Contacts of the helix formed by residues 537 - 549 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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324C SER* 4.3 0.3 + - - -
476C GLU* 5.7 0.9 - - - -
527C PRO* 3.8 17.6 - - - +
530C LEU* 5.3 0.7 - - - -
531C SER* 3.1 26.3 + - - +
535C LYS 3.6 0.9 + - - -
536C PRO* 1.3 74.7 - - - +
538C PRO* 1.3 75.1 - - - +
539C PRO* 3.5 6.6 - - - +
540C TYR* 3.2 30.9 - - - +
541C PHE* 3.4 18.5 + - - +
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Residues in contact with PRO 538 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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464C MET* 4.0 2.9 - - + -
467C LEU* 3.7 35.3 - - + +
468C TYR* 3.5 48.5 - - + +
476C GLU* 5.4 0.2 - - - +
536C PRO 4.1 3.6 - - - +
537C SER* 1.3 85.7 - - - +
539C PRO* 1.3 68.3 - - + +
540C TYR 3.2 2.9 - - - -
541C PHE* 3.8 9.9 - - + -
542C GLY* 2.7 27.0 + - - -
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Residues in contact with PRO 539 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396C LEU* 3.7 25.9 - - + +
464C MET* 3.6 25.8 - - + -
468C TYR* 4.5 2.5 - - - +
519C PHE* 3.7 6.0 - - + -
521C VAL* 5.5 0.2 - - + -
523C VAL* 5.2 5.4 - - + -
525C TYR* 5.0 3.4 - - + +
527C PRO* 3.6 30.1 - - + -
537C SER* 3.2 11.7 - - - +
538C PRO* 1.3 104.1 - - + +
540C TYR* 1.3 62.6 + - + +
543C LEU* 3.1 24.7 + - - +
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Residues in contact with TYR 540 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317C VAL* 4.2 22.3 - - + +
320C ALA* 3.7 17.0 - - + +
321C LEU* 3.7 30.8 - - + +
324C SER* 3.6 10.5 + - - +
368C LEU* 4.4 10.8 - - + +
396C LEU* 3.6 26.0 - - + -
398C VAL* 4.3 12.2 - - + +
527C PRO* 3.9 15.6 - - + +
528C GLU* 2.7 46.9 + - + +
531C SER* 6.1 0.2 - - - +
537C SER* 3.2 23.6 - - - +
539C PRO* 1.3 79.8 - - + +
541C PHE* 1.3 59.1 + - - +
542C GLY 3.3 0.4 - - - -
543C LEU* 3.6 6.3 - - + +
544C LEU* 2.9 27.9 + - - +
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Residues in contact with PHE 541 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324C SER* 3.1 35.1 + - - +
327C ALA* 3.9 24.9 - - + -
328C ILE* 4.5 10.8 - - + -
467C LEU* 5.6 3.6 - - + -
536C PRO* 4.8 12.1 - - + +
537C SER 3.4 15.8 + - - +
538C PRO* 4.0 7.0 - - + +
540C TYR* 1.3 74.5 - - - +
542C GLY* 1.3 60.4 + - - +
544C LEU* 3.0 6.2 + - + +
545C LEU* 2.9 66.1 + - + +
554C TYR* 3.8 31.0 - + - -
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Residues in contact with GLY 542 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467C LEU* 4.3 12.1 - - - -
519C PHE* 3.6 14.5 - - - -
538C PRO 2.7 22.3 + - - -
541C PHE* 1.3 71.3 - - - +
543C LEU* 1.3 64.8 + - - +
545C LEU* 3.1 15.2 + - - +
546C ALA* 2.9 22.5 + - - +
551C LEU* 4.2 5.5 - - - +
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Residues in contact with LEU 543 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301C ILE* 3.6 29.6 - - + -
321C LEU* 5.0 2.0 - - + -
367C VAL 4.0 6.5 - - - +
368C LEU* 4.9 2.2 - - + -
394C PRO* 3.5 35.7 - - + +
395C PHE 4.1 0.4 - - - +
396C LEU* 3.8 26.9 - - + -
519C PHE* 3.5 29.6 - - + -
539C PRO 3.1 21.7 + - - +
540C TYR* 3.6 10.8 - - + +
541C PHE 3.3 0.2 - - - -
542C GLY* 1.3 74.0 - - - +
544C LEU* 1.3 57.1 + - - +
546C ALA* 3.2 1.0 + - - +
547C SER* 2.8 38.5 + - - +
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Residues in contact with LEU 544 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299C CYS* 4.1 29.2 - - + -
321C LEU* 4.9 4.3 - - + +
324C SER* 3.4 39.3 - - - +
325C ALA* 3.7 7.6 - - + +
328C ILE* 3.5 28.7 - - + -
330C HIS* 5.6 1.1 - - + -
331C LYS 5.8 0.9 - - - +
332C LEU* 5.1 11.7 - - + -
540C TYR 2.9 15.3 + - - +
541C PHE* 3.0 11.8 + - + +
543C LEU* 1.3 75.3 - - - +
545C LEU* 1.3 52.9 + - - +
547C SER* 3.0 10.0 + - - -
548C VAL* 2.8 37.6 + - - +
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Residues in contact with LEU 545 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328C ILE* 3.8 17.0 - - + -
467C LEU* 5.1 0.7 - - + -
541C PHE* 2.9 48.5 + - + +
542C GLY* 3.4 9.0 - - - +
544C LEU* 1.3 78.4 - - - +
546C ALA* 1.3 56.2 + - - +
548C VAL* 3.8 4.9 - - - -
549C GLY 2.9 19.2 + - - -
550C ARG* 3.3 28.2 + - + +
551C LEU* 3.1 36.3 + - + +
554C TYR* 3.6 37.2 - - + -
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Residues in contact with ALA 546 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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394C PRO* 3.4 18.2 - - + +
518C PRO* 4.9 3.1 - - + +
519C PHE* 3.5 33.9 - - + -
542C GLY 2.9 13.0 + - - +
543C LEU 3.6 7.0 - - - +
545C LEU* 1.3 74.1 - - - +
547C SER* 1.3 64.9 + - - +
548C VAL 3.2 0.8 + - - -
549C GLY* 3.4 11.4 + - - +
551C LEU* 3.9 12.0 - - + +
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Residues in contact with SER 547 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299C CYS* 5.1 3.1 - - - -
300C SER 5.2 0.7 - - - -
301C ILE* 5.7 1.9 - - - +
365C HIS* 3.7 40.9 - - - +
366C GLY* 3.4 21.2 + - - -
394C PRO* 3.6 10.2 - - - +
543C LEU* 2.8 27.5 + - - +
544C LEU* 3.2 18.8 - - - -
546C ALA* 1.3 74.7 - - - +
548C VAL* 1.3 59.0 + - - +
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Residues in contact with VAL 548 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297C GLU* 4.5 3.8 - - - +
299C CYS* 3.5 29.6 - - - -
328C ILE* 4.0 9.4 - - + -
330C HIS* 3.8 26.7 - - + +
365C HIS* 5.8 0.7 - - - -
544C LEU* 2.8 21.4 + - + +
545C LEU* 3.8 4.5 - - - +
546C ALA 4.1 0.2 - - - -
547C SER* 1.3 76.9 - - - +
549C GLY* 1.3 56.6 + - - +
550C ARG* 3.5 28.0 - - + +
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Residues in contact with GLY 549 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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545C LEU 2.9 11.2 + - - -
546C ALA* 3.4 11.5 + - - -
548C VAL* 1.3 75.1 - - - +
550C ARG* 1.3 54.8 + - - +
551C LEU* 4.1 0.9 - - - -
552C SER* 5.5 3.6 + - - -
553C HIS* 6.0 0.2 - - - +
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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