Contacts of the strand formed by residues 361 - 374 (chain A) in PDB entry 4UHY
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 361 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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296A CYS* 2.0 55.0 - - + -
297A LYS 3.8 2.2 - - - -
325A CYS* 3.7 21.4 - - - +
326A HIS* 3.6 22.4 - - - -
327A GLY 3.2 26.1 + - - +
329A CYS* 3.7 5.0 - - - -
360A CYS* 1.4 76.7 - - - +
362A VAL* 1.4 63.3 + - - +
393A CYS* 4.1 0.4 - - - -
394A GLY 3.6 1.3 - - - -
360B CYS* 4.9 1.0 - - - +
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Residues in contact with VAL 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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325A CYS* 3.5 7.4 - - - -
360A CYS* 3.7 6.1 - - - +
361A CYS* 1.4 73.0 - - - +
363A PRO* 1.4 77.7 - - + +
364A THR* 3.4 1.4 + - - +
394A GLY 2.9 26.1 + - - +
396A ARG* 3.6 36.8 - - + -
360B CYS* 3.5 32.5 - - + -
362B VAL* 3.9 13.2 - - + -
396B ARG* 3.7 27.6 - - + +
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Residues in contact with PRO 363 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325A CYS* 3.2 16.3 - - + +
362A VAL* 1.4 92.1 - - + +
364A THR* 1.3 59.9 + - - +
365A GLU 3.6 0.2 - - - -
366A LEU* 3.7 28.1 - - + +
390A VAL* 3.5 35.2 - - + -
392A GLY 3.3 8.5 - - - +
396A ARG* 5.7 0.2 - - - +
340B THR* 5.4 1.3 - - + +
342B HIS* 4.8 3.1 - - + +
346B GLN* 5.3 3.8 - - - +
396B ARG* 3.4 33.8 - - + +
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Residues in contact with THR 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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338A ASN* 3.0 31.9 + - + -
362A VAL 3.4 15.7 - - - +
363A PRO* 1.3 72.9 - - - +
365A GLU* 1.3 63.6 + - - +
366A LEU* 4.6 3.6 - - - -
392A GLY 2.8 7.7 + - - -
393A CYS 3.3 7.6 + - - -
394A GLY* 3.5 15.3 - - - +
396A ARG* 3.5 44.0 + - + +
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Residues in contact with GLU 365 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338A ASN* 4.6 11.3 + - - +
363A PRO 3.6 0.4 - - - -
364A THR* 1.3 89.9 - - - +
366A LEU* 1.3 65.6 + - - +
390A VAL* 3.7 0.9 - - - -
391A GLU* 2.7 37.9 + - + +
392A GLY* 3.2 24.8 + - - +
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Residues in contact with LEU 366 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363A PRO* 3.7 33.7 - - + +
364A THR 4.6 1.8 - - - -
365A GLU* 1.3 86.4 - - - +
367A SER* 1.3 61.2 + - - +
387A ASP* 3.6 54.7 - - + +
389A VAL 3.0 11.9 - - - +
391A GLU* 4.0 4.6 - - - +
340B THR* 4.6 10.5 - - + +
342B HIS* 3.6 22.4 - - + -
396B ARG* 6.5 0.4 - - - -
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Residues in contact with SER 367 (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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366A LEU* 1.3 75.8 - - - +
368A ALA* 1.3 62.1 + - - +
387A ASP 4.3 2.7 - - - -
388A MET* 2.8 29.3 + - - -
389A VAL* 2.7 27.0 + - - +
391A GLU* 2.9 30.4 + - - +
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Residues in contact with ALA 368 (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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367A SER* 1.3 80.6 + - - +
369A ILE* 1.4 67.8 + - - +
384A ASN* 5.2 3.6 - - + -
385A TYR 3.2 16.4 - - - +
386A GLN* 3.4 35.2 - - - +
387A ASP 4.6 0.2 - - - +
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Residues in contact with ILE 369 (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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317A PRO* 4.5 7.4 - - + -
320A TYR* 3.9 30.5 - - + -
368A ALA* 1.4 78.9 - - - +
370A SER* 1.3 62.3 + - - +
371A MET* 3.5 32.1 - - + -
383A LYS 3.8 0.2 - - - +
384A ASN* 3.4 4.2 - - - -
385A TYR* 2.7 39.2 + - + +
388A MET* 3.8 28.7 - - + +
389A VAL* 3.6 26.5 - - + -
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Residues in contact with SER 370 (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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316A ALA 5.2 0.2 - - - -
317A PRO* 3.9 11.6 - - - +
369A ILE* 1.3 75.1 - - - +
371A MET* 1.3 65.4 + - - +
382A LEU* 4.0 25.3 - - - +
383A LYS 3.5 5.2 - - - -
384A ASN* 2.7 21.9 + - - -
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Residues in contact with MET 371 (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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305A PHE* 3.9 15.3 - - + -
310A TRP* 5.3 0.2 - - + -
313A TRP* 3.9 5.8 - - + -
314A ILE* 3.7 37.9 - - + -
316A ALA 3.4 6.1 - - - +
317A PRO* 4.2 2.2 - - + -
369A ILE* 3.5 26.2 - - + -
370A SER* 1.3 79.2 - - - +
372A LEU* 1.3 66.0 + - - +
373A TYR* 4.2 0.9 + - - -
381A VAL 3.6 0.9 - - - +
382A LEU* 3.5 4.4 - - - -
383A LYS* 2.8 32.8 + - - +
385A TYR* 3.4 50.9 - - + +
388A MET* 3.9 12.6 - - + -
97C LEU* 4.0 4.0 - - + -
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Residues in contact with LEU 372 (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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314A ILE* 3.5 7.3 - - - +
315A VAL* 2.6 43.0 + - + -
316A ALA* 2.7 39.8 + - + +
371A MET* 1.3 74.8 - - - +
373A TYR* 1.3 56.3 + - - +
380A VAL* 3.8 27.1 - - + -
381A VAL 3.4 14.1 - - - +
382A LEU* 3.7 33.2 - - + -
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Residues in contact with TYR 373 (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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313A TRP* 3.4 31.2 - - + +
315A VAL* 3.9 8.1 - - - +
371A MET* 4.5 1.6 - - + -
372A LEU* 1.3 73.1 - - - +
374A LEU* 1.3 73.3 + - - +
375A ASP* 5.3 0.7 - - - -
380A VAL* 3.6 5.4 - - - +
381A VAL* 2.8 73.4 + - + +
383A LYS* 3.6 34.1 + - + +
385A TYR* 3.6 16.6 - - - -
94C ARG* 3.8 11.2 - - + +
95C GLY* 3.6 30.3 + - - -
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Residues in contact with LEU 374 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313A TRP 4.2 3.4 + - - +
315A VAL* 3.7 25.5 - - + +
373A TYR* 1.3 90.2 - - - +
375A ASP* 1.3 63.3 + - - +
378A GLU* 3.9 37.0 - - + +
379A LYS 3.4 12.6 - - - +
380A VAL* 4.0 14.8 - - + -
94C ARG* 3.3 35.5 + - - +
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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