Contacts of the strand formed by residues 618 - 623 (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 ALA 618 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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443C VAL* 3.5 3.8 - - - -
444C SER 3.0 31.5 + - - -
508C THR* 3.5 11.0 - - - +
509C SER* 3.4 9.6 - - - +
510C GLY* 3.9 7.6 - - - +
601C GLN* 3.5 23.8 - - + +
617C LYS* 1.3 78.3 - - - +
619C THR* 1.3 62.9 + - - +
620C GLN* 3.4 20.4 + - - +
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Residues in contact with THR 619 (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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441C GLU* 3.4 41.1 - - + +
442C TYR 3.9 3.6 - - - +
443C VAL* 4.2 15.5 - - + +
507C SER* 3.9 1.4 + - - +
508C THR* 3.5 3.1 - - - -
509C SER* 2.9 39.0 + - - -
562C ASN* 5.2 2.6 + - - -
618C ALA* 1.3 70.7 - - - +
620C GLN* 1.3 59.8 + - - +
621C ARG* 4.5 13.2 + - - +
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Residues in contact with GLN 620 (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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440C GLU 3.9 0.3 - - - +
441C GLU* 3.3 5.5 - - - +
442C TYR* 2.8 76.2 + - + +
444C SER* 3.9 9.9 - - - -
507C SER 3.4 2.2 - - - -
508C THR* 2.6 33.5 + - - -
513C SER* 2.9 22.1 + - - -
515C TRP* 3.7 11.3 - - + -
590C SER* 3.1 18.2 + - - -
601C GLN* 4.1 1.4 - - - +
618C ALA* 3.4 18.1 - - - +
619C THR* 1.3 79.2 - - - +
621C ARG* 1.3 63.7 + - - +
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Residues in contact with ARG 621 (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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439C PHE* 3.5 44.6 - - + -
440C GLU 3.4 4.0 - - - -
441C GLU* 2.9 27.3 + - + +
506C ALA* 3.1 8.8 - - - +
507C SER* 3.0 42.1 + - - +
562C ASN* 5.4 16.4 + - - +
619C THR* 4.5 11.6 + - + +
620C GLN* 1.3 79.3 - - - +
622C VAL* 1.3 63.0 + - - +
623C TYR* 3.6 25.6 + - + -
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Residues in contact with VAL 622 (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* 3.9 20.2 - - + -
439C PHE* 3.4 2.4 - - - -
440C GLU* 2.9 29.9 + - - +
442C TYR* 4.3 7.0 - - + -
483C LEU* 3.7 25.6 - - + -
485C PHE* 4.3 9.2 - - + -
504C LEU* 3.9 16.8 - - + -
505C GLN 3.7 3.1 - - - -
506C ALA* 4.5 5.6 - - + -
515C TRP* 4.8 2.9 - - + -
588C VAL* 3.9 22.9 - - + -
621C ARG* 1.3 72.0 - - - +
623C TYR* 1.3 63.7 + - - +
624C VAL* 3.7 5.3 + - + +
630C SER* 3.7 16.8 - - - +
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Residues in contact with TYR 623 (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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438C GLY* 3.5 16.2 - - - +
439C PHE* 3.6 20.0 - + + -
505C GLN* 2.9 23.5 + - + +
506C ALA* 4.1 1.3 - - - -
507C SER* 3.4 29.6 + - - -
562C ASN 4.5 3.8 + - - -
564C PRO* 3.6 39.7 - - + +
621C ARG* 3.6 35.3 + - + -
622C VAL* 1.3 71.9 - - - +
624C VAL* 1.3 59.0 + - - +
625C SER* 4.7 2.5 - - - +
628C GLN* 3.3 32.1 - - + +
630C SER* 2.7 36.2 + - - -
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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