Contacts of the strand formed by residues 436 - 440 (chain B) in PDB entry 5MKE
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 436 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249B TYR* 5.3 0.4 - - - -
316B LEU* 3.2 39.3 - - + -
427B SER* 2.9 28.3 - - - -
428B VAL 3.5 2.7 - - - -
429B TYR* 3.6 13.2 - + + -
435B LEU* 1.3 75.0 - - - +
437B CYS* 1.3 69.8 + - - +
438B VAL* 4.8 0.9 - - + -
459B PRO 3.1 0.2 - - - -
460B LEU* 2.1 93.7 + - + +
462B LEU* 3.3 33.4 - - + +
536B LEU* 6.2 2.7 - - + -
540B GLU* 6.4 0.4 - - - -
548B PHE* 4.2 20.6 - + + -
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Residues in contact with CYS 437 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249B TYR* 4.4 21.3 - - + +
250B THR* 6.2 5.4 - - - -
253B MET* 5.4 6.1 - - + -
427B SER* 2.1 24.5 + - - -
428B VAL* 2.4 51.6 + - + +
436B PHE* 1.3 75.5 - - - +
438B VAL* 1.3 67.3 + - - +
439B VAL* 5.8 2.2 - - - -
457B PHE* 5.1 9.4 - - - -
458B GLN 3.0 30.5 - - - -
459B PRO* 3.8 7.2 - - + -
460B LEU 4.1 0.4 - - - +
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Residues in contact with VAL 438 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426B PHE 4.4 0.7 - - - +
427B SER* 3.1 22.2 - - - +
436B PHE* 4.7 3.4 - - + -
437B CYS* 1.3 76.8 - - - +
439B VAL* 1.3 62.9 + - - +
440B ARG* 5.3 7.0 - - + +
456B GLN* 5.2 3.1 - - + +
457B PHE* 3.4 21.6 - - - -
458B GLN* 2.7 47.9 + - + +
460B LEU* 5.3 3.1 - - + -
548B PHE* 4.6 5.6 - - + -
549B GLU* 5.8 2.2 - - - -
552B ALA* 3.6 31.2 - - + -
556B ILE* 5.0 5.2 - - + -
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Residues in contact with VAL 439 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257B PHE* 6.3 4.0 - - + -
287B LEU* 5.3 2.0 - - + -
424B ILE 5.3 0.2 - - - +
425B ASP* 3.2 4.9 - - - +
426B PHE* 2.5 90.8 + - + +
428B VAL* 4.6 13.2 - - + -
437B CYS* 5.3 2.2 - - - -
438B VAL* 1.3 78.3 - - - +
440B ARG* 1.3 59.1 + - - +
441B LEU* 4.1 19.1 - - + -
456B GLN 4.0 1.8 - - - -
457B PHE* 4.0 20.6 - - + -
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Residues in contact with ARG 440 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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378B SER 3.0 28.5 + - - -
379B HIS* 3.0 31.2 + - + +
423B PHE* 5.5 1.1 - - + -
425B ASP* 3.1 24.0 + - + +
438B VAL* 5.4 6.5 - - + -
439B VAL* 1.3 73.1 - - - +
441B LEU* 1.3 57.9 + - - +
442B LEU* 5.5 0.2 - - - +
455B TRP 3.4 0.3 - - - -
456B GLN* 2.5 69.1 + - + +
549B GLU* 3.6 34.8 + - + +
553B TYR* 4.4 11.7 - - - +
556B ILE* 4.8 11.4 - - - +
1007B PX6 2.9 29.0 + - - -
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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
------------------------------------------------------------
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