Contacts of the strand formed by residues 583 - 589 (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 ARG 583 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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249A GLN* 5.2 10.4 + - - +
486D VAL* 3.7 32.4 - - + +
487D THR* 3.1 31.3 + - - +
488D GLU* 4.0 13.5 + - - +
489D PRO* 3.6 37.4 - - + +
490D LEU* 4.7 1.1 - - - -
521D ASP* 3.7 5.7 - - - +
522D VAL* 2.9 47.2 + - + +
523D TYR 6.0 0.9 - - - +
525D GLU* 5.8 5.5 + - - -
578D PHE* 4.2 2.5 - - - -
581D GLY 4.8 2.0 - - - +
582D HIS* 1.3 78.7 - - - +
584D VAL* 1.3 63.9 + - - +
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Residues in contact with VAL 584 (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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419D LEU* 3.9 20.6 - - + -
427D LEU* 3.5 2.1 - - + +
486D VAL* 3.4 3.8 - - - +
487D THR* 3.0 47.6 + - + +
490D LEU* 4.2 11.0 - - + -
494D LEU* 4.0 20.4 - - + -
519D LEU* 3.8 26.0 - - + -
520D ILE 3.5 4.9 - - - +
578D PHE* 3.8 29.6 - - + -
583D ARG* 1.3 76.1 - - - +
585D MSE 1.3 63.1 + - - +
634D LEU* 5.3 1.8 - - + -
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Residues in contact with MSE 585 (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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427D LEU* 4.0 1.1 - - - -
477D ASP* 3.9 2.7 - - - +
484D THR* 3.5 22.4 - - + -
485D PHE 3.2 10.8 - - - +
486D VAL* 4.0 16.6 - - + -
519D LEU* 3.6 2.8 - - - +
520D ILE* 2.7 48.2 + - + -
522D VAL* 3.5 26.2 - - + -
537D GLU* 3.5 43.1 - - - +
584D VAL* 1.3 75.7 - - - +
586D VAL* 1.3 80.9 + - - +
587D GLN* 3.7 14.1 - - - -
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Residues in contact with VAL 586 (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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419D LEU* 4.7 2.2 - - + -
421D LEU* 4.4 13.0 - - + -
427D LEU* 3.9 23.8 - - + -
484D THR* 3.6 0.5 - - - -
485D PHE* 2.8 47.8 + - + +
517D VAL* 4.0 19.7 - - + -
518D LYS 3.2 9.9 - - - +
519D LEU* 4.4 7.6 - - + -
585D MSE 1.3 80.5 - - - +
587D GLN* 1.3 66.5 + - - +
588D VAL* 4.1 12.8 - - + -
632D ILE* 3.7 24.0 - - + -
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Residues in contact with GLN 587 (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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473D GLN* 3.8 8.2 + - - +
476D VAL* 3.9 3.9 - - - +
477D ASP* 3.6 18.8 - - - +
482D VAL* 4.1 13.4 - - + +
483D LEU 3.2 4.7 - - - +
484D THR* 3.9 14.8 - - - +
516D VAL 3.6 0.9 - - - +
517D VAL* 3.4 4.7 - - - -
518D LYS* 2.7 78.5 + - + +
520D ILE* 3.6 15.9 - - + +
537D GLU* 3.1 26.3 + - - -
585D MSE 3.7 11.9 - - - +
586D VAL* 1.3 76.7 - - - +
588D VAL* 1.3 63.0 + - - +
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Residues in contact with VAL 588 (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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421D LEU* 4.2 17.5 - - + -
442D TYR* 4.0 13.9 - - + +
482D VAL* 3.6 1.9 - - - -
483D LEU* 2.9 41.1 + - + +
485D PHE* 4.3 7.4 - - + -
504D LEU* 4.8 7.9 - - + -
515D TRP* 4.6 9.0 - - + -
516D VAL 3.2 9.2 - - - +
517D VAL* 4.3 15.0 - - + -
586D VAL* 4.1 16.6 - - + -
587D GLN* 1.3 80.3 - - - +
589D GLN* 1.3 67.9 + - - +
622D VAL* 4.0 22.7 - - + -
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Residues in contact with GLN 589 (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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442D TYR* 3.4 10.4 + - - -
450D VAL* 3.5 21.7 - - + +
451D PRO 4.9 1.0 + - - -
481D ASP 3.8 17.5 - - - +
482D VAL* 3.6 21.1 - - + +
515D TRP* 3.7 2.3 - - - -
516D VAL* 2.8 39.1 + - + +
518D LYS* 2.9 32.7 + - - +
587D GLN* 5.0 0.4 - - - +
588D VAL* 1.3 76.6 - - - +
590D SER* 1.3 63.0 + - - +
591D SER 2.8 25.9 + - - +
592D LEU* 3.6 22.4 - - - +
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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