Contacts of the strand formed by residues 494 - 498 (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 LEU 494 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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429B PHE* 3.9 30.7 - - + -
490B LEU* 4.0 21.1 - - + -
492B GLU 3.5 1.3 + - - +
493B PRO* 1.3 73.1 - - - +
495B GLN* 1.3 59.9 + - - +
496B ILE* 4.6 4.9 - - + -
577B THR* 3.4 0.7 - - - -
578B PHE* 2.8 46.2 + - + -
584B VAL* 4.0 25.8 - - + -
634B LEU* 4.3 10.8 - - + -
636B VAL* 3.8 32.1 - - + -
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Residues in contact with GLN 495 (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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392B ASN* 5.2 2.8 - - - +
395B GLU* 2.9 24.4 + - - -
493B PRO* 4.0 8.8 - - + +
494B LEU* 1.3 78.8 - - - +
496B ILE* 1.3 61.4 + - - +
576B HIS 3.6 5.4 - - - +
577B THR* 3.4 19.6 + - + +
636B VAL* 3.4 8.3 - - - +
637B ARG* 3.0 76.7 + - + +
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Residues in contact with ILE 496 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392B ASN* 5.7 0.2 + - - -
494B LEU* 4.6 3.1 - - + -
495B GLN* 1.3 79.8 - - - +
497B ALA* 1.3 63.6 + - - +
500B PRO* 4.7 6.3 - - + -
519B LEU* 4.0 20.9 - - + -
540B VAL* 4.7 2.7 - - + -
574B ALA* 3.7 28.3 - - + -
575B ASN* 3.4 2.6 - - - +
576B HIS* 2.9 41.9 + - + +
578B PHE* 3.9 28.0 - - + -
634B LEU* 3.7 33.7 - - + -
635B PRO* 3.2 15.0 - - + +
636B VAL* 4.3 7.0 - - + -
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Residues in contact with ALA 497 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404B TRP* 3.5 22.2 - - + -
406B ARG* 3.2 44.5 + - + -
407B SER 3.2 8.9 + - - +
496B ILE* 1.3 76.2 - - - +
498B GLY* 1.3 57.5 + - - +
574B ALA 3.3 5.8 - - - -
575B ASN* 3.8 8.1 - - - +
635B PRO 2.8 12.5 + - - +
637B ARG* 4.1 13.7 - - + -
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Residues in contact with GLY 498 (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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404B TRP* 3.5 6.0 - - - -
405B PRO* 3.7 17.7 - - - -
407B SER 3.9 0.7 - - - -
497B ALA* 1.3 77.8 - - - +
499B ALA* 1.3 60.7 + - - -
500B PRO* 3.4 5.0 - - - +
573B THR* 4.3 4.9 - - - -
574B ALA* 2.9 30.8 + - - +
635B PRO* 3.5 13.7 - - - +
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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