Contacts of the strand formed by residues 438 - 448 (chain C) in PDB entry 5MLE
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 GLU 438 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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367C ASP* 4.1 11.5 - - - +
417C VAL* 3.5 31.4 - - + +
418C LYS 3.8 4.9 - - - +
419C THR* 3.9 19.2 + - - +
436C GLY 3.3 8.5 + - - +
437C MET* 1.3 70.7 - - - +
439C CYS* 1.3 57.8 + - - +
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Residues in contact with CYS 439 (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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363C SER* 3.4 45.8 - - - -
364C VAL* 4.1 7.2 - - - -
367C ASP* 3.9 11.0 - - - -
416C SER 4.2 0.2 - - - +
417C VAL* 3.6 4.2 - - - +
418C LYS* 3.0 35.7 + - + +
420C ILE* 4.0 27.4 - - + -
437C MET* 3.5 3.8 + - + +
438C GLU* 1.3 75.4 - - - +
440C ARG* 1.3 63.0 + - - +
441C GLY 4.0 2.6 + - - +
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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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363C SER 4.1 2.8 - - - +
366C TRP* 3.3 16.8 - - + -
367C ASP* 3.1 28.3 + - - +
371C VAL* 4.3 27.3 - - + +
414C PRO* 3.3 23.7 + - - +
415C ASP* 4.4 18.3 + - - -
416C SER 3.5 9.4 - - - +
417C VAL* 4.4 17.2 - - + +
438C GLU 4.4 0.2 - - - -
439C CYS* 1.3 73.7 - - - +
441C GLY* 1.3 64.8 + - - +
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Residues in contact with GLY 441 (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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363C SER* 2.7 29.1 + - - -
366C TRP* 4.0 14.8 - - - -
412C TRP* 3.6 8.7 - - - -
413C ASP 3.4 13.7 - - - -
414C PRO* 4.5 3.1 + - - -
416C SER 3.0 14.2 + - - -
439C CYS* 4.0 3.7 + - - +
440C ARG* 1.3 74.7 - - - +
442C SER* 1.3 60.0 + - - -
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Residues in contact with SER 442 (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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363C SER* 3.7 7.6 - - - -
412C TRP* 3.5 12.9 - - - -
413C ASP* 2.9 31.6 + - - +
416C SER* 2.3 35.3 + - - -
418C LYS* 4.3 14.0 - - - +
441C GLY* 1.3 74.5 - - - -
443C PRO* 1.3 77.8 + - - +
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Residues in contact with PRO 443 (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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98C ALA 3.5 22.9 - - - +
99C GLY* 3.6 23.8 - - - +
100C GLY* 3.7 4.3 - - - +
363C SER* 4.6 2.9 - - - +
410C VAL* 4.0 11.0 - - + -
411C ILE 4.0 4.7 - - - +
412C TRP* 4.1 11.0 - - + -
413C ASP* 4.5 2.4 - - - +
442C SER* 1.3 95.6 + - - +
444C LEU* 1.3 60.5 + - - +
446C VAL* 3.8 22.2 - - + -
454C LEU* 4.0 10.4 - - + +
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Residues in contact with LEU 444 (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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63C ARG* 4.4 26.2 - - - +
411C ILE* 3.0 28.3 + - + +
412C TRP 4.8 0.2 - - - -
413C ASP* 3.9 32.7 - - + +
442C SER 3.7 1.8 + - - -
443C PRO* 1.3 73.8 - - - +
445C VAL* 1.3 77.9 + - + +
454C LEU* 4.2 10.8 - - - +
455C GLU* 4.3 8.7 - - - -
456C ASP 4.4 4.8 + - - +
457C GLY 5.3 1.6 + - - -
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Residues in contact with VAL 445 (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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58C ILE* 4.3 22.0 - - + -
409C LEU 4.8 0.4 - - - -
410C VAL* 3.3 8.2 - - - +
411C ILE* 3.1 49.1 + - + -
444C LEU* 1.3 97.8 - - + +
446C VAL* 1.3 68.9 + - - +
447C ILE* 4.3 24.7 - - + -
452C ILE* 4.6 6.1 - - + -
454C LEU 3.4 13.9 - - - +
455C GLU* 4.9 11.2 - - + -
456C ASP 5.6 0.4 - - - +
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Residues in contact with VAL 446 (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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97C LEU* 3.6 27.4 - - + +
100C GLY* 4.3 7.6 - - - -
102C THR* 3.9 24.7 - - + -
409C LEU 3.7 4.3 - - - +
410C VAL* 4.6 5.4 - - + -
443C PRO* 3.8 13.9 - - + -
445C VAL* 1.3 80.0 - - - +
447C ILE* 1.3 68.1 + - - +
452C ILE* 3.7 1.7 - - - +
453C VAL* 3.0 39.4 + - + -
454C LEU* 3.1 35.8 + - + +
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Residues in contact with ILE 447 (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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17C LEU* 3.9 12.8 - - + -
19C ILE* 3.5 32.1 - - + -
37C MET* 4.5 3.4 - - - -
58C ILE* 4.8 2.0 - - + -
102C THR* 3.6 8.3 - - - +
407C ALA 3.7 15.3 - - - +
408C ASP* 3.4 4.3 - - - -
409C LEU* 2.9 50.7 + - + +
411C ILE* 5.7 2.0 - - + -
445C VAL* 4.3 14.8 - - + -
446C VAL* 1.3 78.7 - - - +
448C SER* 1.3 62.5 + - - +
450C GLY* 3.7 27.1 - - - +
451C LYS 3.4 3.4 - - - +
452C ILE* 4.2 16.2 - - + -
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Residues in contact with SER 448 (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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97C LEU* 4.1 23.1 - - - -
102C THR* 4.4 9.2 + - - -
132C CYS 4.3 4.6 + - - -
133C CYS* 4.3 19.6 - - - +
134C ASP* 4.8 1.2 + - - -
408C ASP* 4.0 6.8 + - - -
446C VAL 4.3 0.6 + - - -
447C ILE* 1.3 74.5 - - - +
449C GLN* 1.3 73.8 + - - +
450C GLY 3.1 1.6 - - - -
451C LYS* 2.8 31.1 + - - +
453C VAL* 4.7 11.0 - - - +
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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
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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