Contacts of the strand formed by residues 439 - 444 (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 PHE 439 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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437D ALA* 3.3 14.8 + - - +
438D GLY* 1.3 84.3 - - - +
440D GLU* 1.3 76.4 + - - +
441D GLU* 3.7 18.3 + - + -
621D ARG* 3.5 50.0 - - + -
622D VAL 3.3 15.7 - - - +
623D TYR* 3.7 31.9 - + + -
624D VAL* 4.1 6.1 - - - -
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Residues in contact with GLU 440 (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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422D GLN 4.7 0.2 - - - +
423D ALA* 4.1 5.2 - - - +
424D GLY* 3.5 21.8 + - - -
425D GLY* 3.3 25.4 + - - -
437D ALA* 5.2 2.6 - - - +
439D PHE* 1.3 81.8 - - - +
441D GLU* 1.3 61.0 + - - +
483D LEU* 3.9 32.0 - - + +
484D THR 5.2 0.5 - - - +
485D PHE* 3.8 21.9 - - + -
620D GLN 3.9 0.2 - - - +
621D ARG* 3.4 2.6 - - - -
622D VAL 2.9 32.8 + - - +
624D VAL* 4.6 7.9 - - + -
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Residues in contact with GLU 441 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
617A LYS* 6.2 0.3 - - - -
439D PHE* 3.7 18.4 - - + -
440D GLU* 1.3 75.5 - - - +
442D TYR* 1.3 69.5 + - - +
443D VAL* 5.6 2.9 - - + +
480D PRO 5.1 0.3 - - - +
483D LEU* 4.1 7.3 - - - +
619D THR* 3.4 22.7 - - + +
620D GLN 3.3 12.1 - - - +
621D ARG* 3.0 31.5 + - + -
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Residues in contact with TYR 442 (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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441D GLU* 1.3 78.8 - - - +
443D VAL* 1.3 68.3 + - - +
444D SER* 4.4 4.0 - - - -
480D PRO 3.4 21.8 - - - +
481D ASP* 3.7 30.1 - - - -
483D LEU* 3.4 41.5 - - + -
515D TRP* 3.4 12.5 - - - -
588D VAL* 4.0 5.4 - - + +
589D GLN* 3.4 16.5 + - - -
590D SER* 2.8 28.7 + - - -
620D GLN* 2.8 60.7 + - + +
622D VAL* 4.3 9.4 - - + -
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Residues in contact with VAL 443 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480A PRO* 5.1 6.4 - - + +
441D GLU* 5.6 2.5 - - + +
442D TYR* 1.3 78.3 - - - +
444D SER* 1.3 64.4 + - - +
445D ASP* 3.9 4.1 + - + +
480D PRO 4.8 1.7 + - - -
481D ASP* 3.2 23.2 - - - +
617D LYS* 4.1 31.6 - - + -
618D ALA 3.5 10.3 - - - +
619D THR* 4.2 20.4 - - + +
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Residues in contact with SER 444 (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* 3.9 4.6 + - - -
443D VAL* 1.3 72.9 - - - +
445D ASP* 1.3 61.3 + - - +
446D PRO* 4.9 0.7 - - - +
481D ASP* 4.8 4.7 - - - -
590D SER* 3.5 29.8 + - - -
591D SER* 4.9 5.4 + - - -
601D GLN* 2.6 47.8 + - - -
617D LYS* 3.4 0.7 - - - -
618D ALA 3.0 18.8 + - - -
620D GLN* 3.9 12.6 - - - -
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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