Contacts of the strand formed by residues 501 - 508 (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 ASP 501 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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409D ASP* 4.7 8.3 - - - +
499D ALA 3.6 4.0 + - - +
500D PRO* 1.3 75.0 - - - +
502D VAL* 1.3 63.6 + - - +
503D HIS* 3.6 6.6 + - - +
568D GLN* 2.9 32.4 + - - +
569D PHE* 3.2 27.5 + - - +
570D GLY* 3.5 4.8 + - - -
632D ILE* 3.4 3.4 - - - -
633D SER* 2.8 49.1 + - - -
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Residues in contact with VAL 502 (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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501D ASP* 1.3 70.8 - - - +
503D HIS* 1.3 62.8 + - - +
504D LEU* 3.8 26.5 - - + +
517D VAL* 4.0 19.7 - - + -
568D GLN* 3.2 30.0 - - - +
569D PHE* 2.9 40.3 + - + +
571D LEU* 3.5 42.0 - - + -
631D TYR 4.1 4.7 - - - +
632D ILE* 4.4 7.4 - - + -
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Residues in contact with HIS 503 (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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409D ASP* 4.8 6.4 + - - -
501D ASP* 3.6 27.5 + - - -
502D VAL* 1.3 73.2 - - - +
504D LEU* 1.3 59.6 + - - +
505D GLN* 3.8 2.8 + - - +
567D PHE 3.6 4.0 - - - -
568D GLN* 3.3 35.2 + - - +
629D PRO 4.1 2.4 - - - +
630D SER* 3.4 5.4 - - - -
631D TYR* 2.9 83.9 + + + +
633D SER* 4.1 9.1 - - - -
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Residues in contact with LEU 504 (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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421D LEU* 5.0 2.7 - - + -
502D VAL* 3.8 14.8 - - + -
503D HIS* 1.3 72.3 - - - +
505D GLN* 1.3 60.1 + - - +
506D ALA* 3.8 13.0 + - + -
515D TRP* 3.9 44.9 - - + -
517D VAL* 4.8 11.9 - - + -
565D LEU 3.4 2.9 - - - +
566D ALA* 3.5 2.6 - - - -
567D PHE* 2.8 49.0 + - + +
569D PHE* 5.0 1.6 - - + -
588D VAL* 4.8 11.9 - - + -
622D VAL* 3.9 26.0 - - + -
630D SER* 3.8 19.3 - - - +
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Residues in contact with GLN 505 (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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503D HIS 3.8 3.0 + - - +
504D LEU* 1.3 71.1 + - - +
506D ALA* 1.3 61.9 + - - +
564D PRO* 4.5 3.0 - - + +
565D LEU 3.5 15.0 + - - -
566D ALA* 3.5 26.6 + - - +
622D VAL* 3.8 0.7 - - - -
623D TYR* 2.9 32.5 + - + +
628D GLN* 3.8 43.6 + - + +
629D PRO* 3.8 20.3 - - + +
630D SER* 3.0 16.5 + - - +
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Residues in contact with ALA 506 (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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504D LEU* 3.8 21.9 + - + -
505D GLN* 1.3 75.5 - - - +
507D SER* 1.3 60.5 + - - +
515D TRP* 3.8 26.9 - - + -
563D GLN 3.9 0.7 - - - +
564D PRO* 4.1 1.6 - - - -
565D LEU* 3.0 31.4 + - - +
567D PHE* 3.5 12.5 - - + -
621D ARG 3.1 16.8 - - - +
622D VAL* 4.3 2.7 - - - -
623D TYR* 4.1 1.5 - - - -
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Residues in contact with SER 507 (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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506D ALA* 1.3 73.0 - - - +
508D THR* 1.3 62.0 + - - +
515D TRP* 3.5 10.1 - - - -
562D ASN* 3.8 14.9 + - - -
563D GLN 3.2 31.9 - - - -
564D PRO* 3.7 4.3 - - - -
565D LEU* 6.0 0.4 - - - -
619D THR 4.5 0.7 + - - -
620D GLN* 3.5 3.1 - - - -
621D ARG* 3.0 49.8 + - - +
623D TYR* 3.5 11.3 + - - -
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Residues in contact with THR 508 (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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507D SER* 1.3 76.1 - - - +
509D SER* 1.3 62.6 + - - +
510D GLY* 3.2 26.6 + - - +
512D ASP 4.1 1.8 - - - +
513D SER* 3.2 20.3 + - - +
515D TRP* 4.4 3.1 - - + -
559D LEU* 4.0 30.3 - - + -
560D THR 4.1 2.0 + - - +
561D SER* 3.5 0.9 - - - -
562D ASN* 2.8 21.0 + - - +
563D GLN 4.8 0.6 + - - +
618D ALA* 3.6 3.8 - - - +
619D THR 3.4 7.0 - - - -
620D GLN* 2.6 24.7 + - - -
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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