Contacts of the strand formed by residues 537 - 546 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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472A ASP* 2.9 17.7 + - - +
473A GLN* 3.0 37.3 + - + +
474A ARG* 3.5 18.4 - - + +
477A ASP* 2.6 25.7 - - - +
520A ILE* 3.8 14.1 - - + -
522A VAL* 4.3 10.5 - - + +
535A GLY 3.8 10.9 - - - +
536A TYR* 1.3 72.3 - - - +
538A LEU* 1.3 59.4 + - - +
539A PRO* 3.4 9.0 - - - +
585A MSE 3.4 23.4 - - - +
587A GLN* 3.1 22.7 + - - -
455D ARG* 4.7 1.9 + - - -
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Residues in contact with LEU 538 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306A TRP* 4.3 9.9 - - + -
353A LEU* 3.8 22.4 - - + -
393A THR 5.4 2.0 - - - +
470A VAL* 3.7 38.1 - - + +
520A ILE* 3.3 1.7 - - - -
521A ASP* 2.8 45.5 + - + +
523A TYR* 4.0 24.9 - - + +
536A TYR* 3.5 15.1 + - + -
537A GLU* 1.3 72.2 - - - +
539A PRO* 1.3 75.9 - - - +
540A VAL* 3.2 2.6 + - + +
576A HIS* 4.4 21.3 - - + -
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Residues in contact with PRO 539 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306A TRP* 3.2 20.3 + - - -
469A LEU 3.3 25.2 - - - +
470A VAL 4.0 0.7 - - - -
471A HIS 3.3 16.4 - - - +
473A GLN* 3.6 32.1 - - + +
518A LYS* 5.0 1.6 - - + -
519A LEU 3.6 8.3 - - - +
520A ILE* 3.9 8.7 - - + -
537A GLU 3.4 2.0 - - - +
538A LEU* 1.3 89.1 - - + +
540A VAL* 1.3 62.6 + - - +
541A SER* 3.3 2.5 - - - +
542A LEU* 3.9 24.2 - - + -
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Residues in contact with VAL 540 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305A LEU* 4.9 4.7 - - - +
306A TRP* 3.7 22.5 + - + +
393A THR* 5.1 2.2 - - - +
496A ILE* 4.7 6.5 - - + -
519A LEU* 2.9 12.8 + - + +
521A ASP* 3.8 19.3 - - + +
538A LEU* 3.2 5.6 + - + +
539A PRO* 1.3 74.6 - - - +
541A SER* 1.3 62.8 + - - +
572A PRO* 5.3 0.9 - - - +
573A THR 4.7 5.9 - - - +
574A ALA* 3.6 28.9 - - + -
576A HIS* 3.6 49.6 - - + +
578A PHE* 4.2 7.2 - - + -
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Residues in contact with SER 541 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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500A PRO* 4.7 2.2 - - - -
519A LEU* 2.7 46.3 + - - +
539A PRO* 3.3 2.4 - - - -
540A VAL* 1.3 89.2 - - - +
542A LEU* 1.3 55.7 + - - +
571A LEU* 3.2 12.7 - - - +
572A PRO* 2.6 49.8 + - - +
574A ALA* 4.8 2.2 - - - -
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Residues in contact with LEU 542 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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468A TRP* 3.8 31.6 - - + -
469A LEU* 3.9 25.4 - - + +
473A GLN* 5.4 1.8 - - - +
516A VAL* 5.2 3.6 - - + -
517A VAL 3.2 13.5 - - - +
518A LYS* 3.8 24.9 - - + -
539A PRO* 3.9 25.6 - - + -
541A SER* 1.3 76.2 + - - +
543A ALA* 1.3 67.8 + - - +
571A LEU* 4.1 1.8 - - - -
572A PRO* 3.1 23.6 - - - +
592A LEU* 4.4 14.1 - - + -
596A TYR* 6.3 0.4 - - + -
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Residues in contact with ALA 543 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211A ASN* 6.0 1.8 - - - +
212A TYR* 4.9 5.2 - - + -
515A TRP 3.9 0.9 - - - +
516A VAL* 3.4 5.6 - - - +
517A VAL 3.0 31.4 + - - +
542A LEU* 1.3 85.1 - - - +
544A ILE* 1.3 64.5 + - - +
569A PHE* 4.2 10.2 - - + -
570A GLY 3.8 15.3 - - - +
571A LEU* 3.7 16.8 - - + +
572A PRO* 4.1 4.5 - - + -
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Residues in contact with ILE 544 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211A ASN* 3.7 10.3 + - + +
212A TYR* 3.4 25.1 - - - +
214A ALA* 4.0 14.8 - - + -
514A ASP* 3.8 24.2 - - + +
515A TRP 3.4 4.7 - - - +
516A VAL* 3.6 27.4 - - + +
542A LEU* 5.3 0.4 - - - +
543A ALA* 1.3 74.3 - - - +
545A PHE* 1.3 69.1 + - - +
569A PHE* 4.7 0.9 - - - -
591A SER* 5.4 0.9 - - - -
592A LEU* 4.4 9.9 - - + +
596A TYR* 3.5 61.5 - - + +
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Residues in contact with PHE 545 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212A TYR* 3.8 13.9 - + + -
514A ASP* 3.3 4.9 - - - -
515A TRP* 2.9 34.0 + + + +
544A ILE* 1.3 79.4 - - - +
546A ARG* 1.3 79.3 + - - +
547A GLY* 3.4 5.7 + - - -
549A TYR* 3.6 22.7 - - + -
550A ARG* 3.8 21.1 - - - -
553A PHE* 3.7 26.9 - + - -
567A PHE* 4.0 19.1 - + + -
568A GLN 4.3 9.4 - - - -
569A PHE* 3.5 50.9 - + + -
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Residues in contact with ARG 546 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212A TYR 3.2 20.4 + - - +
213A GLY 3.5 15.5 + - - -
214A ALA* 3.6 18.4 - - - +
215A PHE* 3.7 11.1 - - - +
514A ASP* 2.9 38.6 + - - +
545A PHE* 1.3 78.9 - - - +
547A GLY* 1.3 66.5 + - - +
548A ARG* 3.7 22.0 - - + +
549A TYR* 3.1 24.2 + - + -
596A TYR* 5.0 0.4 - - - +
597A ASP* 2.9 48.5 + - - +
599A ASN* 4.0 9.4 - - - +
607A ILE* 3.7 32.2 - - - +
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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