Contacts of the strand formed by residues 516 - 520 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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509B ARG* 2.7 50.3 + - - +
450C TRP* 3.9 29.8 - + + -
502C VAL* 4.3 26.5 - - + -
505C LEU* 3.8 50.9 - - + +
506C ARG* 4.3 13.2 - - + -
508C THR* 4.8 1.7 + - - +
514C LEU 3.1 6.8 + - - +
515C LEU* 1.3 77.6 - - - +
517C MET* 1.3 59.9 + - - +
518C GLY* 3.4 38.6 - - - -
519C TYR* 4.2 1.6 - + - -
527C ILE* 4.2 7.4 - - + -
528C VAL 3.9 8.1 - - - -
529C THR* 4.1 4.5 - - - -
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Residues in contact with MET 517 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
509B ARG* 3.7 20.3 - - - +
510B HIS* 4.0 16.6 - - + +
511B VAL* 3.9 28.0 - - + +
566B TYR* 5.3 0.3 + - - -
450C TRP* 3.6 21.1 - - - +
452C ILE* 5.1 0.2 - - - +
476C TRP* 4.3 25.0 - - + +
477C HIS 5.9 0.4 - - - +
479C ASP 4.9 4.0 - - - +
480C VAL* 3.8 28.0 - - + -
515C LEU* 3.5 5.8 + - + +
516C PHE* 1.3 80.9 - - - +
518C GLY* 1.3 59.5 + - - +
528C VAL* 2.9 19.8 + - + +
529C THR 4.1 0.9 - - - -
530C GLN* 3.7 37.0 - - + +
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Residues in contact with GLY 518 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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450C TRP* 3.3 14.1 - - - -
452C ILE* 4.0 13.7 - - - -
516C PHE* 3.4 21.8 - - - -
517C MET* 1.3 79.8 - - - +
519C TYR* 1.3 55.7 + - - +
527C ILE 3.7 0.2 - - - -
528C VAL* 2.7 36.3 + - - +
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Residues in contact with TYR 519 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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449C ASP* 3.3 27.5 + - - -
450C TRP* 3.0 19.7 + - + -
451C GLU* 3.4 40.0 + - + +
452C ILE* 2.8 28.0 + - - +
457C ILE* 5.3 0.2 - - - -
498C PHE* 3.9 9.6 - + + -
502C VAL* 3.9 42.0 - - + -
506C ARG* 4.5 5.6 + - - -
516C PHE* 4.5 0.7 - + - -
518C GLY* 1.3 74.8 - - - +
520C SER* 1.3 64.3 + - - +
521C THR* 4.1 21.3 - - + -
526C ALA 3.3 12.6 - - - +
527C ILE* 4.9 0.7 - - - -
528C VAL* 4.6 0.7 - - - +
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Residues in contact with SER 520 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451C GLU* 5.2 1.1 - - - -
452C ILE 3.8 14.9 + - - -
454C ASP* 5.1 2.6 - - - -
457C ILE* 3.7 26.7 - - - +
498C PHE* 3.6 4.0 - - - -
519C TYR* 1.3 75.5 - - - +
521C THR* 1.3 63.5 + - - +
522C LYS 3.8 0.5 + - - -
523C PRO* 3.2 26.0 - - - +
524C GLN 3.0 14.7 - - - +
525C LEU* 3.5 1.2 - - - -
526C ALA* 3.0 29.6 + - - +
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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