Contacts of the strand formed by residues 501 - 508 (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 ASP 501 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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409C ASP* 4.8 8.2 - - - +
499C ALA 4.5 3.8 - - - +
500C PRO* 1.3 74.4 - - - +
502C VAL* 1.3 63.9 + - - +
503C HIS* 3.5 7.3 + - - +
568C GLN* 3.6 25.5 + - - +
569C PHE* 3.2 29.8 + - - +
570C GLY* 3.5 4.2 + - - -
632C ILE* 3.4 3.8 - - - -
633C SER* 2.8 49.7 + - - +
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Residues in contact with VAL 502 (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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501C ASP* 1.3 71.0 - - - +
503C HIS* 1.3 63.7 + - - +
504C LEU* 3.6 26.9 - - + +
517C VAL* 4.0 21.5 - - + -
568C GLN* 3.2 30.3 - - - +
569C PHE* 2.9 44.6 + - + +
571C LEU* 3.4 38.6 - - + -
631C TYR 4.1 3.8 - - - +
632C ILE* 4.4 6.7 - - + -
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Residues in contact with HIS 503 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409C ASP* 4.8 6.7 + - - -
501C ASP* 3.5 25.0 - - - +
502C VAL* 1.3 72.0 - - - +
504C LEU* 1.3 61.0 + - - +
505C GLN* 3.7 2.1 + - - +
566C ALA* 6.5 0.2 - - - -
567C PHE 3.7 4.3 - - - -
568C GLN* 3.2 40.3 + - - +
629C PRO 4.0 3.3 - - - +
630C SER* 3.4 4.5 - - - -
631C TYR* 2.8 83.4 + + + +
633C SER* 4.1 11.0 - - - -
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Residues in contact with LEU 504 (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* 4.8 5.6 - - + -
502C VAL* 3.6 14.8 - - + +
503C HIS* 1.3 75.0 - - - +
505C GLN* 1.3 59.4 + - - +
506C ALA* 3.9 12.7 + - + -
515C TRP* 3.8 46.2 - - + -
517C VAL* 4.9 11.0 - - + -
565C LEU 3.4 2.3 - - - +
566C ALA* 3.5 3.1 - - - +
567C PHE* 2.8 47.5 + - + +
569C PHE* 5.0 1.3 - - + -
588C VAL* 4.7 11.2 - - + -
622C VAL* 3.9 24.9 - - + -
630C SER* 3.8 18.2 - - - +
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Residues in contact with GLN 505 (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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503C HIS 3.7 2.4 + - - +
504C LEU* 1.3 72.7 + - - +
506C ALA* 1.3 61.2 + - - +
564C PRO* 4.5 4.4 - - + +
565C LEU* 3.5 16.1 + - - -
566C ALA* 3.6 24.5 + - - +
622C VAL* 3.7 0.9 - - - -
623C TYR* 2.9 34.6 + - + -
628C GLN* 3.9 39.4 + - + +
629C PRO* 3.8 21.6 - - - +
630C SER* 3.0 15.7 + - - +
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Residues in contact with ALA 506 (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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504C LEU* 3.9 21.0 + - + -
505C GLN* 1.3 75.5 - - - +
507C SER* 1.3 60.1 + - - +
515C TRP* 3.7 28.0 - - + -
563C GLN 3.8 0.7 - - - +
564C PRO* 4.1 1.8 - - - -
565C LEU* 3.0 31.3 + - - +
567C PHE* 3.5 11.9 - - + -
621C ARG 3.1 15.5 - - - +
622C VAL* 4.3 3.1 - - + -
623C TYR* 4.1 2.2 - - - -
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Residues in contact with SER 507 (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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506C ALA* 1.3 73.0 - - - +
508C THR* 1.3 61.6 + - - +
515C TRP* 3.7 7.5 - - - -
562C ASN* 3.8 7.8 + - - -
563C GLN 3.2 38.6 - - - -
564C PRO* 3.7 4.0 - - - -
565C LEU* 6.1 0.4 - - - -
619C THR 4.4 0.7 + - - -
620C GLN* 3.4 3.6 - - - -
621C ARG* 3.0 45.0 + - - +
623C TYR* 3.4 17.2 + - - -
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Residues in contact with THR 508 (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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507C SER* 1.3 76.1 - - - +
509C SER* 1.3 60.6 + - - +
510C GLY* 3.2 27.1 + - - +
512C ASP 4.1 1.3 - - - +
513C SER* 3.1 20.8 + - - +
515C TRP* 4.4 2.7 - - + -
559C LEU* 3.9 30.5 - - + -
560C THR 4.1 2.0 + - - +
561C SER* 3.4 1.6 - - - -
562C ASN* 2.8 21.1 + - - +
563C GLN 4.8 0.8 + - - -
618C ALA* 3.5 3.5 - - - +
619C THR 3.5 6.5 - - - -
620C GLN* 2.6 25.7 + - - -
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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