Contacts of the strand formed by residues 581 - 586 (chain A) in PDB entry 2MPF
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 MET 581 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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539A VAL* 5.2 10.8 - - + -
542A MET* 4.8 13.0 - - + -
545A PHE* 5.7 0.7 - - + -
556A MET* 5.4 1.1 - - - +
580A LYS* 1.3 75.3 - - - +
582A TYR* 1.3 56.0 + - - +
583A PHE* 3.9 32.1 - - + -
606A TYR* 3.5 38.6 - - + -
607A PHE 4.3 3.1 - - - -
608A GLY 5.2 2.7 - - - +
632A SER* 2.7 27.9 + - - -
633A LEU* 3.0 33.1 + - + +
635A VAL* 4.5 7.6 - - + +
638A PHE* 4.2 30.3 - - + -
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Residues in contact with TYR 582 (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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565A PHE* 5.8 10.3 - + - -
571A ILE* 4.6 11.7 - - + -
572A ILE* 3.7 28.3 - - + -
579A LYS* 3.4 35.1 + - + +
580A LYS* 3.3 45.8 - - + +
581A MET* 1.3 75.3 - - - +
583A PHE* 1.3 63.9 + - - +
606A TYR* 3.5 2.5 - - - -
607A PHE* 2.9 51.7 + - + +
608A GLY* 5.0 1.6 - - - -
610A ILE* 6.1 0.2 - - + -
630A LEU* 5.5 5.8 - - + -
631A TYR 3.3 8.3 - - - +
632A SER* 3.5 21.5 - - - -
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Residues in contact with PHE 583 (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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535A CYS* 4.8 1.6 - - + -
538A LEU* 3.7 43.5 - - + -
539A VAL* 3.8 31.0 - - + -
560A LEU* 3.8 39.3 - - + -
581A MET* 3.9 24.7 - - + -
582A TYR* 1.3 79.3 - - - +
584A ILE* 1.3 62.3 + - - +
585A GLN 3.5 0.2 + - - -
604A GLY 5.9 0.7 - - - -
605A SER 3.6 11.4 - - - +
606A TYR* 3.9 13.2 - - + +
607A PHE* 4.1 2.8 - - - -
630A LEU* 3.4 5.8 - - - +
631A TYR* 2.8 60.2 + + + +
632A SER* 4.1 4.0 - - - -
633A LEU 4.7 0.2 - - - -
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Residues in contact with ILE 584 (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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538A LEU* 3.6 7.9 - - - +
583A PHE* 1.3 70.4 - - - +
585A GLN* 1.3 58.8 + - - +
586A HIS 4.3 0.2 - - - -
587A GLY 3.6 32.8 - - - +
588A VAL* 5.2 0.4 - - - -
589A VAL* 4.0 16.4 - - + +
601A LEU* 4.2 4.9 - - + +
602A SER 3.8 17.7 - - - +
603A ASP* 3.8 10.3 - - - -
604A GLY* 2.9 28.4 + - - -
605A SER* 2.8 29.3 + - - +
607A PHE* 3.3 39.3 - - + -
628A CYS* 5.5 0.2 - - + -
630A LEU* 3.7 17.5 - - + -
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Residues in contact with GLN 585 (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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535A CYS* 5.6 1.6 - - - -
538A LEU* 3.7 32.0 - - + +
562A PHE* 3.9 16.3 - - - -
583A PHE 3.5 2.2 + - - -
584A ILE* 1.3 72.9 - - - +
586A HIS* 1.3 75.4 + - - +
603A ASP* 4.2 8.1 - - - +
604A GLY 5.0 0.2 + - - -
629A ARG* 2.9 38.2 + - - +
630A LEU 4.7 0.7 - - - +
631A TYR* 4.0 21.9 - - + -
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Residues in contact with HIS 586 (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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584A ILE* 3.6 2.2 - - - -
585A GLN* 1.3 94.7 + - - +
587A GLY* 1.3 61.8 + - - +
603A ASP* 3.9 14.0 - - - -
627A TYR 4.5 3.9 - - - +
628A CYS* 3.7 1.2 - - - -
629A ARG* 2.8 48.7 + - + +
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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