Contacts of the strand formed by residues 574 - 578 (chain A) 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 574 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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305A LEU* 4.6 3.6 - - - -
404A TRP* 3.7 1.7 - - - -
496A ILE* 3.6 20.5 - - + +
497A ALA* 3.2 3.6 + - - -
498A GLY 2.9 34.5 + - - +
500A PRO* 4.9 2.0 - - + -
540A VAL* 3.6 31.2 - - + -
541A SER* 4.8 3.4 - - - -
572A PRO 4.4 4.7 - - - +
573A THR* 1.3 79.8 - - - +
575A ASN* 1.3 60.2 + - - +
576A HIS* 3.7 1.1 - - + -
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Residues in contact with ASN 575 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305A LEU* 4.6 6.2 - - + +
390A ILE* 3.6 21.7 + - + +
391A TYR 3.2 29.8 + - - +
392A ASN* 3.2 13.2 + - - +
393A THR* 3.1 26.3 + - - +
399A ASP* 2.9 28.3 + - - +
404A TRP* 3.6 27.8 - - + -
406A ARG* 5.0 1.4 - - - -
495A GLN* 4.5 4.9 + - - -
496A ILE 3.4 3.5 - - - +
497A ALA* 3.7 11.1 - - - +
574A ALA* 1.3 72.0 - - - +
576A HIS* 1.3 58.7 + - - +
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Residues in contact with HIS 576 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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392A ASN* 3.7 3.3 - - - -
393A THR* 2.7 39.7 + - - +
394A GLY* 3.4 9.7 + - - -
494A LEU 3.7 1.6 - - - +
495A GLN* 3.7 0.5 - - - -
496A ILE* 3.0 40.9 + - + +
521A ASP* 2.8 33.8 + - + +
523A TYR* 5.9 1.1 - + - -
538A LEU* 4.4 11.4 - - + -
540A VAL* 3.6 41.7 - - + +
574A ALA 3.7 0.4 - - - -
575A ASN* 1.3 76.0 - - - +
577A THR* 1.3 73.6 + - - +
578A PHE* 3.9 14.8 + + - -
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Residues in contact with THR 577 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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392A ASN* 3.1 17.5 + - - -
394A GLY* 3.3 17.4 - - - -
395A GLU* 2.7 39.0 + - - +
493A PRO* 3.8 20.6 - - + -
494A LEU 3.4 10.1 - - - +
495A GLN* 3.4 14.4 - - + +
521A ASP* 4.2 1.2 - - - +
576A HIS* 1.3 79.1 + - - +
578A PHE* 1.3 62.3 + - - +
579A GLN* 3.3 27.0 + - - +
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Residues in contact with PHE 578 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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490A LEU* 3.5 22.9 - - + +
493A PRO* 3.4 2.1 - - - +
494A LEU* 2.8 54.2 + - + +
496A ILE* 3.9 34.8 - - + -
519A LEU* 4.4 10.5 - - + -
520A ILE 3.7 14.8 - - - -
521A ASP* 3.6 42.4 - - + +
540A VAL* 4.2 7.2 - - + -
576A HIS* 3.9 13.9 - + - -
577A THR* 1.3 70.5 - - - +
579A GLN* 1.3 63.4 + - - +
582A HIS* 4.9 2.5 - - + -
583A ARG 4.2 2.7 - - - -
584A VAL* 3.9 25.1 - - + -
634A LEU* 5.3 2.0 - - + -
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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