Contacts of the strand formed by residues 501 - 508 (chain B) 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 ASP 501 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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409B ASP* 4.7 8.3 - - - +
499B ALA 3.6 5.1 + - - +
500B PRO* 1.3 75.3 - - - +
502B VAL* 1.3 64.6 + - - +
503B HIS* 3.6 7.3 + - - +
568B GLN* 2.9 31.8 + - - +
569B PHE* 3.1 28.6 + - - +
570B GLY* 3.4 4.7 + - - -
632B ILE* 3.5 2.2 - - - -
633B SER* 2.8 48.1 + - - -
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Residues in contact with VAL 502 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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501B ASP* 1.3 70.3 - - - +
503B HIS* 1.3 62.9 + - - +
504B LEU* 3.7 23.6 - - + +
517B VAL* 4.0 19.1 - - + -
568B GLN* 3.1 30.0 - - - +
569B PHE* 2.8 44.5 + - + +
571B LEU* 3.4 40.6 - - + -
631B TYR 4.1 4.5 - - - +
632B ILE* 4.6 7.4 - - + +
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Residues in contact with HIS 503 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409B ASP* 4.8 6.2 + - - -
501B ASP* 3.6 20.7 + - - -
502B VAL* 1.3 72.0 - - - +
504B LEU* 1.3 59.9 + - - +
505B GLN* 4.8 1.5 - - - +
567B PHE 3.6 3.8 - - - -
568B GLN* 3.2 43.6 + - - +
629B PRO 3.9 3.2 - - - +
630B SER* 3.4 5.5 - - - -
631B TYR* 2.8 83.1 + + + +
633B SER* 4.1 9.3 - - - -
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Residues in contact with LEU 504 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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421B LEU* 5.1 4.9 - - + -
502B VAL* 3.8 16.2 - - + -
503B HIS* 1.3 73.8 - - - +
505B GLN* 1.3 61.3 + - - +
506B ALA* 3.9 12.1 - - + -
515B TRP* 3.7 47.3 - - + -
517B VAL* 4.9 7.6 - - + -
565B LEU 3.5 1.0 - - - +
566B ALA* 3.4 3.8 - - - +
567B PHE* 2.8 47.7 + - + +
569B PHE* 4.8 3.8 - - + -
588B VAL* 5.0 9.2 - - + -
622B VAL* 3.9 25.1 - - + -
630B SER* 3.7 19.1 - - - +
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Residues in contact with GLN 505 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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503B HIS 4.8 1.6 - - - +
504B LEU* 1.3 73.3 - - - +
506B ALA* 1.3 60.6 + - - +
564B PRO* 4.6 4.3 - - + +
565B LEU* 3.5 18.5 + - - -
566B ALA* 3.9 17.4 + - - +
622B VAL* 3.8 0.5 - - - -
623B TYR* 2.8 35.2 + - + +
627B GLU 5.4 1.2 + - - -
628B GLN* 3.9 42.0 + - + +
629B PRO* 3.6 23.1 + - - +
630B SER* 2.9 14.6 + - - +
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Residues in contact with ALA 506 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
504B LEU* 3.8 22.6 - - + -
505B GLN* 1.3 75.3 - - - +
507B SER* 1.3 61.8 + - - +
515B TRP* 3.8 28.9 - - + -
563B GLN 3.8 0.7 - - - +
564B PRO* 4.1 2.0 - - - -
565B LEU* 3.0 32.7 + - - +
567B PHE* 3.6 12.6 - - + -
621B ARG 3.1 14.6 - - - +
622B VAL* 4.4 1.6 - - + -
623B TYR* 4.4 1.8 - - - -
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Residues in contact with SER 507 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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506B ALA* 1.3 74.3 - - - +
508B THR* 1.3 61.1 + - - +
515B TRP* 3.7 6.6 - - - -
562B ASN* 4.2 6.7 - - - -
563B GLN 3.3 36.6 - - - -
564B PRO* 3.7 4.0 - - - -
565B LEU* 6.1 0.4 - - - -
619B THR 3.9 0.9 + - - +
620B GLN* 3.4 4.0 - - - -
621B ARG* 2.9 55.7 + - - +
623B TYR* 3.8 9.1 + - - -
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Residues in contact with THR 508 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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507B SER* 1.3 74.1 - - - +
509B SER* 1.3 60.9 + - - +
510B GLY* 3.1 26.7 + - - +
512B ASP 4.2 1.1 - - - +
513B SER* 3.2 17.5 + - - +
515B TRP* 4.4 2.9 - - + -
559B LEU* 3.9 33.0 - - + -
560B THR 4.2 2.7 + - - +
561B SER* 3.4 2.9 - - - -
562B ASN* 2.8 22.9 + - - -
563B GLN 4.8 0.8 + - - -
618B ALA* 3.5 4.0 - - - +
619B THR 3.4 2.2 - - - -
620B GLN* 2.7 28.4 + - - +
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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