Contacts of the helix formed by residues 421 - 442 (chain B) in PDB entry 3PLZ
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 GLY 421 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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419B GLN 4.2 1.0 + - - -
420B ALA* 1.3 77.9 - - - +
422B ALA* 1.3 66.3 + - - -
423B THR 3.3 3.1 + - - -
424B LEU 3.6 1.0 + - - -
425B ASN* 3.0 21.1 + - - -
516B TYR* 4.5 9.4 + - - -
520B LYS* 6.0 0.8 - - - +
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Residues in contact with ALA 422 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421B GLY* 1.3 72.3 - - - +
423B THR* 1.3 58.4 + - - +
425B ASN* 3.8 4.8 - - - +
426B ASN* 2.9 30.5 + - - +
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Residues in contact with THR 423 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421B GLY 3.3 1.0 - - - -
422B ALA* 1.3 78.9 - - - +
424B LEU* 1.3 63.4 + - - +
426B ASN* 3.2 7.5 + - + +
427B LEU* 3.0 33.2 + - + +
512B GLN 5.6 0.4 - - - +
516B TYR* 3.5 38.1 - - + -
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Residues in contact with LEU 424 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B 470 4.0 43.5 - - + -
342B PHE* 3.6 35.7 - - + -
416B ILE* 5.6 2.5 - - + -
420B ALA* 3.5 26.9 - - + -
421B GLY 3.6 2.4 + - - +
422B ALA 3.5 0.2 - - - -
423B THR* 1.3 78.8 - - - +
425B ASN* 1.3 59.6 + - - +
427B LEU* 3.2 6.1 + - + +
428B MET* 2.8 44.8 + - + +
516B TYR* 3.4 35.0 - - + +
517B LEU* 5.3 1.1 - - + -
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Residues in contact with ASN 425 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413B TYR* 4.1 4.0 + - - -
417B ALA* 2.9 51.9 + - - +
420B ALA* 3.0 21.1 + - - +
421B GLY 3.0 14.8 + - - +
422B ALA* 3.8 6.5 - - - +
424B LEU* 1.3 78.3 - - - +
426B ASN* 1.3 56.9 + - - +
428B MET* 3.5 9.9 + - - +
429B SER* 2.8 35.4 + - - +
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Residues in contact with ASN 426 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
519A TYR* 2.6 29.2 + - - -
523A ASN* 2.9 25.6 + - - +
422B ALA 2.9 18.6 + - - +
423B THR* 3.4 8.1 - - - +
424B LEU 3.2 0.2 - - - -
425B ASN* 1.3 76.0 - - - +
427B LEU* 1.3 63.7 + - - +
429B SER* 3.3 8.1 + - - -
430B HIS* 3.0 34.9 + - - -
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Residues in contact with LEU 427 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
519A TYR* 4.1 23.1 - - + +
1B 470 3.8 16.7 - - + +
423B THR* 3.0 26.6 + - + +
424B LEU* 3.7 9.2 - - + +
426B ASN* 1.3 75.3 - - - +
428B MET* 1.3 62.8 + - - +
430B HIS* 3.2 7.8 + - + +
431B ALA* 3.1 21.3 + - - +
509B ILE* 4.2 20.3 - - + +
512B GLN* 3.9 30.7 - - + +
513B ALA* 3.7 26.7 - - + -
516B TYR* 4.1 19.7 - - + -
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Residues in contact with MET 428 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B 470 3.7 34.9 - - + -
413B TYR* 3.1 28.7 - - + +
416B ILE* 3.5 34.8 - - + +
417B ALA* 4.0 9.0 - - - +
420B ALA* 5.0 1.6 - - + -
424B LEU* 2.8 41.6 + - + +
425B ASN* 3.8 22.7 - - - +
427B LEU* 1.3 76.9 - - - +
429B SER* 1.3 55.0 + - - +
431B ALA* 3.2 9.8 + - - +
432B GLN* 3.0 31.7 + - - +
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Residues in contact with SER 429 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413B TYR* 3.5 10.7 + - - -
425B ASN* 2.8 23.8 + - - +
426B ASN* 3.6 8.0 - - - -
428B MET* 1.3 72.7 - - - +
430B HIS* 1.3 66.5 + - - +
432B GLN* 3.4 5.0 + - - +
433B GLU* 3.1 29.5 + - - +
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Residues in contact with HIS 430 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
519A TYR* 4.0 13.4 - + - -
522A LEU* 3.5 40.5 - - + +
523A ASN* 2.9 28.1 + - - -
426B ASN* 3.0 39.1 + - - -
427B LEU* 3.2 10.1 + - + +
429B SER* 1.3 75.5 - - - +
431B ALA* 1.3 64.3 + - - +
433B GLU* 3.2 9.0 + - - +
434B LEU* 3.1 30.5 + - - +
509B ILE* 3.7 25.9 - - + +
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Residues in contact with ALA 431 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B 470 4.0 27.1 - - + -
387B ILE* 5.4 8.5 - - + -
390B HIS* 4.8 6.7 - - + -
391B ILE* 4.2 5.5 - - + +
427B LEU 3.1 13.2 + - - +
428B MET 3.2 9.4 + - - +
430B HIS* 1.3 77.4 - - - +
432B GLN* 1.3 64.3 + - - +
434B LEU* 3.2 16.7 + - - +
435B VAL* 3.0 27.7 + - - +
509B ILE* 4.7 4.6 - - + +
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Residues in contact with GLN 432 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B 470 4.0 4.5 - - + -
390B HIS* 3.1 28.6 + - - -
394B GLN* 4.1 7.5 + - - +
402B SER 5.3 2.6 + - - -
403B ILE* 3.6 20.8 - - + +
413B TYR* 4.1 20.6 - - + +
428B MET 3.0 16.6 + - - +
429B SER* 3.4 5.6 + - - +
430B HIS 3.3 0.2 - - - -
431B ALA* 1.3 76.4 - - - +
433B GLU* 1.3 56.4 + - - +
435B VAL* 3.3 27.5 + - - +
436B ALA* 2.9 27.2 + - - +
439B ARG* 6.0 0.4 - - - +
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Residues in contact with GLU 433 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429B SER* 3.1 20.3 + - - +
430B HIS* 3.5 12.8 - - - +
431B ALA 3.2 0.2 - - - -
432B GLN* 1.3 74.1 - - - +
434B LEU* 1.3 67.3 + - + +
436B ALA* 3.4 7.5 + - - +
437B LYS* 3.0 38.3 + - - +
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Residues in contact with LEU 434 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
522A LEU* 6.3 0.2 - - + -
387B ILE* 4.9 2.7 - - + -
391B ILE* 3.6 32.5 - - + -
430B HIS* 3.1 19.0 + - - +
431B ALA* 3.3 11.2 - - - +
433B GLU* 1.3 77.2 - - + +
435B VAL* 1.3 65.1 + - - +
437B LYS* 3.4 10.3 + - + +
438B LEU* 3.0 31.4 + - + +
502B ARG* 5.2 7.8 - - + +
505B GLU* 3.9 24.7 - - + +
506B ILE* 3.8 20.6 - - + +
509B ILE* 3.5 29.4 - - + -
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Residues in contact with VAL 435 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391B ILE* 3.9 26.9 - - + -
394B GLN* 3.7 36.8 - - + -
395B VAL* 4.0 6.9 - - + +
431B ALA 3.0 18.9 + - - +
432B GLN* 3.4 26.0 - - - +
433B GLU 3.3 0.2 - - - -
434B LEU* 1.3 76.3 - - - +
436B ALA* 1.3 57.4 + - - +
438B LEU* 3.3 1.7 + - - +
439B ARG* 2.9 53.5 + - - +
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Residues in contact with ALA 436 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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432B GLN 2.9 16.9 + - - +
433B GLU* 3.6 9.2 - - - +
434B LEU 3.3 0.2 - - - -
435B VAL* 1.3 78.3 - - - +
437B LYS* 1.3 63.0 + - + +
439B ARG* 3.4 8.9 + - - +
440B SER* 3.1 23.3 + - - -
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Residues in contact with LYS 437 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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433B GLU* 3.0 29.6 + - - +
434B LEU* 3.7 8.6 - - - +
436B ALA* 1.3 76.2 - - + +
438B LEU* 1.3 58.8 + - - +
440B SER* 3.3 9.7 + - - -
441B LEU* 3.0 33.2 + - + +
502B ARG* 3.7 45.1 - - - +
505B GLU* 4.7 10.5 + - - +
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Residues in contact with LEU 438 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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388B LEU* 5.4 5.2 - - + -
391B ILE* 3.3 32.5 - - + -
395B VAL* 4.0 7.9 - - + -
434B LEU* 3.0 20.4 + - + +
435B VAL 3.9 2.5 - - - +
437B LYS* 1.3 72.9 - - - +
439B ARG* 1.3 66.2 + - - +
441B LEU* 3.2 7.2 + - + +
442B GLN 3.2 4.5 + - - -
443B PHE* 3.1 69.2 + - + +
451B LEU* 5.3 2.5 - - + -
499B LEU* 4.0 16.6 - - + -
502B ARG* 4.0 32.1 - - + -
506B ILE* 5.6 1.8 - - + -
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Residues in contact with ARG 439 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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394B GLN* 2.7 26.6 + - - +
395B VAL* 3.1 44.3 + - + +
396B VAL 5.1 0.8 + - - -
398B GLY* 3.3 28.4 + - - +
399B LYS* 5.1 3.2 + - - +
432B GLN* 6.0 0.6 - - - +
435B VAL* 2.9 32.7 + - - +
436B ALA* 3.5 9.1 - - - +
438B LEU* 1.3 75.5 - - - +
440B SER* 1.3 58.2 + - - +
442B GLN* 3.0 23.5 + - - +
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Residues in contact with SER 440 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436B ALA 3.1 10.8 + - - -
437B LYS* 3.3 12.8 + - - -
439B ARG* 1.3 79.7 - - - +
441B LEU* 1.3 63.2 + - - +
442B GLN* 3.5 9.2 + - - +
492B GLN* 4.8 2.3 - - - +
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Residues in contact with LEU 441 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437B LYS* 3.0 24.0 + - + +
438B LEU* 3.7 12.6 - - + +
439B ARG 3.2 0.4 - - - -
440B SER* 1.3 76.1 - - - +
442B GLN* 1.3 69.2 + - - +
443B PHE 4.6 1.6 - - - +
492B GLN* 3.0 26.9 + - - +
495B LYS* 3.1 19.6 + - + -
498B GLN* 3.2 66.9 - - + +
499B LEU* 4.5 13.9 - - + -
502B ARG* 4.2 9.6 - - - +
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Residues in contact with GLN 442 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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395B VAL* 6.2 0.2 - - - -
438B LEU 3.2 0.2 + - - -
439B ARG 3.0 16.7 + - - +
440B SER 4.2 8.4 + - - +
441B LEU* 1.3 81.0 - - - +
443B PHE* 1.3 66.0 + - - +
444B ASP* 3.4 2.3 + - - +
489B TYR* 3.7 30.8 + - + +
492B GLN* 3.9 13.4 + - - +
495B LYS* 2.9 15.7 + - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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