Contacts of the strand formed by residues 372 - 382 (chain A) in PDB entry 5E2Q
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 ASP 372 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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301A ILE 5.4 0.2 - - - +
304A LYS* 3.4 26.2 - - + +
305A GLY* 2.4 35.9 + - - -
306A PRO* 4.2 2.3 - - - +
309A GLU* 4.7 1.5 - - - +
344A GLU* 5.2 4.3 - - - +
371A PRO* 1.3 72.2 - - - +
373A PHE* 1.3 63.2 + - - +
374A THR* 3.6 19.5 - - - +
404A PHE 3.6 5.3 + - - -
405A LYS* 3.6 28.0 - - + -
406A ASN* 2.7 37.1 + - - -
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Residues in contact with PHE 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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340A SER 4.1 0.7 - - - +
343A PHE* 3.5 49.6 - + + +
344A GLU* 3.5 24.6 - - - +
346A LEU* 4.6 1.8 - - + -
347A VAL* 3.6 17.6 - - + +
371A PRO 3.6 1.4 + - - -
372A ASP* 1.3 78.6 + - - +
374A THR* 1.3 63.7 + - - +
406A ASN* 3.2 35.7 - - + +
407A VAL 4.0 1.8 - - - -
408A SER* 3.9 19.3 - - - -
447A VAL* 4.6 4.5 - - + -
448A GLY* 3.5 34.5 - - - -
451A ALA* 4.7 3.8 - - + -
452A LEU* 3.8 27.1 - - + -
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Residues in contact with THR 374 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305A GLY* 4.6 8.7 - - - -
306A PRO* 5.6 0.7 - - + -
309A GLU* 4.9 5.7 + - - -
335A VAL* 3.8 25.4 - - + +
340A SER* 3.5 12.6 - - - +
343A PHE* 4.7 2.2 - - - -
344A GLU* 4.4 7.4 - - - +
372A ASP* 3.6 21.1 + - - +
373A PHE* 1.3 83.0 - - - +
375A SER* 1.3 61.3 + - - +
376A LEU* 3.2 21.8 - - - +
406A ASN 3.2 5.1 + - - -
407A VAL* 3.4 12.6 - - - +
408A SER 3.0 23.6 + - - -
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Residues in contact with SER 375 (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 VAL 3.7 0.3 - - - -
336A ASN* 2.8 28.3 + - - +
339A MET* 3.4 52.8 - - - +
340A SER* 2.6 19.1 + - - +
343A PHE* 3.8 12.2 - - - -
374A THR* 1.3 71.7 - - - +
376A LEU* 1.3 63.3 + - - +
377A ASP* 5.5 0.2 + - - -
408A SER* 3.3 11.0 + - - +
410A GLY* 3.9 5.7 - - - -
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Residues in contact with LEU 376 (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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309A GLU* 4.2 10.3 - - + -
331A PHE* 3.9 19.7 - - + -
333A ALA* 3.6 28.7 - - + -
334A VAL 3.8 3.4 - - - +
335A VAL* 4.1 12.1 - - + -
374A THR* 3.2 33.4 - - - +
375A SER* 1.3 79.7 + - - +
377A ASP* 1.3 66.4 + - - +
378A VAL 3.8 0.2 - - - -
407A VAL* 3.6 25.8 - - + -
408A SER 2.8 10.8 + - - +
409A LEU* 3.4 19.3 - - + -
410A GLY* 2.7 28.3 + - - -
411A ASN* 3.4 4.0 - - - +
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Residues in contact with ASP 377 (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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18A ASP 5.1 4.3 - - - +
19A SER* 5.6 2.0 - - - -
22A ALA* 3.5 27.9 + - + +
333A ALA* 3.3 2.5 - - - -
334A VAL* 2.9 37.5 + - - +
336A ASN* 3.3 31.0 + - - +
339A MET* 5.1 3.5 - - - +
375A SER* 5.5 0.2 + - - -
376A LEU* 1.3 75.6 - - - +
378A VAL* 1.3 66.2 + - - +
379A LEU* 3.4 5.4 + - - +
410A GLY* 4.4 2.8 - - - -
411A ASN* 3.4 26.3 + - + +
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Residues in contact with VAL 378 (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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17A LEU* 3.4 25.9 - - + +
19A SER* 2.9 21.7 + - - -
331A PHE* 5.3 0.7 - - + -
332A VAL 4.3 0.9 - - - +
333A ALA* 3.8 9.6 - - + -
377A ASP* 1.3 69.8 - - - +
379A LEU* 1.3 60.3 + - - +
380A THR 3.6 27.8 - - - +
381A PHE* 3.8 18.4 - - + +
386A ILE* 5.4 1.1 - - + -
409A LEU* 3.8 42.4 - - + -
411A ASN* 2.8 22.2 + - - +
412A VAL* 4.0 5.6 - - + -
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Residues in contact with LEU 379 (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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17A LEU* 5.1 0.2 - - - -
19A SER* 3.6 34.1 - - - +
22A ALA* 5.3 0.9 - - + -
23A PHE* 4.2 20.4 - - + +
26A LEU* 4.3 7.6 - - + -
34A ALA* 4.2 24.9 - - + -
38A SER* 5.1 2.7 - - - +
308A VAL* 5.8 0.4 - - + -
332A VAL* 2.9 19.5 + - + +
333A ALA* 4.7 0.2 - - - -
334A VAL* 3.8 30.1 - - + +
377A ASP 3.4 3.1 + - - +
378A VAL* 1.3 76.2 - - - +
380A THR* 1.3 68.1 + - - +
674A GLN* 4.2 2.4 - - - +
675A PRO* 3.6 28.8 - - + +
677A THR* 5.7 8.5 - - + -
686A LEU* 4.8 7.9 - - + -
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Residues in contact with THR 380 (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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38A SER* 3.2 27.1 + - - +
41A ALA* 4.0 22.9 - - + -
42A TRP* 3.2 41.8 + - + +
331A PHE* 3.1 6.2 - - - +
332A VAL* 2.8 35.3 + - - +
378A VAL* 3.6 3.2 - - - +
379A LEU* 1.3 82.4 + - - +
381A PHE* 1.3 63.7 + - - +
382A ALA 4.1 2.5 - - - +
674A GLN* 3.4 4.3 - - - -
675A PRO 4.6 2.8 + - - -
677A THR* 5.9 1.6 - - - +
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Residues in contact with PHE 381 (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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42A TRP* 4.4 1.1 - - - -
329A GLU* 4.0 18.8 - - + -
330A GLY 3.7 2.9 - - - -
331A PHE* 3.4 31.6 - + + -
378A VAL* 3.8 14.1 - - + -
380A THR* 1.3 71.8 - - - +
382A ALA* 1.3 76.5 + - - +
383A GLY 5.1 1.0 - - - +
385A GLY 4.0 15.6 - - - +
386A ILE* 4.1 16.9 - - + +
387A PRO* 3.5 21.1 - - + -
390A ILE* 3.6 23.1 - - + -
409A LEU* 3.7 30.7 - - + -
674A GLN* 2.6 37.4 + - - +
2B ARG* 4.0 3.8 - - - -
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Residues in contact with ALA 382 (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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41A ALA* 3.2 38.1 - - + +
42A TRP* 3.7 25.4 - - + +
45A GLY* 4.2 5.4 - - - -
329A GLU* 3.9 4.7 - - - +
330A GLY 3.0 28.1 + - - +
380A THR* 4.0 1.8 - - - +
381A PHE* 1.3 90.3 - - - +
383A GLY* 1.3 60.2 + - - +
385A GLY 5.0 0.7 - - - +
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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