Contacts of the helix formed by residues 392 - 410 (chain A) in PDB entry 3PU3
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 PRO 392 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27A EDO 3.9 8.5 - - - +
33A EDO 5.8 3.8 - - - -
390A GLN 3.8 4.2 - - - +
391A LEU* 1.3 97.8 - - + +
393A PRO* 1.3 76.8 - - + +
394A HIS* 4.0 19.5 - - + +
395A LEU* 3.2 34.7 + - + +
396A VAL* 3.3 8.0 + - - +
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Residues in contact with PRO 393 (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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27A EDO 4.2 20.6 - - - +
33A EDO 5.9 3.6 - - - +
391A LEU 3.5 2.0 - - - +
392A PRO* 1.3 87.1 - - + +
394A HIS* 1.3 58.4 + - - +
396A VAL* 3.2 8.8 + - + +
397A GLN* 2.9 30.5 + - - +
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Residues in contact with HIS 394 (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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6A EDO 5.1 3.2 + - - -
33A EDO 3.8 31.2 - - - +
119A GLU* 6.0 4.9 - - + -
339A SER* 3.4 27.9 + - - +
340A LEU* 3.8 21.7 - - + +
342A VAL* 5.2 1.4 - - - +
392A PRO* 3.2 22.6 + - + +
393A PRO* 1.3 80.7 - - - +
395A LEU* 1.3 76.8 + - + +
397A GLN* 3.6 6.2 + - - +
398A GLY* 2.9 22.9 + - - -
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Residues in contact with LEU 395 (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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6A EDO 3.7 39.3 - - - +
339A SER* 3.9 10.8 - - - +
342A VAL* 6.2 1.1 - - + -
373A MET* 4.7 1.3 - - + -
376A HIS* 5.6 1.3 - - + -
377A LEU* 4.4 20.7 - - + +
380A ALA* 5.9 1.8 - - + -
381A PHE* 5.5 0.2 - - - -
391A LEU* 4.5 20.4 - - + -
392A PRO* 3.2 35.7 + - + +
394A HIS* 1.3 98.5 - - + +
396A VAL* 1.3 61.6 + - - +
398A GLY* 3.0 2.7 + - - +
399A ALA* 2.7 30.2 + - - +
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Residues in contact with VAL 396 (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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381A PHE* 4.2 13.0 - - + -
391A LEU* 3.6 26.0 - - + +
392A PRO 3.3 13.7 + - - +
393A PRO* 3.2 9.7 + - + +
395A LEU* 1.3 75.4 - - - +
397A GLN* 1.3 62.5 + - - +
399A ALA* 3.2 8.7 + - - +
400A LYS* 3.1 26.6 + - + +
439A ILE* 4.3 21.3 - - + +
442A SER* 3.9 24.9 - - - +
443A GLU* 5.0 6.7 - - + -
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Residues in contact with GLN 397 (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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393A PRO 2.9 16.8 + - - +
394A HIS* 3.9 6.7 - - - +
396A VAL* 1.3 73.8 - - - +
398A GLY* 1.3 63.8 + - - +
400A LYS* 3.4 19.2 + - - +
401A ILE* 3.0 38.0 + - + +
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Residues in contact with GLY 398 (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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342A VAL* 3.9 28.9 - - - -
373A MET* 6.5 0.2 - - - -
377A LEU* 4.4 6.5 - - - -
394A HIS 2.9 16.9 + - - -
395A LEU* 3.0 5.6 + - - -
397A GLN* 1.3 73.8 - - - +
399A ALA* 1.3 65.5 + - - +
401A ILE* 3.0 4.8 + - - +
402A LEU* 2.9 26.7 + - - +
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Residues in contact with ALA 399 (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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377A LEU* 3.8 18.4 - - + +
381A PHE* 3.6 24.9 - - + -
395A LEU 2.7 13.6 + - - +
396A VAL 3.2 10.3 + - - +
398A GLY* 1.3 72.6 - - - +
400A LYS* 1.3 63.2 + - - +
402A LEU* 3.3 2.0 + - - +
403A ASN* 2.8 26.7 + - - +
435A LEU* 4.6 7.6 - - + +
439A ILE* 3.6 19.7 - - + +
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Residues in contact with LYS 400 (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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396A VAL* 3.1 13.4 + - - +
397A GLN* 3.6 22.4 - - - +
398A GLY 3.2 0.2 - - - -
399A ALA* 1.3 79.2 - - - +
401A ILE* 1.3 63.8 + - + +
403A ASN* 3.7 3.3 - - - +
404A GLY* 3.0 20.3 + - - -
439A ILE* 3.8 23.8 - - + -
443A GLU* 4.1 18.1 + - - +
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Residues in contact with ILE 401 (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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342A VAL* 3.7 11.4 - - + +
343A GLU* 4.1 32.8 - - + +
346A MET* 3.5 34.3 - - + -
397A GLN* 3.0 29.0 + - + +
398A GLY* 3.0 9.9 + - - +
400A LYS* 1.3 78.4 - - + +
402A LEU* 1.3 62.1 + - - +
404A GLY* 3.3 3.3 + - - -
405A ALA* 3.0 20.1 + - - +
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Residues in contact with LEU 402 (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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217A TRP* 4.5 7.9 - - + -
342A VAL* 4.1 15.0 - - + -
346A MET* 4.6 8.7 - - - -
370A CYS* 3.8 37.0 - - + +
373A MET* 3.6 32.1 - - + -
374A GLY* 4.4 6.3 - - - +
377A LEU* 3.6 20.9 - - + -
398A GLY* 2.9 18.6 + - - +
399A ALA* 3.9 3.8 - - - +
401A ILE* 1.3 69.4 - - - +
403A ASN* 1.3 56.1 - - - +
405A ALA* 3.1 5.4 + - + +
406A PHE* 2.7 54.8 + - + -
435A LEU* 6.4 0.2 - - + -
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Residues in contact with ASN 403 (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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399A ALA 2.8 19.2 + - - +
400A LYS* 3.7 5.4 - - - +
402A LEU* 1.3 77.1 - - - +
404A GLY* 1.3 62.6 - - - +
406A PHE* 3.1 7.9 + - - +
407A ARG* 2.9 51.7 + - - +
432A ILE* 3.1 46.3 + - - +
435A LEU* 3.7 18.0 - - + +
436A ALA* 3.3 18.4 - - - +
439A ILE* 4.4 4.4 - - + +
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Residues in contact with GLY 404 (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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36A EDO 4.8 4.2 + - - -
400A LYS 3.0 13.6 + - - -
401A ILE 3.7 4.3 - - - -
402A LEU 3.3 0.2 - - - -
403A ASN* 1.3 77.0 - - - +
405A ALA* 1.3 60.4 + - - +
407A ARG* 3.4 15.3 + - - +
408A SER* 3.0 22.5 + - - -
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Residues in contact with ALA 405 (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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346A MET* 3.4 33.2 - - + -
401A ILE 3.0 11.7 + - - +
402A LEU* 3.1 11.0 + - + +
404A GLY* 1.3 74.8 - - - +
406A PHE* 1.3 63.5 + - - +
408A SER* 3.0 11.3 + - - -
409A TRP* 2.9 44.2 + - + +
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Residues in contact with PHE 406 (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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370A CYS* 3.3 31.0 - - + -
371A TRP* 3.5 49.4 - + + -
374A GLY* 3.8 22.7 - - - -
402A LEU* 2.7 40.0 + - + -
403A ASN* 3.4 18.2 - - - +
405A ALA* 1.3 72.1 - - - +
407A ARG* 1.3 61.0 + - - +
409A TRP* 3.1 31.3 + + - -
410A THR* 2.8 25.6 + - - +
431A LEU* 4.2 2.9 - - + -
432A ILE* 3.8 12.6 - - + -
435A LEU* 4.2 12.8 - - + -
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Residues in contact with ARG 407 (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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36A EDO 3.4 46.1 + - - +
403A ASN* 2.9 49.0 + - - +
404A GLY* 3.6 11.1 - - - +
406A PHE* 1.3 74.3 - - - +
408A SER* 1.3 61.5 + - - +
410A THR* 3.3 25.0 + - - +
432A ILE* 3.5 29.3 - - + +
436A ALA* 3.5 19.6 - - - +
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Residues in contact with SER 408 (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 EDO 2.7 34.3 + - - -
36A EDO 5.2 2.2 + - - -
404A GLY 3.0 13.8 + - - -
405A ALA* 3.1 16.6 - - - -
407A ARG* 1.3 78.9 - - - +
409A TRP* 1.3 61.7 + - - +
410A THR 3.5 0.7 + - - +
412A LYS* 4.0 8.3 - - - +
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Residues in contact with TRP 409 (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 EDO 4.9 0.4 - - - -
346A MET* 4.1 11.6 - - + +
349A TYR* 4.4 12.9 - + - -
366A PHE* 4.8 0.7 - + - -
367A GLU* 3.7 47.2 + - + -
370A CYS* 3.8 22.4 - - + -
371A TRP* 3.6 24.7 - + + +
405A ALA* 2.9 35.7 + - + +
406A PHE* 3.1 30.7 + + - +
408A SER* 1.3 84.0 - - - +
410A THR* 1.3 64.6 + - + +
412A LYS* 4.4 0.9 - - - -
415A LEU* 3.4 11.1 + - - -
418A HIS* 3.4 54.8 - + + +
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Residues in contact with THR 410 (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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371A TRP* 3.9 16.6 - - + -
406A PHE 2.8 17.9 + - - +
407A ARG* 3.3 14.9 + - - +
408A SER 3.3 1.0 - - - -
409A TRP* 1.3 84.5 - - + +
411A LYS* 1.3 63.4 + - - +
412A LYS* 2.6 19.9 + - - +
415A LEU* 5.7 0.2 - - - +
422A LEU* 5.9 0.4 - - + -
428A PRO* 3.8 31.0 - - + -
429A SER* 5.9 0.4 - - - -
432A ILE* 3.5 15.3 - - - +
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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