Contacts of the strand formed by residues 583 - 589 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249B GLN* 5.1 11.4 + - - +
486C VAL* 3.7 30.2 - - + +
487C THR* 3.1 36.6 + - - +
488C GLU* 4.2 13.9 + - - -
489C PRO* 3.8 35.8 - - + +
490C LEU* 4.8 1.1 - - - -
521C ASP* 3.7 6.1 - - - +
522C VAL* 2.9 49.0 + - + +
523C TYR 5.9 0.7 - - - +
525C GLU* 5.7 4.0 + - - -
578C PHE* 4.2 2.8 - - - -
581C GLY 4.8 1.6 - - - +
582C HIS* 1.3 78.6 - - - +
584C VAL* 1.3 63.5 + - - +
585C MSE 6.1 0.2 - - - -
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Residues in contact with VAL 584 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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419C LEU* 3.9 21.3 - - + -
427C LEU* 3.6 3.0 - - + +
486C VAL* 3.4 4.2 - - - +
487C THR* 3.0 46.1 + - + +
490C LEU* 4.3 10.8 - - + -
494C LEU* 4.0 20.4 - - + -
519C LEU* 3.8 26.0 - - + -
520C ILE 3.6 5.2 - - - +
578C PHE* 3.9 29.4 - - + -
583C ARG* 1.3 75.3 - - - +
585C MSE 1.3 63.0 + - - +
634C LEU* 5.4 2.2 - - + -
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Residues in contact with MSE 585 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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427C LEU* 4.0 0.9 - - - -
477C ASP* 3.7 2.5 - - - +
484C THR* 3.7 22.2 - - + -
485C PHE 3.2 11.7 - - - +
486C VAL* 4.0 15.0 - - + -
519C LEU* 3.6 2.3 - - - +
520C ILE* 2.8 50.0 + - + +
522C VAL* 3.5 33.4 - - + -
537C GLU* 3.4 37.7 - - - +
584C VAL* 1.3 76.2 - - - +
586C VAL* 1.3 77.7 + - - +
587C GLN* 3.7 17.3 - - + -
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Residues in contact with VAL 586 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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419C LEU* 4.8 1.6 - - + -
421C LEU* 4.5 11.7 - - + -
427C LEU* 3.8 24.7 - - + -
484C THR* 3.7 1.9 - - - -
485C PHE* 2.9 42.4 + - + +
517C VAL* 3.9 22.0 - - + -
518C LYS 3.1 9.9 - - - +
519C LEU* 4.4 7.6 - - + -
585C MSE 1.3 80.4 - - - +
587C GLN* 1.3 66.1 + - - +
588C VAL* 4.2 12.6 - - + -
632C ILE* 3.5 26.0 - - + -
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Residues in contact with GLN 587 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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473C GLN* 3.8 8.0 + - - +
476C VAL* 3.9 4.6 - - - +
477C ASP* 3.6 17.6 - - - +
482C VAL* 4.1 12.8 - - + +
483C LEU 3.2 4.9 - - - +
484C THR* 3.8 14.8 - - - +
516C VAL 3.6 0.9 - - - +
517C VAL* 3.4 4.9 - - - -
518C LYS* 2.8 69.5 + - + +
520C ILE* 3.6 18.6 - - + +
537C GLU* 3.1 26.5 + - - -
585C MSE 3.7 12.1 - - - -
586C VAL* 1.3 76.3 - - - +
588C VAL* 1.3 61.0 + - - +
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Residues in contact with VAL 588 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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421C LEU* 4.3 9.4 - - + -
442C TYR* 3.9 13.8 - - + +
481C ASP 4.4 0.2 - - - +
482C VAL* 3.5 2.1 - - - -
483C LEU* 2.8 40.2 + - + +
485C PHE* 4.2 17.3 - - + -
504C LEU* 4.7 6.3 - - + -
515C TRP* 4.6 8.5 - - + -
516C VAL 3.2 9.0 - - - +
517C VAL* 4.5 13.9 - - + -
586C VAL* 4.2 16.2 - - + -
587C GLN* 1.3 79.2 - - - +
589C GLN* 1.3 68.9 + - - +
622C VAL* 3.9 24.2 - - + -
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Residues in contact with GLN 589 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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442C TYR* 3.5 10.4 + - - -
450C VAL* 3.4 21.7 - - + +
451C PRO 4.9 0.8 + - - -
481C ASP 3.8 16.8 - - - +
482C VAL* 3.6 20.0 - - + +
515C TRP* 3.7 2.3 - - - -
516C VAL* 2.8 40.8 + - + +
518C LYS* 3.0 33.6 + - - +
587C GLN* 4.9 0.2 - - - +
588C VAL* 1.3 76.0 - - - +
590C SER* 1.3 63.4 + - - +
591C SER 2.8 26.9 + - - +
592C LEU* 3.6 20.2 - - - +
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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