Contacts of the strand formed by residues 362 - 374 (chain A) in PDB entry 5O67
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 ALA 362 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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340A LEU* 4.4 5.4 - - + -
341A ILE* 3.5 6.6 - - - +
342A GLN* 3.0 47.9 + - + +
360A SER 4.6 2.5 - - - +
361A ASP* 1.3 76.2 - - - +
363A ASN* 1.3 63.2 + - - +
364A ALA* 5.2 2.0 - - + +
392A ASP* 3.4 20.4 - - + +
118B ARG* 5.2 3.1 - - - +
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Residues in contact with ASN 363 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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339A ASP* 2.6 40.7 + - - +
340A LEU 3.4 5.4 - - - -
341A ILE* 4.2 12.3 - - + +
362A ALA* 1.3 76.8 - - - +
364A ALA* 1.3 53.0 + - - +
365A GLY 3.8 2.8 + - - -
390A THR* 2.7 28.1 + - - +
392A ASP* 3.0 17.8 + - - +
116B TYR* 3.5 21.2 + - - -
118B ARG* 3.8 38.7 + - - +
396B PHE* 4.0 5.3 - - - -
502B LDA 5.7 0.2 - - - +
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Residues in contact with ALA 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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339A ASP* 3.4 3.7 - - - -
340A LEU* 3.0 40.6 + - + +
362A ALA* 4.3 1.5 - - + -
363A ASN* 1.3 73.6 + - - +
365A GLY* 1.3 62.3 + - - +
366A TYR* 3.3 26.8 - - + +
390A THR* 3.4 5.2 - - - -
392A ASP* 4.0 20.4 - - + +
393A ALA* 4.1 3.6 - - + -
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Residues in contact with GLY 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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338A SER 3.5 4.5 - - - -
339A ASP* 3.4 14.1 + - - -
363A ASN* 3.8 2.0 + - - -
364A ALA* 1.3 73.7 - - - +
366A TYR* 1.3 68.6 + - - -
389A MET* 3.2 39.1 + - - -
390A THR* 3.4 14.3 + - - +
393A ALA* 3.8 5.4 - - - +
396B PHE* 4.5 1.1 - - - -
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Residues in contact with TYR 366 (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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337A VAL* 3.3 8.3 - - - +
338A SER* 2.8 53.7 + - - +
340A LEU* 5.4 0.2 - - + -
364A ALA* 3.3 29.9 - - + +
365A GLY* 1.3 74.9 - - - -
367A PHE* 1.3 59.5 + - - +
368A ASN* 4.2 12.2 + - - +
386A ALA* 4.4 17.9 - - + -
387A ILE 3.6 4.7 - - - +
388A GLY* 4.5 9.2 - - - -
389A MET* 3.5 5.8 - - - +
392A ASP 5.1 0.3 + - - -
393A ALA* 3.6 18.1 - - + +
394A PRO* 3.5 29.7 - - + +
397A THR* 4.9 5.8 - - - -
501A LDA 4.2 27.0 - - + +
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Residues in contact with PHE 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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335A PHE* 4.6 13.9 - + + -
336A SER 3.3 22.7 - - - -
337A VAL* 4.5 0.2 - - - +
366A TYR* 1.3 73.1 - - - +
368A ASN* 1.3 61.0 + - - +
369A VAL* 3.7 28.0 - - + -
386A ALA* 3.5 0.3 - - - -
387A ILE* 2.8 59.7 + - + +
389A MET* 4.0 11.3 - - + -
335B PHE* 6.1 0.4 - + - -
367B PHE* 4.5 8.3 - + - -
369B VAL* 3.9 28.5 - - + -
385B LEU* 3.6 18.2 - - + -
387B ILE* 3.8 22.7 - - + -
367C PHE* 4.3 17.5 - + - -
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Residues in contact with ASN 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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334A SER* 3.9 0.9 + - - +
335A PHE* 3.7 3.8 - - - -
336A SER* 2.9 59.0 + - - +
337A VAL 4.4 1.0 - - - +
338A SER* 4.0 18.4 + - - -
366A TYR* 4.3 8.8 + - - +
367A PHE* 1.3 76.3 - - - +
369A VAL* 1.3 68.5 + - - +
384A ASN* 3.7 14.9 + - - +
385A LEU 3.3 4.9 - - - +
386A ALA* 3.1 27.2 - - - +
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Residues in contact with VAL 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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333A MET* 4.0 26.7 - - + -
334A SER 3.7 6.7 - - - +
335A PHE* 4.5 10.3 - - + -
367A PHE* 3.7 28.3 - - + -
368A ASN* 1.3 79.7 - - - +
370A GLY* 1.3 60.3 + - - +
384A ASN* 3.2 5.3 - - - +
385A LEU* 2.8 40.3 + - + +
387A ILE* 5.6 1.6 - - + -
335C PHE* 5.4 2.0 - - + -
367C PHE* 4.1 19.7 - - + -
505C C8E 4.1 28.4 - - + +
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Residues in contact with GLY 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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333A MET* 3.3 7.4 - - - +
334A SER* 2.9 40.9 + - - +
369A VAL* 1.3 78.7 - - - +
371A MET* 1.3 65.1 + - - +
383A PRO 3.5 6.3 - - - -
384A ASN* 3.4 13.2 - - - -
505C C8E 5.0 3.1 - - - -
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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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98A GLU* 5.9 0.2 - - - +
327A LEU* 3.9 22.2 - - + -
331A MET* 4.2 24.9 - - + -
332A SER* 3.2 18.6 - - - +
333A MET* 4.4 9.9 - - + +
370A GLY* 1.3 78.8 - - - +
372A THR* 1.3 68.5 + - - +
373A ILE* 4.6 11.7 - - + -
382A VAL* 3.5 9.2 - - - +
383A PRO* 3.2 38.9 + - + +
280C ALA* 5.4 0.4 - - + -
282C LEU* 4.1 22.4 - - + -
323C VAL* 4.5 13.7 - - + -
505C C8E 4.0 26.2 - - + +
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Residues in contact with THR 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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91A SER* 4.5 2.2 - - - +
94A ASN* 3.4 44.9 + - + +
95A LEU* 5.6 0.4 - - - -
98A GLU* 4.6 6.2 - - - +
330A ARG 3.4 3.3 - - - +
331A MET* 3.2 8.2 - - - +
332A SER* 2.9 49.5 + - - +
371A MET* 1.3 78.5 + - - +
373A ILE* 1.3 65.3 + - - +
380A THR* 4.7 0.9 - - + -
381A ILE 3.6 4.0 - - - -
382A VAL* 3.8 20.6 - - - +
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Residues in contact with ILE 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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330A ARG* 3.7 3.4 - - + -
331A MET* 4.7 17.5 - - + -
371A MET* 4.6 22.0 - - + -
372A THR* 1.3 84.9 - - - +
374A ALA* 1.3 69.1 + - - +
375A ALA* 3.3 1.7 + - - -
380A THR* 3.3 6.8 - - - +
381A ILE* 2.8 60.6 + - + +
383A PRO* 4.8 6.1 - - + -
282C LEU* 4.4 23.3 - - + -
505C C8E 5.2 11.0 - - + -
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Residues in contact with ALA 374 (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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90A GLN* 3.6 39.9 - - + +
94A ASN* 4.2 9.6 - - - +
330A ARG* 3.1 49.0 + - + +
373A ILE* 1.3 75.2 - - - +
375A ALA* 1.3 62.0 + - - +
376A SER 4.1 0.9 - - - +
379A LEU 3.9 5.4 - - - +
380A THR* 4.3 3.7 - - - +
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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