYS 4.7 3.9 + - - +
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Residues in contact with ILE 354 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225I ALA* 4.1 25.4 - - + -
270I THR* 4.7 0.4 - - + -
294I PHE* 3.8 12.2 - - + +
295I CYS* 3.2 4.2 - - - -
296I LEU* 2.8 49.1 + - + +
298I ILE* 3.8 22.9 - - + -
304I VAL* 4.6 8.5 - - + -
307I LEU* 5.2 2.5 - - + -
346I LEU* 4.1 17.3 - - + -
348I VAL* 5.1 0.4 - - + -
353I GLU* 1.3 73.6 - - - +
355I TYR* 1.3 65.7 + - - +
376I LEU* 3.7 37.5 - - + -
377I ASP 3.9 3.4 - - - +
378I PHE* 3.8 12.6 - - + -
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Residues in contact with TYR 355 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293D ALA* 3.5 22.6 - - + -
294D PHE* 3.2 33.2 + - - -
295D CYS* 3.5 10.4 + - + -
355D TYR* 4.4 16.6 - + - -
294I PHE* 3.4 8.5 - - - -
295I CYS* 3.6 21.1 - - + -
353I GLU* 2.9 43.5 + - + -
354I ILE* 1.3 81.3 - - - +
356I GLY* 1.3 59.0 + - - +
376I LEU* 3.6 3.1 - - - -
377I ASP* 2.8 43.9 + - + +
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Residues in contact with GLY 356 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293I ALA* 3.3 4.7 - - - +
294I PHE* 2.7 48.9 + - - +
355I TYR* 1.3 77.2 - - - +
357I THR* 1.3 60.6 + - - +
375I ASP* 3.0 16.6 - - - -
376I LEU* 4.3 0.4 - - - -
377I ASP* 4.6 2.0 - - - -
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Residues in contact with THR 357 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291I THR* 4.0 21.8 - - + +
292I SER 3.4 8.5 - - - -
293I ALA* 4.2 13.7 - - + -
294I PHE* 3.6 2.3 - - - -
356I GLY* 1.3 79.2 - - - +
358I ILE* 1.3 61.9 + - - +
359I SER* 5.0 2.8 + - - -
373I THR 3.7 0.3 + - - +
374I VAL* 3.5 2.3 - - - -
375I ASP* 2.9 47.8 + - + +
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Residues in contact with ILE 358 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221I LEU* 5.9 0.9 - - + -
223I VAL* 4.9 8.1 - - + -
275I ILE* 3.9 37.9 - - + -
290I PHE* 4.1 4.7 - - + -
291I THR* 3.9 0.2 - - - -
292I SER* 2.9 31.9 + - - +
294I PHE* 3.5 24.0 - - + -
307I LEU* 6.4 0.9 - - + -
309I THR* 4.9 11.4 - - + -
340I PHE* 5.3 3.4 - - + -
357I THR* 1.3 75.7 - - - +
359I SER* 1.3 68.7 + - - +
360I MET* 5.3 4.3 - - + -
372I PHE* 4.3 21.3 - - + -
373I THR 3.3 6.7 - - - +
374I VAL* 4.3 18.6 - - + -
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Residues in contact with SER 359 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290I PHE 3.0 9.4 - - - -
291I THR* 3.1 31.8 + - - +
357I THR* 5.0 2.3 + - - -
358I ILE* 1.3 76.5 - - - +
360I MET* 1.3 62.1 + - - +
361I LYS* 6.0 1.6 - - - -
372I PHE* 3.2 6.9 - - - +
373I THR* 2.8 47.6 + - - +
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Residues in contact with MET 360 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190I CYS 5.1 2.0 - - - +
192I PHE* 3.6 45.8 - - + -
221I LEU* 4.9 6.7 - - - -
288I LEU* 3.6 19.0 - - + +
289I SER* 3.3 4.9 - - - -
290I PHE* 3.1 51.8 + - + -
358I ILE* 5.3 2.7 - - + -
359I SER* 1.3 75.2 - - - +
361I LYS* 1.3 65.1 + - - +
362I PRO* 6.0 0.2 - - + -
370I LEU* 3.8 19.7 - - + -
371I ASP 3.0 13.5 - - - +
372I PHE* 3.6 33.9 - - + -
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Residues in contact with LYS 361 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288I LEU 4.9 0.2 - - - -
289I SER* 3.8 14.4 - - - +
290I PHE 5.7 0.4 - - - +
359I SER* 6.0 1.6 - - - -
360I MET* 1.3 78.1 - - - +
362I PRO* 1.3 81.8 + - + +
364I ALA* 5.7 5.4 - - - +
370I LEU* 3.6 10.3 - - - +
371I ASP* 2.9 49.9 + - + +
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Residues in contact with PRO 362 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195I SER* 4.0 14.6 - - - +
198I ASN* 5.1 7.2 - - - +
288I LEU* 4.7 9.9 - - + +
289I SER* 3.5 16.6 - - - +
360I MET* 6.0 0.4 - - + -
361I LYS* 1.3 102.7 + - + +
363I ASN* 1.3 66.4 + - - +
364I ALA* 3.6 1.9 + - - -
367I VAL* 3.7 33.9 - - + +
369I ASP 3.6 7.6 - - - +
370I LEU* 4.6 5.4 - - + -
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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