Contacts of the strand formed by residues 355 - 365 (chain A) in PDB entry 4Y5U
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 CYS 355 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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225A GLN* 4.3 4.0 - - - -
294A ARG* 3.7 28.7 - - - +
299A LEU* 3.8 10.6 - - - +
348A GLU 3.9 0.5 - - - +
349A ASN* 3.5 2.9 - - - -
350A SER* 3.0 33.0 + - - +
353A GLY* 3.5 24.5 - - - +
354A ASN* 1.3 79.2 - - - +
356A CYS* 1.3 60.0 + - - +
357A SER* 4.3 16.6 - - - -
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Residues in contact with CYS 356 (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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225A GLN* 4.9 0.2 + - - -
294A ARG* 3.5 4.8 - - - +
295A PHE* 2.8 44.7 + - - +
298A GLY* 3.8 13.9 - - - -
299A LEU* 4.5 0.8 - - - +
302A LEU* 3.8 17.7 - - - -
347A LEU* 3.5 29.8 - - - -
348A GLU 3.4 11.0 - - - -
349A ASN* 3.2 26.0 - - - +
355A CYS* 1.3 72.9 - - - +
357A SER* 1.3 62.3 + - - +
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Residues in contact with SER 357 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276A GLU* 4.6 5.4 - - - -
293A VAL 3.3 12.1 - - - -
294A ARG* 4.3 8.5 - - - -
346A PRO 3.9 2.1 - - - +
347A LEU* 3.6 7.2 - - - -
348A GLU* 3.4 25.4 + - - +
355A CYS* 4.3 16.8 - - - -
356A CYS* 1.3 77.9 - - - +
358A ALA* 1.3 58.9 + - - +
359A LEU* 3.8 22.3 + - - +
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Residues in contact with ALA 358 (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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292A GLY* 3.5 1.4 - - - -
293A VAL* 2.8 51.4 + - + +
311A VAL* 4.0 13.2 - - + -
345A VAL* 4.1 4.5 - - + -
346A PRO 3.9 14.6 - - - +
347A LEU* 3.5 11.7 - - + +
357A SER* 1.3 71.8 - - - +
359A LEU* 1.3 65.4 + - - +
360A PHE* 3.8 12.3 - - + -
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Residues in contact with LEU 359 (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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276A GLU* 5.3 5.4 - - - +
291A ALA 3.9 3.1 - - - +
292A GLY* 4.4 11.7 - - - -
293A VAL 4.9 0.4 - - - +
345A VAL* 3.4 20.6 - - - +
357A SER* 3.8 24.5 + - - +
358A ALA* 1.3 82.0 - - - +
360A PHE* 1.3 62.8 + - - +
361A LYS* 3.6 25.3 + - + +
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Residues in contact with PHE 360 (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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289A PHE 4.0 0.7 - - - +
290A GLN* 3.3 6.9 - - - +
291A ALA 2.9 33.9 + - - +
293A VAL* 4.3 3.4 - - + -
311A VAL* 3.8 22.0 - - + -
313A ALA* 3.9 8.1 - - + -
342A ASN 5.2 0.7 - - - +
343A ASN 3.6 23.8 - - - -
345A VAL* 3.5 28.3 - - + -
358A ALA* 3.8 22.9 - - + -
359A LEU* 1.3 75.5 - - - +
361A LYS* 1.3 61.9 + - - +
362A ASN 3.6 1.3 - - - -
363A LEU* 3.5 42.4 - - + -
388A PHE* 3.8 31.4 - + - -
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Residues in contact with LYS 361 (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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290A GLN* 1.4 51.9 + - - +
345A VAL* 5.5 0.2 - - - +
359A LEU* 3.6 27.8 + - + +
360A PHE* 1.3 72.5 - - - +
362A ASN* 1.3 71.1 + - - +
363A LEU 4.0 0.4 - - - -
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Residues in contact with ASN 362 (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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288A LYS* 3.6 34.7 - - + +
289A PHE 3.7 2.5 - - - -
290A GLN* 4.1 2.1 + - - -
342A ASN* 3.2 33.6 + - - +
361A LYS* 1.3 92.2 - - - +
363A LEU* 1.3 65.1 + - - +
364A LEU* 3.5 3.6 + - - +
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Residues in contact with LEU 363 (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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288A LYS* 3.1 6.1 - - - -
289A PHE* 2.8 62.5 + - + +
291A ALA* 4.3 19.7 - - + +
313A ALA* 4.5 10.1 - - + -
340A ILE* 4.0 12.1 - - + -
341A ILE 3.8 2.7 - - - +
342A ASN 3.2 24.5 - - - +
343A ASN* 3.9 12.6 - - + -
360A PHE* 3.5 43.7 - - + -
361A LYS 4.0 0.2 - - - -
362A ASN* 1.3 73.7 - - - +
364A LEU* 1.3 57.8 + - - +
386A VAL* 5.4 3.1 - - + -
388A PHE* 4.9 3.1 - - + -
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Residues in contact with LEU 364 (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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286A GLN* 3.4 43.1 - - + +
287A THR* 4.0 3.4 - - - +
288A LYS* 4.5 14.1 - - + -
340A ILE* 3.1 18.1 - - - +
341A ILE* 3.3 42.8 + - + +
342A ASN* 5.6 0.4 - - + -
362A ASN 3.5 4.0 + - - +
363A LEU* 1.3 76.3 - - - +
365A LEU* 1.3 63.5 + - - +
366A LYS* 3.4 33.4 + - + -
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Residues in contact with LEU 365 (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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283A LEU* 4.2 11.2 - - + -
284A LYS 4.3 8.7 - - - +
285A THR* 3.2 19.0 - - + -
286A GLN 2.3 34.5 + - - -
287A THR 3.8 5.1 + - - -
289A PHE* 3.9 13.4 - - + -
315A MET* 3.3 37.5 - - + -
339A GLU* 3.5 21.8 - - + +
340A ILE* 3.6 17.9 - - + -
364A LEU* 1.3 76.8 - - - +
366A LYS* 1.3 60.4 + - - +
412A VAL* 3.7 19.5 - - + -
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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