Contacts of the strand formed by residues 537 - 546 (chain C) in PDB entry 1MPX
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 GLU 537 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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455B ARG* 4.8 1.7 + - - -
472C ASP* 3.0 16.8 + - - +
473C GLN* 3.0 37.3 + - + +
474C ARG* 3.4 19.4 - - + +
477C ASP* 2.5 25.5 - - - +
520C ILE* 3.7 15.0 - - + -
521C ASP 3.9 0.2 - - - -
522C VAL* 4.3 10.5 - - + +
535C GLY 3.7 12.2 - - - +
536C TYR* 1.3 71.0 - - - +
538C LEU* 1.3 61.5 + - - +
539C PRO* 3.4 6.8 - - - +
585C MSE 3.4 21.2 - - - +
587C GLN* 3.1 22.7 + - - -
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Residues in contact with LEU 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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306C TRP* 4.3 10.8 - - + -
353C LEU* 3.7 31.6 - - + -
393C THR 5.5 2.9 - - - +
470C VAL* 3.6 32.8 - - + +
520C ILE* 3.3 2.3 - - - -
521C ASP* 2.8 45.0 + - + +
523C TYR* 4.1 24.9 - - + +
536C TYR* 3.5 14.9 + - + -
537C GLU* 1.3 72.1 - - - +
539C PRO* 1.3 70.0 - - - +
540C VAL* 3.1 6.2 + - + +
576C HIS* 4.6 19.3 - - + -
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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
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306C TRP* 3.2 18.4 + - - -
469C LEU 3.3 26.3 - - - +
470C VAL 3.9 1.1 - - - -
471C HIS 3.3 15.7 - - - +
473C GLN* 3.6 31.2 - - + +
518C LYS* 5.0 2.2 - - + -
519C LEU 3.6 8.7 - - - +
520C ILE* 3.9 9.2 - - + -
537C GLU 3.4 2.2 - - - +
538C LEU* 1.3 89.3 - - + +
540C VAL* 1.3 64.2 + - - +
541C SER 3.3 2.0 - - - +
542C LEU* 3.9 23.8 - - + -
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Residues in contact with VAL 540 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305C LEU* 4.9 4.2 - - - +
306C TRP* 3.7 21.2 + - + +
393C THR* 4.9 3.4 - - - +
496C ILE* 4.8 5.2 - - + -
519C LEU* 2.9 14.2 + - + +
521C ASP* 3.8 20.6 - - + +
538C LEU* 3.1 7.6 + - + +
539C PRO* 1.3 74.4 - - - +
541C SER* 1.3 62.4 + - - +
572C PRO* 5.4 0.9 - - - +
573C THR 4.7 5.9 - - - +
574C ALA* 3.6 28.5 - - + -
576C HIS* 3.4 48.2 - - + +
578C PHE* 4.3 5.2 - - + -
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Residues in contact with SER 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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500C PRO* 4.8 0.9 - - - -
517C VAL 4.2 0.2 - - - +
519C LEU* 2.7 48.0 + - - +
539C PRO 3.3 1.7 - - - -
540C VAL* 1.3 88.9 - - - +
542C LEU* 1.3 58.1 + - - +
571C LEU* 3.2 11.4 - - - +
572C PRO* 2.6 49.9 + - - +
574C ALA* 4.7 3.6 - - - -
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Residues in contact with LEU 542 (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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311C MSE 5.7 0.2 - - - +
468C TRP* 3.9 30.3 - - + +
469C LEU* 3.9 26.1 - - + +
473C GLN* 5.5 1.6 - - - +
516C VAL* 5.1 3.4 - - + -
517C VAL 3.2 13.7 - - - +
518C LYS* 3.8 22.9 - - + -
539C PRO* 3.9 26.2 - - + -
541C SER* 1.3 76.1 + - - +
543C ALA* 1.3 69.7 + - - +
571C LEU* 4.4 1.8 - - - -
572C PRO* 3.1 23.9 - - - +
592C LEU* 4.4 14.6 - - + -
596C TYR* 6.3 0.4 - - + -
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Residues in contact with ALA 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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211C ASN* 6.0 2.7 - - - +
212C TYR* 4.6 6.1 - - + -
515C TRP 3.9 0.7 - - - +
516C VAL* 3.4 5.1 - - - +
517C VAL 3.0 31.3 + - - -
542C LEU* 1.3 85.8 - - - +
544C ILE* 1.3 63.4 + - - +
569C PHE* 4.4 10.0 - - + -
570C GLY 3.9 15.3 - - - +
571C LEU* 3.9 17.4 - - + +
572C PRO* 4.2 5.4 - - + -
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Residues in contact with ILE 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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211C ASN* 3.5 8.8 + - + +
212C TYR* 3.3 24.4 - - - +
214C ALA* 4.0 13.0 - - + -
514C ASP* 3.8 29.2 - - + +
515C TRP 3.5 4.7 - - - +
516C VAL* 3.6 26.9 - - + +
543C ALA* 1.3 75.6 - - - +
545C PHE* 1.3 63.5 + - - +
546C ARG 4.3 0.2 - - - -
569C PHE* 4.8 0.7 - - - -
591C SER* 5.4 0.4 - - - -
592C LEU* 4.4 11.7 - - + +
596C TYR* 3.4 62.6 - - + +
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Residues in contact with PHE 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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212C TYR* 3.7 13.2 - + + -
514C ASP* 3.4 0.9 - - - -
515C TRP* 2.9 33.4 + + + +
544C ILE* 1.3 78.8 - - - +
546C ARG* 1.3 75.4 + - - +
547C GLY* 3.2 7.4 + - - -
549C TYR 3.5 23.1 - - - -
550C ARG* 3.9 20.9 - - - -
553C PHE* 3.6 28.0 - + - -
567C PHE* 4.0 21.8 - + + -
568C GLN 4.3 9.4 - - - -
569C PHE* 3.6 52.5 - + + -
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Residues in contact with ARG 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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212C TYR 3.2 21.2 + - - +
213C GLY 3.5 13.7 + - - -
214C ALA* 3.6 20.9 - - - +
215C PHE* 3.7 11.5 - - - +
514C ASP* 2.9 40.6 + - - +
544C ILE 4.3 0.4 - - - -
545C PHE* 1.3 77.6 - - - +
547C GLY* 1.3 64.7 - - - +
548C ARG* 3.7 20.6 - - + +
549C TYR* 3.0 25.8 + - + +
597C ASP* 2.9 48.9 + - - +
598C ARG 4.3 0.2 - - - -
599C ASN* 4.0 10.4 - - - +
607C ILE* 3.8 31.3 - - - +
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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