Contacts of the strand formed by residues 516 - 520 (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 PHE 516 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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509F ARG* 3.4 52.6 + - - +
450G TRP* 4.0 26.7 - + + -
502G VAL* 4.2 24.9 - - + -
505G LEU* 3.8 47.8 - - + +
506G ARG* 4.2 14.1 - - + -
508G THR* 4.8 2.1 + - - +
514G LEU 3.1 6.8 + - - -
515G LEU* 1.3 76.2 - - - +
517G MET* 1.3 64.7 + - - +
518G GLY* 3.5 40.6 - - - -
519G TYR 4.0 2.2 - - - -
527G ILE* 4.3 9.4 - - + -
528G VAL 4.0 6.1 - - - -
529G THR* 4.2 5.8 - - - -
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Residues in contact with MET 517 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
509F ARG* 3.2 20.9 - - - +
510F HIS* 3.9 34.8 - - + +
511F VAL* 4.0 11.4 - - + +
566F TYR* 5.1 0.9 + - - -
450G TRP* 3.8 18.3 - - - +
476G TRP* 4.1 27.7 - - + +
477G HIS 5.6 1.1 - - - +
479G ASP 5.2 2.9 - - - +
480G VAL* 3.9 27.4 - - + -
515G LEU* 4.0 10.1 - - + +
516G PHE* 1.3 82.4 - - - +
518G GLY* 1.3 60.0 + - - +
528G VAL* 2.8 22.7 + - + +
529G THR 4.2 0.2 - - - -
530G GLN* 4.0 28.3 - - + +
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Residues in contact with GLY 518 (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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450G TRP 3.1 14.4 - - - -
452G ILE* 4.0 8.5 - - - -
516G PHE* 3.5 21.7 - - - -
517G MET* 1.3 80.1 - - - +
519G TYR* 1.3 58.2 + - - +
527G ILE 3.7 0.2 - - - -
528G VAL* 2.7 40.3 + - - +
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Residues in contact with TYR 519 (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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327D SER* 4.6 10.2 + - - -
449G ASP* 4.4 10.8 + - - -
450G TRP* 3.1 19.4 + - + -
451G GLU* 3.4 48.4 + - + +
452G ILE* 2.9 29.3 + - - +
498G PHE* 3.7 27.4 - + + -
502G VAL* 3.9 33.9 - - + -
506G ARG* 6.6 0.2 - - - -
516G PHE* 4.5 0.9 - + + -
518G GLY* 1.3 75.3 - - - +
520G SER* 1.3 65.6 + - - +
521G THR* 5.1 4.3 - - - -
526G ALA 3.2 13.5 - - - +
527G ILE* 4.7 1.3 - - + -
528G VAL* 4.6 1.1 - - - +
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Residues in contact with SER 520 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451G GLU* 5.2 1.3 - - - -
452G ILE* 3.1 20.6 + - - +
453G PRO 4.8 1.4 + - - -
454G ASP* 4.9 0.5 - - - -
457G ILE* 3.8 27.8 - - - +
498G PHE* 3.5 8.8 - - - -
519G TYR* 1.3 77.8 - - - +
521G THR* 1.3 63.7 + - - +
522G LYS 3.4 17.5 + - - -
524G GLN 4.0 2.2 - - - -
525G LEU* 3.4 2.4 - - - -
526G ALA* 3.0 37.0 + - - -
528G VAL* 5.3 0.4 - - - +
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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