Contacts of the helix formed by residues 537 - 549 (chain B) in PDB entry 5U03
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 SER 537 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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324B SER* 4.3 0.3 + - - -
476B GLU* 5.7 1.1 - - - -
527B PRO* 3.8 17.9 - - - +
530B LEU* 5.3 1.1 - - - -
531B SER* 3.1 26.9 + - - -
535B LYS 3.6 1.3 + - - -
536B PRO* 1.3 74.3 - - - +
538B PRO* 1.3 74.0 - - - +
539B PRO* 3.5 6.2 - - - +
540B TYR* 3.2 31.2 + - - +
541B PHE* 3.4 17.8 + - - +
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Residues in contact with PRO 538 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464B MET* 4.0 2.9 - - + -
467B LEU* 3.7 36.4 - - + +
468B TYR* 3.5 48.0 - - + +
476B GLU* 5.4 0.4 - - - +
536B PRO 4.1 4.0 - - - +
537B SER* 1.3 85.5 - - - +
539B PRO* 1.3 68.8 - - + +
540B TYR 3.2 2.7 - - - -
541B PHE* 3.8 9.9 - - + -
542B GLY* 2.7 27.0 + - - -
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Residues in contact with PRO 539 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396B LEU* 3.7 26.3 - - + +
464B MET* 3.6 26.0 - - + -
468B TYR* 4.5 2.7 - - - +
519B PHE* 3.7 6.6 - - + -
521B VAL* 5.5 0.2 - - + -
523B VAL* 5.2 5.4 - - + -
525B TYR* 5.0 3.4 - - + +
527B PRO* 3.6 29.6 - - + -
537B SER* 3.2 11.7 - - - +
538B PRO* 1.3 103.9 - - + +
540B TYR* 1.3 62.6 + - + +
543B LEU* 3.1 24.8 + - - +
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Residues in contact with TYR 540 (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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317B VAL* 4.2 21.7 - - + +
320B ALA* 3.7 17.3 - - + +
321B LEU* 3.7 30.8 - - + +
324B SER* 3.6 10.5 + - - +
368B LEU* 4.4 10.6 - - + +
396B LEU* 3.6 25.8 - - + -
398B VAL* 4.3 12.2 - - + +
527B PRO* 3.9 15.4 - - + +
528B GLU* 2.7 47.6 + - + +
531B SER* 6.1 0.2 - - - +
537B SER* 3.2 22.9 - - - +
538B PRO 3.2 0.4 - - - -
539B PRO* 1.3 80.4 - - + +
541B PHE* 1.3 59.2 + - - +
542B GLY 3.3 0.2 - - - -
543B LEU* 3.6 6.5 - - + +
544B LEU* 2.9 27.4 + - - +
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Residues in contact with PHE 541 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324B SER* 3.1 35.2 + - - +
327B ALA* 3.9 24.5 - - + -
328B ILE* 4.5 10.5 - - + -
467B LEU* 5.6 3.4 - - + -
536B PRO* 4.8 11.9 - - + +
537B SER 3.4 14.9 + - - +
538B PRO* 4.0 7.6 - - + +
540B TYR* 1.3 74.7 - - - +
542B GLY* 1.3 58.9 + - - +
544B LEU* 3.0 6.5 + - + +
545B LEU* 2.9 67.3 + - + +
554B TYR* 3.8 31.2 - + - -
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Residues in contact with GLY 542 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467B LEU* 4.2 12.6 - - - -
519B PHE* 3.6 14.1 - - - -
538B PRO 2.7 21.9 + - - -
541B PHE* 1.3 70.6 - - - +
543B LEU* 1.3 64.6 + - - +
545B LEU* 3.1 16.2 + - - +
546B ALA* 2.9 22.7 + - - +
551B LEU* 4.2 5.8 - - - +
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Residues in contact with LEU 543 (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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301B ILE* 3.6 30.3 - - + -
321B LEU* 5.0 2.2 - - + -
366B GLY* 5.4 0.2 - - - -
367B VAL 4.0 5.6 - - - +
368B LEU* 4.9 2.0 - - + -
394B PRO* 3.5 35.9 - - + +
395B PHE 4.1 0.9 - - - +
396B LEU* 3.8 26.7 - - + -
519B PHE* 3.5 29.8 - - + -
539B PRO 3.1 20.9 + - - +
540B TYR* 3.6 11.2 - - + +
542B GLY* 1.3 73.9 - - - +
544B LEU* 1.3 59.0 + - - +
546B ALA* 3.2 1.4 + - - +
547B SER* 2.8 38.1 + - - +
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Residues in contact with LEU 544 (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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299B CYS* 4.1 29.2 - - + -
321B LEU* 4.9 4.3 - - + +
324B SER* 3.4 39.3 - - - +
325B ALA* 3.7 7.4 - - + +
328B ILE* 3.5 30.1 - - + -
330B HIS* 5.8 1.1 - - + -
331B LYS 5.8 0.9 - - - +
332B LEU* 5.1 11.7 - - + -
540B TYR 2.9 15.1 + - - +
541B PHE* 3.0 12.3 + - + +
543B LEU* 1.3 75.9 - - - +
545B LEU* 1.3 53.0 + - - +
547B SER* 3.0 10.0 + - - -
548B VAL* 2.8 38.2 + - + +
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Residues in contact with LEU 545 (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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328B ILE* 3.8 17.5 - - + -
467B LEU* 5.1 0.4 - - + -
541B PHE* 2.9 46.8 + - + +
542B GLY* 3.4 9.2 - - - +
544B LEU* 1.3 78.6 - - - +
546B ALA* 1.3 56.0 + - - +
548B VAL* 3.8 4.3 - - - -
549B GLY 2.9 19.6 + - - -
550B ARG* 3.3 28.7 + - + +
551B LEU* 3.1 34.8 + - + +
554B TYR* 3.6 37.2 - - + -
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Residues in contact with ALA 546 (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 PRO* 3.4 18.4 - - + +
518B PRO* 4.9 3.4 - - + +
519B PHE* 3.5 34.1 - - + -
542B GLY 2.9 12.8 + - - +
543B LEU 3.6 6.7 - - - +
545B LEU* 1.3 74.9 - - - +
547B SER* 1.3 65.0 + - - +
548B VAL 3.2 0.4 + - - -
549B GLY* 3.4 11.9 + - - +
551B LEU* 3.9 11.8 - - + +
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Residues in contact with SER 547 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299B CYS* 5.1 3.1 - - - -
300B SER 5.1 0.8 + - - -
301B ILE* 5.7 1.9 - - - +
365B HIS* 3.7 40.9 - - - +
366B GLY* 3.4 20.8 - - - -
394B PRO* 3.6 10.2 - - - +
543B LEU* 2.8 27.9 + - - +
544B LEU* 3.2 18.9 - - - -
546B ALA* 1.3 74.9 - - - +
548B VAL* 1.3 59.9 + - - +
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Residues in contact with VAL 548 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297B GLU* 4.5 3.8 - - - +
299B CYS* 3.5 30.7 - - - -
328B ILE* 4.0 9.2 - - + -
330B HIS* 3.8 26.7 - - + +
365B HIS* 5.8 0.2 - - - -
544B LEU* 2.8 21.0 + - + +
545B LEU* 3.8 4.0 - - - +
547B SER* 1.3 76.2 - - - +
549B GLY* 1.3 57.4 + - - +
550B ARG* 3.5 28.0 - - + +
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Residues in contact with GLY 549 (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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545B LEU 2.9 10.6 + - - -
546B ALA* 3.4 11.9 + - - -
548B VAL* 1.3 75.3 - - - +
550B ARG* 1.3 55.5 + - - +
551B LEU* 4.7 0.7 - - - -
552B SER* 5.5 3.8 + - - -
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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