Contacts of the strand formed by residues 537 - 546 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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455A ARG* 4.9 1.6 + - - -
472D ASP* 3.0 17.1 + - - +
473D GLN* 3.0 36.3 + - + +
474D ARG* 3.5 17.9 - - + +
477D ASP* 2.6 26.4 - - - +
520D ILE* 3.7 15.3 - - + -
521D ASP 4.0 0.4 - - - -
522D VAL* 4.2 11.1 - - + +
535D GLY 3.8 11.1 - - - +
536D TYR* 1.3 72.2 - - - +
538D LEU* 1.3 62.0 + - - +
539D PRO* 3.4 6.9 - - - +
585D MSE 3.5 22.9 - - - +
587D GLN* 3.1 22.9 + - - -
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Residues in contact with LEU 538 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306D TRP* 4.3 9.2 - - + -
353D LEU* 3.7 31.4 - - + -
393D THR 5.5 2.0 - - - +
470D VAL* 3.6 32.5 - - + +
520D ILE* 3.3 2.3 - - - -
521D ASP* 2.8 46.2 + - + +
523D TYR* 4.0 25.8 - - + +
536D TYR* 3.5 15.0 + - + -
537D GLU* 1.3 71.8 - - - +
539D PRO* 1.3 74.0 - - - +
540D VAL* 3.2 2.6 + - + +
576D HIS* 4.4 22.2 - - + -
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Residues in contact with PRO 539 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306D TRP* 3.2 18.7 + - - -
469D LEU 3.3 24.5 - - - +
470D VAL 3.9 0.7 - - - -
471D HIS 3.3 24.2 - - - +
473D GLN* 3.6 22.7 - - + +
518D LYS* 5.0 2.0 - - + -
519D LEU 3.6 8.1 - - - +
520D ILE* 3.9 9.4 - - + -
537D GLU 3.4 2.0 - - - +
538D LEU* 1.3 89.0 - - + +
540D VAL* 1.3 63.6 + - - +
541D SER 3.3 2.7 - - - +
542D LEU* 4.0 23.6 - - + -
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Residues in contact with VAL 540 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305D LEU* 4.9 4.2 - - - +
306D TRP* 3.7 20.7 + - + +
393D THR* 5.1 3.1 - - - +
496D ILE* 4.5 6.7 - - + -
519D LEU* 2.9 12.8 + - + +
521D ASP* 3.8 33.4 - - + +
538D LEU* 3.2 6.0 + - + +
539D PRO* 1.3 74.9 - - - +
541D SER* 1.3 62.2 + - - +
572D PRO* 5.3 0.7 - - - +
573D THR 4.8 5.7 - - - +
574D ALA* 3.6 28.7 - - + -
576D HIS* 3.8 35.4 - - + +
578D PHE* 4.1 7.4 - - + -
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Residues in contact with SER 541 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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500D PRO* 4.8 2.2 - - - -
518D LYS* 3.7 0.2 - - - -
519D LEU* 2.8 47.7 + - - +
539D PRO 3.3 1.5 - - - -
540D VAL* 1.3 89.8 - - - +
542D LEU* 1.3 57.7 + - - +
571D LEU* 3.2 12.4 - - - +
572D PRO* 2.6 49.6 + - - +
574D ALA* 4.8 1.8 - - - -
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Residues in contact with LEU 542 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311D MSE 5.7 0.2 - - - +
468D TRP* 3.8 30.7 - - + +
469D LEU* 3.7 27.7 - - + +
473D GLN* 5.6 1.8 - - - +
516D VAL* 5.0 4.0 - - + -
517D VAL 3.3 13.7 - - - +
518D LYS* 3.9 21.8 - - + -
539D PRO* 4.0 25.6 - - + -
541D SER* 1.3 76.4 + - - +
543D ALA* 1.3 67.5 + - - +
544D ILE 5.2 0.2 - - - +
571D LEU* 4.3 1.3 - - - -
572D PRO* 3.1 23.7 - - - +
592D LEU* 4.2 15.5 - - + -
596D TYR* 6.2 0.4 - - + -
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Residues in contact with ALA 543 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211D ASN* 6.0 1.8 - - - -
212D TYR* 4.6 5.8 - - + -
515D TRP 4.0 0.9 - - - +
516D VAL* 3.4 4.1 - - - +
517D VAL 3.0 31.6 + - - +
542D LEU* 1.3 85.7 - - - +
544D ILE* 1.3 63.1 + - - +
569D PHE* 4.3 10.7 - - + -
570D GLY 3.9 15.3 - - - +
571D LEU* 3.6 19.2 - - + +
572D PRO* 4.1 4.5 - - + -
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Residues in contact with ILE 544 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211D ASN* 3.6 15.6 + - + +
212D TYR* 3.3 25.8 - - - +
214D ALA* 3.9 9.6 - - + -
514D ASP* 3.8 25.1 - - + +
515D TRP 3.5 4.9 - - - +
516D VAL* 3.7 25.4 - - + +
543D ALA* 1.3 75.1 - - - +
545D PHE* 1.3 67.5 + - - +
569D PHE* 4.7 0.9 - - - -
591D SER* 5.4 0.7 - - - -
592D LEU* 4.5 9.0 - - + +
596D TYR* 3.4 64.6 - - + +
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Residues in contact with PHE 545 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212D TYR* 3.8 14.4 - + + -
514D ASP* 3.4 1.2 - - - -
515D TRP* 2.9 34.4 + + + +
544D ILE* 1.3 78.9 - - - +
546D ARG* 1.3 78.2 + - - +
547D GLY* 3.3 4.6 + - - -
549D TYR* 3.5 22.7 - - + -
550D ARG* 3.9 21.3 - - - -
553D PHE* 3.6 28.3 - + - -
567D PHE* 4.0 20.6 - + + -
568D GLN 4.4 9.4 - - - -
569D PHE* 3.5 53.6 - + + -
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Residues in contact with ARG 546 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212D TYR 3.3 20.8 + - - +
213D GLY 3.5 22.2 + - - -
214D ALA* 3.6 17.4 - - - +
215D PHE* 3.6 5.7 - - - +
514D ASP* 2.9 34.9 + - - +
544D ILE* 4.9 0.8 - - - +
545D PHE* 1.3 79.7 - - - +
547D GLY* 1.3 63.6 + - - +
548D ARG* 3.7 21.8 - - + +
549D TYR* 3.1 24.2 + - + +
596D TYR* 5.0 0.4 - - - +
597D ASP* 2.9 53.7 + - - +
599D ASN* 4.0 10.3 - - - +
607D ILE* 3.7 29.8 - - - +
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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