Contacts of the strand formed by residues 479 - 484 (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 ASP 479 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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473G LYS* 3.8 27.3 + - - -
474G GLY 3.5 5.9 - - - +
475G LYS* 3.9 18.5 - - - +
477G HIS 5.2 0.2 - - - +
478G GLY* 1.3 71.8 - - - -
480G VAL* 1.3 62.5 + - - +
517G MET* 5.2 3.3 - - - +
530G GLN* 4.7 1.4 - - - -
531G TRP* 3.6 33.6 + - + +
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Residues in contact with VAL 480 (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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457G ILE* 5.1 0.4 - - + -
473G LYS* 4.3 0.3 - - - +
474G GLY 3.1 38.0 + - - +
475G LYS 4.2 0.4 - - - +
476G TRP* 3.4 36.6 - - + +
477G HIS 5.0 0.7 - - - +
478G GLY 3.7 1.8 - - - +
479G ASP* 1.3 80.4 - - - +
481G ALA* 1.3 61.8 + - - +
482G VAL* 3.9 15.3 - - + -
517G MET* 3.9 21.5 - - + -
528G VAL* 3.7 20.6 - - + -
529G THR 3.4 11.2 - - - +
531G TRP* 3.6 17.2 - - - +
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Residues in contact with ALA 481 (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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471G VAL* 4.4 12.3 - - + -
472G TYR 3.7 6.5 - - - +
480G VAL* 1.3 75.8 - - - +
482G VAL* 1.3 61.3 + - - +
483G LYS* 3.9 0.5 + - - +
514G LEU* 6.1 0.9 - - + -
527G ILE 3.2 5.0 - - - +
528G VAL* 3.5 0.3 - - - -
529G THR* 2.7 42.1 + - - +
530G GLN 3.5 17.0 + - - +
531G TRP* 3.9 17.7 - - + -
532G CYS 5.6 0.2 - - - +
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Residues in contact with VAL 482 (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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457G ILE* 3.9 24.0 - - + -
459G VAL* 4.9 8.3 - - + -
470G THR 3.8 1.0 - - - +
471G VAL* 3.4 2.5 - - - -
472G TYR* 2.8 45.4 + - + +
474G GLY* 4.3 12.3 - - - -
480G VAL* 3.9 20.4 - - + -
481G ALA* 1.3 74.0 - - - +
483G LYS* 1.3 60.7 + - - +
484G MET* 4.2 15.7 - - + -
526G ALA* 3.7 27.6 - - + -
527G ILE 3.3 4.5 - - - +
528G VAL* 4.6 8.7 - - + -
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Residues in contact with LYS 483 (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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470G THR* 3.5 17.5 - - - +
471G VAL* 3.8 26.0 - - + +
481G ALA 3.9 1.2 + - - +
482G VAL* 1.3 72.2 - - - +
484G MET* 1.3 63.6 + - - +
498G PHE* 5.5 0.2 - - - -
501G GLU* 2.6 38.5 + - - +
525G LEU 4.2 0.2 - - - +
526G ALA* 3.2 3.5 - - - -
527G ILE* 2.7 54.1 + - + +
594G ASP* 3.4 30.7 + - - +
595G PHE 4.7 0.4 - - - +
596G GLY* 4.2 3.0 - - - -
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Residues in contact with MET 484 (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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459G VAL* 4.7 17.7 - - + -
470G THR* 2.9 37.2 + - - +
472G TYR* 3.6 32.1 - - + -
482G VAL* 3.9 12.3 + - + -
483G LYS* 1.3 76.3 - - - +
485G LEU* 1.3 61.1 + - - +
486G ASN* 3.8 12.1 + - - +
524G GLN* 3.1 34.8 - - + +
525G LEU 3.6 6.7 - - - +
526G ALA* 3.6 23.6 - - + -
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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