Contacts of the strand formed by residues 352 - 363 (chain A) in PDB entry 2QQM
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 LYS 352 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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344A ALA 4.0 3.4 - - - -
345A ILE* 4.5 8.3 - - + +
350A LYS 4.2 9.2 - - - +
351A LYS* 1.3 76.0 - - - +
353A TYR* 1.3 61.2 + - - +
354A TYR* 4.8 7.0 - - + -
387A PRO* 3.9 32.5 - - + -
412A GLU* 3.9 2.5 - - + +
413A THR* 2.9 28.4 + - - +
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Residues in contact with TYR 353 (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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301A TRP* 4.5 15.0 - + - -
316A THR* 5.4 4.3 - - + -
343A GLY* 4.2 0.2 - - - -
344A ALA 2.8 38.5 + - - +
346A SER* 4.1 13.4 - - - -
349A THR* 4.7 2.1 + - - -
351A LYS* 3.6 43.6 - - + +
352A LYS* 1.3 74.5 - - - +
354A TYR* 1.3 69.2 + - - +
387A PRO* 3.8 2.1 - - - +
412A GLU 3.6 3.6 - - - -
413A THR* 3.2 32.0 - - + +
414A GLY* 3.5 24.5 - - - +
415A ILE 5.3 0.9 - - - -
416A SER* 3.4 22.9 - - - -
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Residues in contact with TYR 354 (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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343A GLY* 3.7 8.3 - - - -
352A LYS* 5.0 7.4 - - + -
353A TYR* 1.3 82.6 - - - +
355A VAL* 1.3 62.6 + - - +
356A LYS* 3.8 12.8 - - + +
384A ASN* 3.4 29.6 - - + -
385A THR* 3.2 26.6 + - - -
386A ASN* 3.4 35.7 - - - +
387A PRO* 3.6 6.7 - - + -
411A TRP* 3.3 4.3 - - - +
412A GLU* 2.8 68.0 + - + +
414A GLY 3.9 2.1 + - - -
416A SER 3.7 9.9 - - - -
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Residues in contact with VAL 355 (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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341A THR* 4.9 0.4 + - - +
343A GLY* 5.0 0.2 - - - -
354A TYR* 1.3 74.8 - - - +
356A LYS* 1.3 60.4 + - - +
357A THR 3.2 29.8 - - - +
358A TYR* 4.3 10.3 - - + -
383A GLY* 3.9 2.3 - - - -
384A ASN* 3.0 29.2 + - - +
408A PRO* 4.0 17.0 - - + -
410A THR 3.2 8.3 - - - +
411A TRP* 3.9 2.7 - - + -
415A ILE* 3.9 22.7 - - + -
416A SER 3.8 4.9 + - - +
417A MET* 3.3 39.7 - - + +
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Residues in contact with LYS 356 (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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354A TYR* 3.8 18.8 - - + +
355A VAL* 1.3 75.0 - - - +
357A THR* 1.3 66.1 + - + +
382A GLN* 3.5 8.6 + - - +
383A GLY* 2.8 24.9 + - - -
384A ASN 3.5 18.6 - - - +
385A THR* 6.0 0.4 - - + -
410A THR* 2.8 23.2 + - - +
411A TRP* 3.4 33.1 + - - +
412A GLU* 3.9 15.4 + - - +
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Residues in contact with THR 357 (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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355A VAL* 3.2 8.4 - - - +
356A LYS* 1.3 89.9 - - + +
358A TYR* 1.3 57.2 + - - +
380A LEU* 4.5 16.5 - - + +
381A PHE 3.2 15.0 - - - +
382A GLN* 4.8 10.1 - - - +
383A GLY 4.2 1.1 - - - +
409A ALA* 2.8 34.0 + - - +
410A THR* 2.7 35.1 + - + +
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Residues in contact with TYR 358 (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 VAL* 3.2 36.2 + - + +
341A THR* 3.7 27.5 - - + +
355A VAL* 4.3 9.2 - - + -
357A THR* 1.3 79.6 - - - +
359A LYS* 1.3 64.4 + - - +
360A ILE* 3.4 36.1 - - + -
379A VAL 3.6 1.6 - - - +
380A LEU* 3.7 1.8 - - - +
381A PHE* 2.8 51.7 + + + -
382A GLN 3.9 17.4 + - - -
383A GLY* 4.2 4.3 - - - -
391A VAL 5.1 0.7 + - - -
393A ALA* 3.7 11.6 - - - +
406A ILE* 3.9 13.2 - - + -
407A LYS 3.4 19.3 - - - +
408A PRO* 4.0 4.5 - - + -
409A ALA* 3.9 3.6 - - - +
417A MET* 4.8 1.6 - - + -
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Residues in contact with LYS 359 (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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358A TYR* 1.3 77.6 - - - +
360A ILE* 1.3 68.5 + - - +
371A THR* 4.8 5.2 - - + -
378A PRO* 3.9 29.7 - - + +
379A VAL 3.6 19.1 - - - +
380A LEU* 4.0 21.3 - - + -
381A PHE* 4.3 0.2 - - - -
407A LYS* 2.9 61.3 + - + +
409A ALA* 4.6 9.6 - - + -
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Residues in contact with ILE 360 (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 VAL* 4.2 10.5 - - + -
358A TYR* 3.4 28.7 - - + -
359A LYS* 1.3 75.7 - - - +
361A ASP* 1.3 83.6 + - - +
362A VAL* 3.8 7.6 - - + -
371A THR* 3.5 2.3 - - - +
372A ILE* 3.0 45.5 + - + +
379A VAL 4.7 0.2 + - - -
381A PHE* 3.5 34.5 - - + -
395A PHE* 4.4 7.6 - - + -
404A VAL* 4.0 9.6 - - + -
405A ARG 3.3 4.3 - - - +
406A ILE* 3.5 24.2 - - + -
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Residues in contact with ASP 361 (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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360A ILE* 1.3 83.5 - - - +
362A VAL* 1.3 62.1 - - - +
369A TRP* 3.6 28.6 - - + +
370A ILE 3.2 8.5 - - - +
371A THR* 2.7 28.7 + - - -
405A ARG* 2.8 43.8 + - + -
407A LYS* 2.9 34.2 + - - +
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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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360A ILE* 3.8 16.4 - - + -
361A ASP* 1.3 79.6 - - - +
363A SER* 1.3 62.4 + - - +
368A ASP 4.0 0.3 - - - +
369A TRP* 3.6 3.0 - - - -
370A ILE* 2.9 49.2 + - + +
372A ILE* 4.3 6.7 - - + -
395A PHE* 4.8 3.4 - - + -
399A LEU* 4.2 29.2 - - + -
401A THR* 3.5 22.7 - - + +
403A PHE 3.4 9.9 - - - +
404A VAL* 4.5 6.1 - - + -
547A ASP* 4.4 1.2 - - - +
548A THR* 4.6 9.6 + - + +
604A EDO 4.5 6.1 - - - -
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Residues in contact with SER 363 (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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362A VAL* 1.3 72.6 - - - +
364A SER* 1.3 60.0 + - - +
365A ASN* 3.0 9.7 + - - -
366A GLY* 2.8 29.1 + - - -
368A ASP 2.9 24.5 + - - -
369A TRP* 3.6 23.1 - - - -
401A THR* 3.0 10.4 + - - -
402A ARG 3.1 0.5 + - - -
403A PHE* 2.9 34.3 + - - +
547A ASP* 3.6 2.7 - - - -
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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