Contacts of the strand formed by residues 537 - 546 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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471B HIS 3.5 3.3 - - - +
472B ASP* 3.0 19.0 + - - +
473B GLN* 3.0 36.0 + - + +
474B ARG* 3.4 19.7 - - + +
477B ASP* 2.6 26.2 - - - +
520B ILE* 3.7 15.0 - - + -
521B ASP 3.9 0.2 - - - -
522B VAL* 4.2 9.6 - - + +
535B GLY 3.8 10.7 - - - +
536B TYR* 1.3 72.7 - - - +
538B LEU* 1.3 61.6 + - - +
539B PRO* 3.5 2.3 - - - +
585B MSE 3.5 22.8 - - - +
587B GLN* 3.0 23.2 + - - -
455C ARG* 4.7 2.3 + - - -
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Residues in contact with LEU 538 (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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306B TRP* 4.3 11.7 - - + -
353B LEU* 3.9 21.8 - - + -
393B THR 5.5 2.2 - - - +
470B VAL* 3.6 36.3 - - + +
520B ILE* 3.2 1.9 - - - -
521B ASP* 2.8 44.8 + - + +
523B TYR* 4.0 26.9 - - + +
536B TYR* 3.5 15.5 + - + -
537B GLU* 1.3 72.1 - - - +
539B PRO* 1.3 79.5 - - + +
540B VAL* 3.2 2.9 + - + +
576B HIS* 4.5 18.8 - - + -
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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
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306B TRP* 3.2 18.0 + - - -
469B LEU 3.3 25.1 - - - +
470B VAL 4.0 0.9 - - - -
471B HIS 3.3 16.2 - - - +
473B GLN* 3.6 31.9 - - + +
518B LYS* 5.0 2.2 - - + -
519B LEU 3.6 7.9 - - - +
520B ILE* 3.8 9.6 - - + -
537B GLU 3.5 1.8 - - - +
538B LEU* 1.3 87.8 - - + +
540B VAL* 1.3 64.9 + - - +
541B SER 3.3 2.2 - - - +
542B LEU* 3.9 23.3 - - + -
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Residues in contact with VAL 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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305B LEU* 4.9 4.5 - - - +
306B TRP* 3.8 21.4 + - + +
393B THR* 5.0 2.7 - - - +
496B ILE* 4.7 7.2 - - + -
519B LEU* 2.8 12.8 + - + +
521B ASP* 3.8 20.0 - - + +
538B LEU* 3.2 6.9 + - + +
539B PRO* 1.3 74.2 - - - +
541B SER* 1.3 62.1 + - - +
572B PRO* 5.3 0.7 - - - +
573B THR 4.8 5.7 - - - +
574B ALA* 3.6 27.8 - - + -
576B HIS* 3.7 49.8 - - + +
578B PHE* 4.3 6.5 - - + -
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Residues in contact with SER 541 (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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500B PRO* 4.9 1.1 - - - -
517B VAL 4.2 0.3 - - - +
519B LEU* 2.8 44.4 + - - +
539B PRO* 3.3 2.6 - - - -
540B VAL* 1.3 88.9 - - - +
542B LEU* 1.3 59.2 + - - +
571B LEU* 3.2 11.6 - - - +
572B PRO* 2.6 49.0 + - - +
574B ALA* 4.8 2.9 - - - -
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Residues in contact with LEU 542 (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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468B TRP* 3.8 32.3 - - + -
469B LEU* 3.9 26.6 - - + +
473B GLN* 5.4 1.6 - - - +
516B VAL* 5.3 2.7 - - + -
517B VAL 3.3 12.8 - - - +
518B LYS* 3.8 25.1 - - + -
539B PRO* 3.9 26.0 - - + -
541B SER* 1.3 76.2 + - - +
543B ALA* 1.3 67.9 + - - +
571B LEU* 4.3 1.6 - - - -
572B PRO* 3.1 24.3 - - - +
592B LEU* 4.4 13.5 - - + -
596B TYR* 6.3 0.2 - - + -
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Residues in contact with ALA 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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211B ASN* 6.1 1.1 - - - -
212B TYR* 4.9 4.3 - - + -
515B TRP 3.9 1.0 - - - +
516B VAL* 3.3 6.2 - - - +
517B VAL 3.0 32.2 + - - -
542B LEU* 1.3 83.7 - - - +
544B ILE* 1.3 62.8 + - - +
569B PHE* 4.2 11.2 - - + -
570B GLY 3.8 15.3 - - - +
571B LEU* 3.6 19.5 - - + +
572B PRO* 4.2 3.8 - - + -
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Residues in contact with ILE 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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211B ASN* 3.7 10.2 + - + +
212B TYR* 3.4 23.7 - - - +
214B ALA* 4.0 12.6 - - + -
514B ASP* 3.8 28.9 - - + +
515B TRP 3.4 4.0 - - - +
516B VAL* 3.6 28.0 - - + +
543B ALA* 1.3 75.8 - - - +
545B PHE* 1.3 64.7 + - - +
569B PHE* 4.8 0.9 - - - -
591B SER* 5.3 0.7 - - - -
592B LEU* 4.4 9.2 - - + +
596B TYR* 3.4 63.9 - - + +
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Residues in contact with PHE 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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212B TYR* 3.7 13.9 - + + -
514B ASP* 3.3 3.5 - - - -
515B TRP* 2.9 35.8 + + + +
544B ILE* 1.3 79.1 - - - +
546B ARG* 1.3 79.3 + - - +
547B GLY* 3.4 7.5 + - - -
549B TYR* 3.6 22.4 - - + -
550B ARG* 3.8 21.1 - - - -
553B PHE* 3.7 28.3 - + - -
567B PHE* 4.1 16.4 - + + -
568B GLN 4.3 9.6 - - - -
569B PHE* 3.5 50.7 - + + -
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Residues in contact with ARG 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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212B TYR 3.3 20.8 + - - +
213B GLY 3.5 13.2 + - - -
214B ALA* 3.6 20.6 - - - +
215B PHE* 3.7 10.7 - - - +
514B ASP* 2.9 35.2 + - - +
545B PHE* 1.3 80.1 - - - +
547B GLY* 1.3 64.8 + - - +
548B ARG* 3.8 20.2 - - + +
549B TYR* 3.1 24.3 + - + -
596B TYR* 5.0 0.2 - - - +
597B ASP* 2.8 53.7 + - - +
599B ASN* 4.0 10.9 - - - +
607B ILE* 3.8 31.6 - - - +
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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