Contacts of the strand formed by residues 443 - 454 (chain C) in PDB entry 5SUY
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 MET 443 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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442C ARG* 1.3 76.8 - - - +
444C TRP* 1.3 72.8 + - - +
445C LEU* 3.7 41.1 - - + -
445D LEU 3.8 0.5 - - - +
446D LYS* 3.5 5.4 - - - +
447D ILE* 2.9 44.5 + - + +
449D ILE* 3.3 40.6 - - + -
452D ALA* 4.8 3.1 - - + -
491D THR* 3.5 23.8 - - - +
492D VAL* 4.8 5.8 - - + -
502D TYR* 3.5 28.5 - - + +
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Residues in contact with TRP 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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454A LEU* 5.4 11.4 - - + -
456A SER* 5.7 3.4 - - - -
457A ASP* 4.1 14.5 + - - -
438B GLU* 4.8 17.9 + - - +
442C ARG* 5.0 4.3 - - + +
443C MET* 1.3 82.3 - - - +
445C LEU* 1.3 61.9 + - - +
444D TRP* 4.2 45.2 - + + -
445D LEU 3.4 16.2 - - - -
446D LYS* 3.7 52.1 - - + +
500D GLN 5.3 1.7 - - - +
502D TYR* 3.4 41.7 - + + +
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Residues in contact with LEU 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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443C MET* 3.7 16.8 - - + -
444C TRP* 1.3 76.5 - - - +
446C LYS* 1.4 70.0 + - - +
447C ILE* 3.6 26.2 + - + +
443D MET 3.6 1.2 - - - +
444D TRP* 3.5 9.1 - - - -
445D LEU* 2.9 42.8 + - + +
447D ILE* 5.3 7.4 - - + -
492D VAL* 4.2 35.7 - - + -
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Residues in contact with LYS 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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445C LEU* 1.4 79.6 - - - +
447C ILE* 1.3 66.9 + - - +
448C THR* 4.2 13.2 + - - -
442D ARG* 4.2 36.7 - - + +
443D MET 3.4 9.4 - - - +
444D TRP* 3.9 35.2 - - + -
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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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445C LEU* 3.6 39.9 - - + +
446C LYS* 1.3 77.2 - - - +
448C THR* 1.3 67.1 + - - +
449C ILE* 3.5 23.0 + - + -
442D ARG* 3.3 3.6 - - - +
443D MET* 2.9 61.7 + - + +
445D LEU* 4.9 7.2 - - + -
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Residues in contact with THR 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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446C LYS* 4.2 14.1 + - - -
447C ILE* 1.3 74.6 - - - +
449C ILE* 1.3 63.6 + - - +
450C PRO* 3.9 16.4 - - + +
441D ASP* 3.3 24.4 + - + +
442D ARG* 4.5 2.1 - - - +
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Residues in contact with ILE 449 (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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447C ILE* 3.5 22.9 + - + +
448C THR* 1.3 78.8 - - - +
450C PRO* 1.3 73.3 - - + +
451C ASN 3.3 2.1 + - - -
452C ALA* 3.4 22.1 + - + +
491C THR* 3.9 14.8 - - + -
504C VAL* 3.9 19.5 - - + -
440D ARG 3.4 13.0 - - - +
441D ASP* 3.1 10.5 + - - -
443D MET* 3.5 38.6 - - + +
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Residues in contact with PRO 450 (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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448C THR* 3.9 16.4 - - + +
449C ILE* 1.3 93.1 - - + +
451C ASN* 1.3 78.2 + - - +
452C ALA 3.4 0.3 + - - -
504C VAL* 4.7 3.8 - - - +
441D ASP* 4.1 12.8 - - + -
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Residues in contact with ASN 451 (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 ILE 3.3 1.0 + - - -
450C PRO* 1.3 81.4 - - - +
452C ALA* 1.3 59.7 + - - +
453C PHE* 3.4 21.8 - - - -
504C VAL* 4.4 4.7 - - - +
505C PHE* 5.2 4.9 + - + -
439D VAL* 3.9 27.6 - - + +
440D ARG 3.6 9.4 + - - -
441D ASP* 4.4 0.8 - - - +
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Residues in contact with ALA 452 (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 ILE* 3.6 32.1 - - + +
450C PRO 3.3 0.8 - - - -
451C ASN* 1.3 77.9 - - - +
453C PHE* 1.3 61.0 + - - +
491C THR* 5.1 2.2 - - + -
502C TYR* 4.8 17.7 - - + -
503C TYR 3.4 12.3 - - - +
504C VAL* 4.2 3.6 - - + -
439D VAL* 3.3 5.2 - - - -
440D ARG* 2.9 35.0 + - - +
442D ARG 5.3 2.0 - - - +
443D MET* 5.2 4.7 - - + -
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Residues in contact with PHE 453 (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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451C ASN 3.4 19.5 - - - -
452C ALA* 1.3 73.9 - - - +
454C LEU* 1.3 64.4 + - - +
457C ASP* 5.2 0.2 - - + -
458C VAL* 3.4 30.1 - - + -
488C ILE* 4.0 12.3 - - + -
502C TYR* 4.3 6.2 - - - -
503C TYR* 2.7 55.1 + - + +
504C VAL* 3.5 25.8 - - - -
505C PHE* 3.6 38.6 - + - -
430D MET* 5.0 0.2 - - + -
437D LEU* 4.1 16.2 - - + -
438D GLU 3.6 20.4 - - - +
439D VAL* 4.1 4.5 - - + +
440D ARG* 5.7 2.2 - - - -
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Residues in contact with LEU 454 (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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500A GLN* 4.1 16.6 - - - +
453C PHE* 1.3 74.7 - - - +
455C GLY* 1.3 64.2 + - - +
456C SER* 3.9 20.6 - - - +
457C ASP* 3.0 28.4 + - - +
458C VAL* 3.2 12.9 + - - +
499C GLU 4.2 2.0 - - - +
500C GLN* 3.5 29.2 - - - +
501C CYS 3.5 7.2 - - - +
502C TYR* 3.6 34.1 - - + +
503C TYR* 4.4 0.4 - - - -
438D GLU 5.1 0.2 + - - -
440D ARG* 3.6 30.3 - - - +
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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