Contacts of the strand formed by residues 362 - 374 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118A ARG* 5.7 0.2 - - - -
340C LEU* 4.3 4.0 - - + -
341C ILE* 3.7 5.0 - - - +
342C GLN* 3.1 45.5 + - + +
360C SER 4.7 2.5 - - - +
361C ASP* 1.3 78.8 + - - +
363C ASN* 1.3 63.1 + - - +
364C ALA* 4.3 2.0 - - + +
392C ASP* 3.5 21.8 - - + +
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Residues in contact with ASN 363 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A TYR* 4.2 7.1 + - - -
118A ARG* 3.9 47.1 - - - +
120A ASP* 5.4 0.7 - - - +
396A PHE* 4.4 6.4 - - - -
339C ASP* 2.6 40.8 + - - +
340C LEU 3.4 4.7 - - - -
341C ILE* 3.7 16.0 - - - +
362C ALA* 1.3 74.0 - - - +
364C ALA* 1.3 52.8 + - - +
365C GLY 4.0 1.2 + - - -
390C THR* 2.8 25.9 + - - +
392C ASP* 3.0 21.2 + - - +
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Residues in contact with ALA 364 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339C ASP* 3.5 3.8 - - - -
340C LEU* 3.0 44.4 + - + +
362C ALA* 4.3 2.2 - - + -
363C ASN* 1.3 70.3 + - - +
365C GLY* 1.3 59.5 + - - +
366C TYR* 3.6 29.2 - - + +
390C THR* 3.4 3.6 - - - -
392C ASP* 3.4 23.1 - - + +
393C ALA* 4.3 2.5 - - + -
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Residues in contact with GLY 365 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396A PHE* 4.7 4.3 - - - -
338C SER 3.3 8.7 - - - -
339C ASP* 3.4 12.3 + - - -
363C ASN* 4.0 1.0 + - - -
364C ALA* 1.3 72.1 - - - +
366C TYR* 1.3 66.4 + - - -
388C GLY* 3.9 2.9 - - - -
389C MET* 3.2 31.3 + - - -
390C THR* 3.1 16.4 + - - +
393C ALA* 4.1 3.6 - - - +
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Residues in contact with TYR 366 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337C VAL* 3.3 10.1 - - - +
338C SER* 2.8 47.5 + - - +
339C ASP* 5.7 0.4 - - - -
340C LEU* 5.4 6.1 - - + -
364C ALA* 3.6 28.7 - - + +
365C GLY* 1.3 76.3 - - - -
367C PHE* 1.3 60.2 + - - +
368C ASN* 4.4 10.8 - - - +
386C ALA* 4.4 19.5 - - + -
387C ILE 3.4 10.8 - - - -
388C GLY* 4.6 3.4 - - - -
389C MET* 3.8 7.5 - - - -
392C ASP 5.1 0.2 + - - -
393C ALA* 4.1 11.1 - - + +
394C PRO* 3.4 36.7 - - + +
397C THR* 5.0 1.3 - - - -
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Residues in contact with PHE 367 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335A PHE* 6.2 0.4 - + - -
367A PHE* 4.3 14.8 - + - -
369A VAL* 4.1 27.4 - - + -
385A LEU* 4.0 15.3 - - + -
387A ILE* 3.9 24.2 - - + -
367B PHE* 4.3 11.0 - + - -
335C PHE* 4.5 13.0 - + + -
336C SER 3.4 20.0 - - - -
337C VAL* 4.6 0.2 - - - +
366C TYR* 1.3 74.1 - - - +
368C ASN* 1.3 64.3 + - - +
369C VAL* 3.9 27.5 + - + -
386C ALA* 3.6 0.9 - - - -
387C ILE* 2.9 55.5 + - + +
389C MET* 4.1 9.1 - - + -
505C C8E 4.3 11.9 - - + -
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Residues in contact with ASN 368 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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334C SER 3.7 1.0 - - - +
335C PHE* 3.4 7.1 - - - +
336C SER* 2.9 58.3 + - - +
337C VAL* 4.7 1.2 - - - +
338C SER* 4.6 7.7 + - - -
366C TYR* 4.4 14.2 + - - +
367C PHE* 1.3 78.1 - - - +
369C VAL* 1.3 64.4 + - - +
384C ASN* 3.2 20.2 + - - +
385C LEU 3.4 4.0 - - - +
386C ALA* 3.1 28.9 - - - +
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Residues in contact with VAL 369 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335B PHE* 5.3 4.3 - - + -
367B PHE* 4.0 25.1 - - + -
333C MET* 3.7 29.2 - - + -
334C SER 3.4 6.7 - - - +
335C PHE* 4.1 12.8 - - + -
367C PHE* 3.9 27.1 + - + -
368C ASN* 1.3 78.5 - - - +
370C GLY* 1.3 61.2 + - - +
384C ASN* 3.3 4.1 - - - +
385C LEU* 3.0 39.4 + - + +
387C ILE* 6.0 0.9 - - + -
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Residues in contact with GLY 370 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333C MET* 3.4 5.7 - - - +
334C SER* 3.0 41.2 + - - -
369C VAL* 1.3 77.3 - - - +
371C MET* 1.3 69.5 + - - +
383C PRO 3.4 10.8 - - - -
384C ASN* 3.8 9.1 + - - -
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Residues in contact with MET 371 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282B LEU* 4.0 17.9 - - + -
323B VAL* 3.9 33.7 - - + -
98C GLU* 5.7 0.2 - - - +
327C LEU* 3.6 31.6 - - + -
331C MET* 4.6 12.8 - - + -
332C SER* 3.3 14.4 - - - +
333C MET* 3.9 12.1 - - + -
334C SER* 5.6 0.9 - - - -
370C GLY* 1.3 78.8 - - - +
372C THR* 1.3 69.7 + - - +
373C ILE* 3.8 20.0 - - + -
382C VAL* 3.5 12.0 - - - +
383C PRO* 3.0 31.1 + - + +
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Residues in contact with THR 372 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91C SER 4.5 1.2 + - - -
94C ASN* 3.7 32.7 + - + +
95C LEU* 4.1 1.4 + - - +
98C GLU* 4.2 25.4 - - + -
330C ARG 3.5 1.5 + - - +
331C MET* 3.1 8.7 - - - +
332C SER* 2.6 51.8 + - - +
371C MET* 1.3 79.7 - - - +
373C ILE* 1.3 61.7 + - - +
380C THR* 4.1 4.7 - - - -
381C ILE 3.6 4.0 - - - -
382C VAL* 4.1 16.6 - - + -
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Residues in contact with ILE 373 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282B LEU* 5.1 10.5 - - + -
94C ASN* 4.6 0.7 - - - -
330C ARG* 3.8 4.9 - - + -
331C MET* 4.4 30.7 - - + +
371C MET* 3.8 20.6 - - + -
372C THR* 1.3 79.0 - - - +
374C ALA* 1.3 70.0 + - - +
375C ALA* 3.3 7.9 + - - +
380C THR* 3.3 6.5 - - - -
381C ILE* 2.9 52.2 + - + +
383C PRO* 3.7 31.0 - - + -
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Residues in contact with ALA 374 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90C GLN* 4.8 11.4 - - + -
94C ASN* 3.9 16.4 - - - +
330C ARG* 3.1 61.2 + - - +
373C ILE* 1.3 75.1 - - - +
375C ALA* 1.3 66.2 + - - +
376C SER 3.3 7.6 - - - +
379C LEU 4.0 5.2 - - - -
380C THR* 4.6 0.4 - - - +
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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