Contacts of the strand formed by residues 574 - 578 (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 ALA 574 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305D LEU* 4.6 2.5 - - - -
404D TRP* 3.8 1.2 - - - -
496D ILE* 3.5 29.4 - - + +
497D ALA* 3.2 4.5 + - - -
498D GLY 2.9 35.1 + - - +
500D PRO* 4.8 4.3 - - + -
540D VAL* 3.6 22.7 - - + -
541D SER* 4.8 2.7 - - - -
572D PRO 4.3 4.5 - - - +
573D THR* 1.3 79.4 - - - +
575D ASN* 1.3 60.0 + - - +
576D HIS* 3.7 1.3 - - + -
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Residues in contact with ASN 575 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305D LEU* 4.6 6.7 - - + +
390D ILE* 3.6 19.7 + - + +
391D TYR 3.1 31.3 + - - +
392D ASN* 3.1 14.9 + - - +
393D THR* 3.1 26.0 + - - +
399D ASP* 3.0 26.7 + - - +
404D TRP* 3.4 30.1 - - + -
406D ARG* 5.0 1.6 - - - -
495D GLN* 4.6 4.0 + - - -
496D ILE 3.4 3.6 - - - +
497D ALA* 3.7 9.5 - - - +
574D ALA* 1.3 72.5 - - - +
576D HIS* 1.3 59.0 + - - +
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Residues in contact with HIS 576 (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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306D TRP* 5.7 0.4 - - - -
392D ASN* 3.6 3.1 - - - +
393D THR* 2.8 29.9 + - - +
394D GLY* 3.3 20.6 + - - -
494D LEU 3.7 1.7 - - - +
495D GLN* 3.7 0.6 - - - -
496D ILE* 3.0 40.6 + - + +
521D ASP* 2.6 33.0 + - + +
523D TYR* 5.8 1.1 - - - -
538D LEU* 4.4 11.9 - - + -
540D VAL* 3.8 39.2 - - + +
574D ALA 3.7 0.4 - - - -
575D ASN* 1.3 76.2 - - - +
577D THR* 1.3 74.8 + - - +
578D PHE* 3.8 13.8 + + - -
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Residues in contact with THR 577 (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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392D ASN* 3.2 17.2 + - - -
394D GLY* 3.4 17.6 - - - -
395D GLU* 2.7 38.5 + - - +
493D PRO* 3.8 28.0 - - + -
494D LEU 3.5 10.5 - - - +
495D GLN* 3.4 14.6 - - + +
521D ASP* 4.4 0.9 - - - +
576D HIS* 1.3 78.3 + - - +
578D PHE* 1.3 59.3 + - - +
579D GLN* 3.2 24.0 + - - +
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Residues in contact with PHE 578 (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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490D LEU* 3.4 23.9 - - + +
493D PRO* 3.5 1.4 - - - +
494D LEU* 2.8 52.1 + - + +
496D ILE* 3.8 37.2 - - + -
519D LEU* 4.5 10.5 - - + -
520D ILE 3.7 9.4 - - - -
521D ASP* 3.6 47.8 - - + -
540D VAL* 4.1 8.1 - - + -
576D HIS* 4.0 12.8 - + - -
577D THR* 1.3 69.4 - - - +
579D GLN* 1.3 64.2 + - - +
582D HIS* 4.8 2.5 - - + -
583D ARG 4.2 2.9 - - - -
584D VAL* 3.8 26.7 - - + -
634D LEU* 5.2 2.2 - - + -
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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