Contacts of the strand formed by residues 526 - 530 (chain G) in PDB entry 4MNE
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 526 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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457G ILE* 5.3 2.9 - - + -
482G VAL* 3.7 17.0 - - + -
483G LYS 3.2 6.1 - - - -
484G MET* 3.6 20.4 - - + -
498G PHE* 3.3 9.2 - - - -
519G TYR* 3.2 5.7 - - - -
520G SER* 3.0 38.3 + - - -
524G GLN 3.5 5.8 + - - +
525G LEU* 1.3 76.9 - - - +
527G ILE* 1.3 64.3 + - - +
528G VAL* 4.1 0.4 - - + -
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Residues in contact with ILE 527 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481G ALA 3.2 4.2 - - - +
482G VAL* 3.3 1.3 - - - -
483G LYS* 2.7 54.2 + - + +
498G PHE* 3.7 19.1 - - + -
501G GLU* 3.6 44.2 - - + +
502G VAL* 4.0 19.7 - - + -
505G LEU* 3.6 24.5 - - + -
516G PHE* 4.3 7.9 - - + -
518G GLY 3.8 1.8 - - - -
519G TYR* 4.7 0.4 - - + -
526G ALA* 1.3 78.6 - - - +
528G VAL* 1.3 62.1 + - - +
529G THR* 4.0 14.6 + - + +
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Residues in contact with VAL 528 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452G ILE* 4.0 8.3 - - + -
457G ILE* 3.6 32.1 - - + -
476G TRP* 4.4 11.2 - - + -
480G VAL* 3.7 32.1 - - + -
481G ALA 3.5 3.6 - - - -
482G VAL* 4.6 12.3 - - + -
516G PHE* 4.0 1.7 - - - -
517G MET* 2.8 37.1 + - + -
518G GLY 2.7 25.4 + - - +
519G TYR* 5.1 2.2 - - - -
526G ALA 5.2 1.8 - - - +
527G ILE* 1.3 74.0 - - - +
529G THR* 1.3 65.0 + - - +
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Residues in contact with THR 529 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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480G VAL* 3.4 6.6 - - - +
481G ALA* 2.7 43.7 + - - +
505G LEU* 4.8 7.6 - - + -
514G LEU* 3.7 31.5 - - + +
515G LEU 3.2 15.3 - - - +
516G PHE* 4.2 8.5 - - - +
517G MET* 4.0 6.7 - - - +
527G ILE* 4.0 20.0 - - + +
528G VAL* 1.3 80.0 - - - +
530G GLN* 1.3 65.9 + - - +
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Residues in contact with GLN 530 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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511F VAL* 3.6 33.4 - - + +
801F CL 4.4 7.5 - - - +
479G ASP 4.8 0.4 - - - -
480G VAL* 4.6 1.3 - - - +
481G ALA* 3.5 5.5 - - - +
513G ILE 4.1 0.7 - - - +
514G LEU* 3.8 18.5 - - + +
515G LEU* 2.8 46.7 + - + +
517G MET* 4.0 15.0 - - + -
529G THR* 1.3 87.7 + - - +
531G TRP* 1.3 63.6 + - - +
532G CYS* 4.0 3.6 + - - -
585G HIS* 4.6 15.0 + - - -
591G LYS* 3.6 33.2 + - - +
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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