Contacts of the strand formed by residues 436 - 440 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249C TYR* 5.3 0.2 - - - -
316C LEU* 3.2 38.4 - - + -
427C SER* 2.9 28.9 - - - -
428C VAL 3.5 3.4 - - - -
429C TYR* 3.6 12.6 - - + +
435C LEU* 1.3 76.0 - - - +
437C CYS* 1.3 68.4 + - - +
438C VAL* 4.8 0.4 - - + -
459C PRO 3.1 0.7 - - - -
460C LEU* 2.1 93.7 + - + +
462C LEU* 3.3 33.0 - - + -
536C LEU* 6.2 2.9 - - + -
540C GLU* 6.4 0.7 - - - -
548C PHE* 4.2 20.9 - + + -
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Residues in contact with CYS 437 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249C TYR* 4.4 20.9 - - + +
250C THR* 6.2 5.4 - - - -
253C MET* 5.4 5.4 - - - -
427C SER* 2.1 23.9 + - - -
428C VAL* 2.4 50.3 + - + +
436C PHE* 1.3 76.1 - - - +
438C VAL* 1.3 65.6 - - - +
439C VAL* 5.3 2.5 - - - -
457C PHE* 5.1 9.2 - - - -
458C GLN 3.0 30.5 - - - -
459C PRO* 3.8 6.5 - - + -
460C LEU 4.1 0.4 - - - +
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Residues in contact with VAL 438 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426C PHE 4.3 1.3 - - - +
427C SER* 3.1 21.5 - - - +
436C PHE* 4.7 3.1 - - + -
437C CYS* 1.3 78.2 - - - +
439C VAL* 1.3 63.1 + - - +
440C ARG* 5.3 7.6 - - + +
456C GLN* 3.8 2.9 - - + +
457C PHE* 3.4 21.0 - - - +
458C GLN* 2.7 47.8 + - + +
460C LEU* 5.3 3.6 - - + -
548C PHE* 4.6 5.4 - - + -
549C GLU* 5.8 2.9 - - - -
552C ALA* 3.6 31.2 - - + -
556C ILE* 5.0 4.9 - - + -
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Residues in contact with VAL 439 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257C PHE* 6.3 4.3 - - + -
287C LEU* 5.3 2.0 - - + -
425C ASP* 3.2 4.0 - - - +
426C PHE* 2.5 91.6 + - + +
427C SER* 4.6 0.2 - - - -
428C VAL* 4.6 13.0 - - + -
437C CYS* 5.3 2.2 - - - -
438C VAL* 1.3 77.6 - - - +
440C ARG* 1.3 60.3 + - - +
441C LEU* 4.1 19.5 - - + -
456C GLN 4.0 2.0 - - - -
457C PHE* 4.0 21.3 - - + -
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Residues in contact with ARG 440 (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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378C SER 3.0 28.9 + - - -
379C HIS* 3.0 30.9 + - + +
423C PHE* 5.9 0.9 - - + -
425C ASP* 3.1 22.5 + - + +
438C VAL* 5.4 6.5 - - + -
439C VAL* 1.3 73.0 - - - +
441C LEU* 1.3 60.9 + - - +
442C LEU* 5.5 0.2 - - - +
456C GLN* 2.5 70.9 + - + +
549C GLU* 3.6 34.9 + - + +
553C TYR* 4.4 10.3 - - - -
556C ILE* 4.8 11.0 - - - +
1007C PX6 2.9 28.9 + - - -
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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