Contacts of the strand formed by residues 482 - 486 (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 VAL 482 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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450B VAL* 3.8 22.2 - - + -
476B VAL* 3.8 26.5 - - + +
477B ASP* 5.1 0.9 - - - -
478B GLY 5.2 0.3 + - - -
479B ARG* 3.1 7.8 + - + +
480B PRO 3.3 1.0 + - - -
481B ASP* 1.3 91.1 - - - +
483B LEU* 1.3 71.7 + - - +
484B THR* 3.8 4.8 + - - +
587B GLN* 4.1 22.0 - - + +
588B VAL 3.5 7.2 - - - +
589B GLN* 3.7 26.0 - - + +
448C LYS* 2.8 26.3 + - - -
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Residues in contact with LEU 483 (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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440B GLU* 3.8 35.9 - - + +
441B GLU 4.0 15.0 - - - +
442B TYR* 3.4 38.1 - - + -
480B PRO 5.2 0.4 - - - +
482B VAL* 1.3 75.2 - - - +
484B THR* 1.3 61.5 + - - +
485B PHE* 3.8 16.6 - - + -
586B VAL 3.8 0.6 - - - +
587B GLN* 3.2 7.4 - - - +
588B VAL* 2.8 35.9 + - + +
622B VAL* 3.6 27.8 - - + -
448C LYS* 4.4 9.4 - - - +
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Residues in contact with THR 484 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425B GLY* 3.4 19.9 - - - +
440B GLU* 4.7 3.2 + - - +
477B ASP* 2.6 32.0 + - - +
478B GLY 4.7 0.3 + - - -
482B VAL* 3.8 6.8 + - - +
483B LEU* 1.3 76.2 + - - +
485B PHE* 1.3 67.6 + - - +
486B VAL* 4.9 4.9 - - + -
585B MSE 3.7 34.8 - - + -
586B VAL 3.7 2.7 - - - -
587B GLN* 3.8 8.8 - - - +
448C LYS* 4.9 5.9 - - - +
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Residues in contact with PHE 485 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421B LEU* 3.6 35.2 - - + -
422B GLN 3.3 31.9 - - - -
425B GLY* 3.4 9.2 - - - -
426B LYS 3.4 13.9 - - - +
427B LEU* 4.0 15.8 - - + +
440B GLU* 3.6 33.4 - - + -
483B LEU* 3.8 29.8 - - + -
484B THR* 1.3 75.6 - - - +
486B VAL* 1.3 62.2 + - - +
585B MSE 3.3 4.7 - - - +
586B VAL* 2.8 45.5 + - + +
588B VAL* 4.3 6.5 - - + -
622B VAL* 4.4 6.7 - - + -
624B VAL* 4.2 2.5 - - + -
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Residues in contact with VAL 486 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425B GLY 3.0 15.7 + - - +
426B LYS* 3.5 9.5 - - - +
427B LEU* 3.3 19.7 + - - +
484B THR* 4.9 4.3 - - + -
485B PHE* 1.3 75.4 - - - +
487B THR* 1.3 74.3 + - - +
488B GLU* 5.7 0.3 - - - +
522B VAL* 4.3 0.4 - - + -
583B ARG* 3.8 30.5 - - + +
584B VAL 3.4 13.7 - - - +
585B MSE 4.0 27.1 - - + -
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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