Contacts of the strand formed by residues 331 - 342 (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 MET 331 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91A SER* 3.6 4.0 - - - -
327A LEU* 2.9 26.9 + - + -
328A ASN* 2.8 31.5 + - - +
330A ARG* 1.3 83.6 - - + +
332A SER* 1.3 61.8 + - - +
371A MET* 4.2 18.8 - - + -
372A THR 3.2 8.1 - - - +
373A ILE* 4.7 18.6 - - + -
277C PHE* 3.3 51.4 - - + -
280C ALA* 4.2 19.3 - - - -
282C LEU* 3.8 14.4 - - + -
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Residues in contact with SER 332 (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 4.1 13.9 - - - -
95A LEU* 4.2 15.1 - - - +
324A ALA* 5.9 0.8 - - - +
325A PHE 3.3 15.3 - - - -
326A ALA* 4.3 4.5 - - - -
327A LEU* 3.9 4.5 - - - +
331A MET* 1.3 75.6 - - - +
333A MET* 1.3 63.7 + - - +
334A SER* 6.0 0.7 - - - -
371A MET* 3.2 9.9 - - - +
372A THR* 2.9 54.5 + - - +
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Residues in contact with MET 333 (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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324A ALA* 3.4 2.7 - - - +
325A PHE* 3.0 37.5 + - + +
327A LEU* 3.4 20.6 - - + +
332A SER* 1.3 77.3 - - - +
334A SER* 1.3 63.3 + - - +
335A PHE* 3.7 35.4 - - + -
369A VAL* 4.0 22.2 - - + -
370A GLY 3.3 9.6 - - - +
371A MET* 4.6 7.6 - - + -
323C VAL* 4.1 22.7 - - + -
325C PHE* 3.8 28.7 - - - -
335C PHE* 4.1 12.6 - - + -
505C C8E 5.4 1.3 - - + -
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Residues in contact with SER 334 (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* 6.1 4.9 - - - +
283A PHE* 4.0 17.1 - - - -
323A VAL 3.6 7.4 - - - -
324A ALA* 4.2 10.5 - - - -
332A SER* 6.0 0.4 - - - -
333A MET* 1.3 76.7 - - - +
335A PHE* 1.3 72.4 + - - +
336A SER* 4.6 3.1 + - - -
368A ASN* 3.9 0.5 + - - +
369A VAL* 3.7 6.4 - - - +
370A GLY* 2.9 40.2 + - - -
384A ASN* 5.6 0.9 + - - -
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Residues in contact with PHE 335 (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 PHE* 4.2 0.2 - - - -
322A GLY* 3.2 2.8 - - - -
323A VAL* 2.8 40.1 + - + +
325A PHE* 4.1 24.2 - + - -
333A MET* 3.7 37.7 - - + -
334A SER* 1.3 79.5 + - - +
336A SER* 1.3 61.6 + - - +
367A PHE* 4.6 14.1 - + + -
368A ASN 3.7 2.5 - - - +
369A VAL* 4.5 17.3 - - + -
333B MET* 3.9 23.1 - - + -
335B PHE* 4.0 21.8 - + - -
369B VAL* 5.4 2.7 - - + -
335C PHE* 3.9 34.8 - + - -
367C PHE* 6.2 0.4 - + - -
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Residues in contact with SER 336 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A PHE* 4.2 15.7 - - - -
321A VAL 3.5 13.9 - - - -
322A GLY* 4.0 4.5 - - - -
334A SER* 4.6 3.6 - - - -
335A PHE* 1.3 77.1 - - - +
337A VAL* 1.3 63.7 + - - +
367A PHE* 3.3 14.1 - - - -
368A ASN* 2.9 57.9 + - - +
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Residues in contact with VAL 337 (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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320A GLY* 3.1 2.9 - - - -
321A VAL* 3.0 51.2 + - + +
336A SER* 1.3 82.2 + - - +
338A SER* 1.3 66.9 + - - +
366A TYR 3.3 13.5 - - - +
367A PHE* 4.8 0.2 - - + -
368A ASN* 4.5 0.7 - - - +
389A MET* 4.2 7.4 - - + -
385B LEU* 4.0 32.1 - - + -
398B PHE* 3.7 32.1 - - + -
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Residues in contact with SER 338 (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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319A PHE* 3.3 16.6 - - - -
320A GLY* 4.0 4.7 - - - -
337A VAL* 1.3 81.3 - - - +
339A ASP* 1.3 61.7 + - - +
364A ALA 4.1 0.8 - - - +
365A GLY* 3.5 1.7 - - - -
366A TYR* 2.8 52.3 + - - +
368A ASN* 4.0 8.4 + - - -
389A MET* 4.4 0.9 - - - +
501A LDA 4.3 24.2 - - - +
398B PHE* 5.2 0.9 - - - -
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Residues in contact with ASP 339 (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 PHE 4.2 0.7 - - - +
318A GLN* 3.5 3.0 - - - -
319A PHE* 3.0 44.8 + - + -
338A SER* 1.3 76.5 - - - +
340A LEU* 1.3 63.0 + - - +
341A ILE* 3.8 13.8 - - - +
363A ASN* 2.6 41.2 + - - +
364A ALA 3.8 1.3 - - - -
365A GLY* 3.4 14.0 + - - -
501A LDA 5.5 1.8 - - - -
116B TYR* 4.5 4.3 - - - -
396B PHE* 3.5 18.0 - - - -
398B PHE* 4.1 17.3 - - + -
502B LDA 4.8 1.4 - - - +
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Residues in contact with LEU 340 (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 SER* 4.8 0.2 - - - -
317A PHE 3.6 3.1 - - - -
318A GLN* 3.3 38.4 - - + +
339A ASP* 1.3 72.5 + - - +
341A ILE* 1.3 75.9 + - - +
342A GLN* 4.3 18.4 - - + +
362A ALA* 5.4 3.6 - - + +
363A ASN* 3.4 6.2 - - - +
364A ALA* 3.0 48.6 + - + +
366A TYR* 5.4 0.2 - - + -
501A LDA 4.2 21.1 - - + +
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Residues in contact with ILE 341 (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 SER* 3.1 6.9 - - - -
317A PHE* 2.9 65.0 + - + +
319A PHE* 5.2 2.0 - - + -
339A ASP* 3.8 20.4 - - - +
340A LEU* 1.3 82.0 - - - +
342A GLN* 1.3 66.5 + - - +
343A ARG* 4.1 0.8 + - - +
362A ALA 3.5 9.4 - - - +
363A ASN* 4.2 10.1 - - + +
502B LDA 3.5 45.8 - - + -
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Residues in contact with GLN 342 (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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291A ASN* 4.7 1.9 + - - +
313A LEU* 5.1 3.8 - - - +
314A GLY 2.7 39.3 + - - +
315A ASP 3.8 1.6 - - - -
316A SER* 3.6 14.2 + - - -
340A LEU* 4.3 12.0 - - + +
341A ILE* 1.3 76.9 - - - +
343A ARG* 1.3 70.9 + - - +
345A SER* 4.3 4.8 + - - -
360A SER 4.1 15.5 - - - +
361A ASP* 3.4 5.4 - - - +
362A ALA* 3.0 42.2 + - + +
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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