Contacts of the strand formed by residues 618 - 623 (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 ALA 618 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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443D VAL* 3.5 5.1 - - - +
444D SER 3.0 29.9 + - - -
508D THR* 3.6 10.8 - - - +
509D SER* 3.4 9.9 - - - +
510D GLY* 4.0 7.4 - - - +
601D GLN* 3.5 24.7 - - + +
617D LYS* 1.3 77.2 - - - +
619D THR* 1.3 64.0 + - - +
620D GLN* 3.5 18.8 + - - +
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Residues in contact with THR 619 (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* 3.4 41.3 - - + +
442D TYR 3.9 3.6 - - - +
443D VAL* 4.2 15.0 - - + +
507D SER* 4.0 1.0 + - - +
508D THR* 3.4 2.6 - - - -
509D SER* 2.9 40.2 + - - -
562D ASN* 4.7 4.0 + - - -
618D ALA* 1.3 68.9 - - - +
620D GLN* 1.3 60.0 + - - +
621D ARG* 4.2 15.7 + - - +
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Residues in contact with GLN 620 (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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440D GLU 3.9 0.2 - - - +
441D GLU* 3.3 5.7 - - - +
442D TYR* 2.8 77.9 + - + +
444D SER* 3.9 9.9 - - - -
507D SER 3.5 2.7 - - - -
508D THR* 2.6 29.6 + - - -
513D SER* 2.8 22.7 + - - -
515D TRP* 3.7 12.2 - - + -
590D SER* 3.1 18.5 + - - -
601D GLN* 4.0 1.0 - - - +
618D ALA* 3.5 16.2 - - - +
619D THR* 1.3 77.7 - - - +
621D ARG* 1.3 63.9 + - - +
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Residues in contact with ARG 621 (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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439D PHE* 3.5 42.8 - - + -
440D GLU 3.4 4.0 - - - -
441D GLU* 3.0 25.8 + - + +
506D ALA* 3.1 8.2 - - - +
507D SER* 3.0 46.0 + - - +
562D ASN* 4.6 23.4 + - - +
619D THR* 4.2 13.9 + - + +
620D GLN* 1.3 79.2 - - - +
622D VAL* 1.3 63.3 + - - +
623D TYR* 3.8 25.3 + - + -
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Residues in contact with VAL 622 (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* 3.9 20.9 - - + -
439D PHE* 3.3 1.9 - - - -
440D GLU* 2.9 29.1 + - - +
442D TYR* 4.3 6.5 - - + -
483D LEU* 3.6 27.6 - - + -
485D PHE* 4.3 8.3 - - + -
504D LEU* 3.9 16.2 - - + -
505D GLN 3.8 2.7 - - - -
506D ALA* 4.3 4.3 - - + -
515D TRP* 4.9 2.9 - - + -
588D VAL* 4.0 22.2 - - + -
621D ARG* 1.3 73.3 - - - +
623D TYR* 1.3 64.4 + - - +
624D VAL* 3.6 5.3 + - + +
630D SER* 3.7 17.5 - - - +
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Residues in contact with TYR 623 (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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438D GLY 3.6 16.2 - - - +
439D PHE* 3.7 23.0 - + + -
505D GLN* 2.9 25.8 + - + +
506D ALA* 4.1 1.1 - - - -
507D SER* 3.5 28.2 + - - -
562D ASN 4.5 3.5 + - - -
564D PRO* 3.6 37.8 - - + +
621D ARG* 3.8 28.9 + - + -
622D VAL* 1.3 71.9 - - - +
624D VAL* 1.3 59.2 + - - +
625D SER* 4.8 2.7 - - - +
628D GLN* 3.3 32.5 - - + +
630D SER* 2.6 36.0 + - - -
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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