Contacts of the strand formed by residues 583 - 589 (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 ARG 583 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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486A VAL* 3.7 27.6 - - + +
487A THR* 3.1 37.2 + - - +
488A GLU* 4.0 16.7 + - - +
489A PRO* 3.7 34.5 - - + +
490A LEU* 4.8 1.1 - - - -
521A ASP* 3.7 5.7 - - - +
522A VAL* 2.9 49.3 + - + +
523A TYR 5.7 1.1 - - - +
525A GLU* 5.6 9.1 + - - +
578A PHE* 4.2 2.6 - - - -
581A GLY 4.8 2.4 + - - +
582A HIS* 1.3 80.1 - - - +
584A VAL* 1.3 64.6 + - - +
585A MSE 6.1 0.2 - - - -
249D GLN* 5.0 12.4 + - - +
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Residues in contact with VAL 584 (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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419A LEU* 3.9 20.6 - - + -
427A LEU* 3.5 4.8 - - + +
486A VAL* 3.4 3.1 - - - +
487A THR* 3.0 44.6 + - + +
490A LEU* 4.4 11.0 - - + -
494A LEU* 3.9 25.8 - - + -
519A LEU* 3.9 26.5 - - + -
520A ILE 3.5 5.8 - - - +
578A PHE* 3.9 24.5 - - + -
583A ARG* 1.3 75.5 - - - +
585A MSE 1.3 63.5 + - - +
634A LEU* 5.5 1.6 - - + -
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Residues in contact with MSE 585 (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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427A LEU* 4.0 0.7 - - - -
477A ASP* 3.8 2.9 - - - +
484A THR* 3.6 21.1 - - + -
485A PHE 3.2 12.1 - - - +
486A VAL* 3.9 16.2 - - + -
519A LEU* 3.6 2.9 - - - +
520A ILE* 2.7 47.8 + - + -
522A VAL* 3.5 31.0 - - + -
537A GLU* 3.4 44.0 - - - +
583A ARG* 6.1 0.2 - - - -
584A VAL* 1.3 76.4 - - - +
586A VAL* 1.3 79.9 + - - +
587A GLN* 3.7 15.0 - - - -
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Residues in contact with VAL 586 (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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419A LEU* 4.6 1.8 - - + -
421A LEU* 4.3 12.8 - - + -
427A LEU* 3.8 23.3 - - + -
484A THR* 3.6 1.9 - - - -
485A PHE* 2.8 44.3 + - + +
517A VAL* 4.0 21.3 - - + -
518A LYS 3.2 9.0 - - - +
519A LEU* 4.3 7.4 - - + -
585A MSE 1.3 81.3 - - - +
587A GLN* 1.3 67.6 + - - +
588A VAL* 4.1 12.6 - - + -
632A ILE* 3.5 25.6 - - + -
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Residues in contact with GLN 587 (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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473A GLN* 3.8 7.7 + - - +
476A VAL* 3.8 6.7 - - - +
477A ASP* 3.7 17.6 - - - +
482A VAL* 4.0 13.4 - - + +
483A LEU 3.2 4.7 - - - +
484A THR* 3.7 15.7 - - - +
516A VAL 3.6 1.0 - - - +
517A VAL* 3.4 4.5 - - - -
518A LYS* 2.8 73.2 + - + +
520A ILE* 3.7 11.4 - - + -
537A GLU* 3.1 26.9 + - - -
585A MSE 3.7 11.9 - - - +
586A VAL* 1.3 77.4 - - - +
588A VAL* 1.3 63.1 + - - +
589A GLN* 5.0 0.7 - - - +
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Residues in contact with VAL 588 (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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421A LEU* 4.2 17.0 - - + -
442A TYR* 4.0 15.0 - - + +
481A ASP 4.4 0.2 - - - +
482A VAL* 3.5 1.3 - - - -
483A LEU* 2.9 42.5 + - + +
485A PHE* 4.3 7.6 - - + -
504A LEU* 4.9 7.6 - - + -
515A TRP* 4.6 9.0 - - + -
516A VAL 3.2 10.8 - - - +
517A VAL* 4.5 13.9 - - + -
586A VAL* 4.1 16.6 - - + -
587A GLN* 1.3 80.4 - - - +
589A GLN* 1.3 68.9 + - - +
622A VAL* 4.0 19.7 - - + -
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Residues in contact with GLN 589 (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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442A TYR* 3.4 10.9 + - - -
450A VAL* 3.4 23.4 - - + +
451A PRO 4.9 0.8 + - - -
481A ASP 3.7 17.0 - - - +
482A VAL* 3.7 19.4 - - + +
515A TRP* 3.7 2.6 - - - -
516A VAL* 2.9 40.1 + - + +
518A LYS* 2.9 34.2 + - - +
587A GLN* 5.0 0.6 - - - +
588A VAL* 1.3 76.3 - - - +
590A SER* 1.3 62.5 + - - +
591A SER 2.8 26.5 + - - +
592A LEU* 3.7 20.6 - - - +
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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