Contacts of the helix formed by residues 464 - 481 (chain C) in PDB entry 5MS0
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 464 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52C ALA* 6.1 3.4 - - + -
460C ALA 2.9 16.9 + - - +
461C GLU* 3.2 7.6 + - - +
463C GLN* 1.3 77.2 - - - +
465C ARG* 1.3 59.3 + - - +
466C VAL 3.1 2.0 - - - -
467C GLY* 3.1 6.7 + - - +
468C LEU* 3.0 24.5 + - - +
498C ILE* 5.9 0.9 - - - +
502C VAL* 5.8 2.7 - - + -
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Residues in contact with ARG 465 (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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52C ALA* 5.1 14.5 - - + +
393C ASP 5.6 0.2 - - - +
461C GLU 2.9 17.2 + - - +
462C ASN* 4.4 6.5 - - - +
464C PHE* 1.3 72.7 - - - +
466C VAL* 1.3 64.4 + - - +
468C LEU* 3.7 11.0 - - - +
469C VAL* 3.5 21.3 + - - +
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Residues in contact with VAL 466 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462C ASN 4.6 9.4 + - - +
463C GLN* 4.5 6.7 - - - +
464C PHE* 3.1 1.2 - - - +
465C ARG* 1.3 79.9 - - - +
467C GLY* 1.3 60.5 + - - +
469C VAL* 3.7 9.5 + - - +
470C ARG* 3.7 10.6 + - - +
501C ALA* 4.4 18.2 - - + -
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Residues in contact with GLY 467 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464C PHE* 3.1 10.6 + - - +
466C VAL* 1.3 77.4 - - - +
468C LEU* 1.3 59.6 + - - +
470C ARG* 3.4 5.6 + - - +
471C VAL* 3.0 30.4 + - - +
497C PRO* 4.2 8.0 - - - +
498C ILE* 4.1 30.5 + - - +
501C ALA* 4.6 5.6 - - - +
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Residues in contact with LEU 468 (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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52C ALA* 5.1 11.0 - - + +
55C SER* 6.5 0.7 - - - -
56C VAL* 4.7 12.8 - - + +
464C PHE 3.0 14.8 + - - +
465C ARG* 3.8 12.8 - - + +
466C VAL 3.3 0.2 - - - -
467C GLY* 1.3 78.1 - - - +
469C VAL* 1.3 57.0 + - - +
471C VAL* 3.3 4.7 + - - +
472C GLU* 3.0 30.0 + - - +
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Residues in contact with VAL 469 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393C ASP* 3.9 36.3 - - + +
465C ARG 3.5 12.7 + - - +
466C VAL* 3.7 4.4 + - - +
467C GLY 3.3 0.6 - - - -
468C LEU* 1.3 79.5 - - - +
470C ARG* 1.3 60.6 + - - +
472C GLU* 4.1 7.1 - - - +
473C ARG* 3.9 14.4 + - - +
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Residues in contact with ARG 470 (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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466C VAL 3.7 10.2 + - - +
467C GLY* 3.4 8.4 + - - +
468C LEU 3.2 0.2 - - - -
469C VAL* 1.3 78.0 - - - +
471C VAL* 1.3 59.4 + - - +
472C GLU 3.2 0.2 - - - -
473C ARG* 3.1 9.4 + - - +
474C ALA* 3.0 23.2 + - - +
497C PRO* 4.0 22.2 - - + +
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Residues in contact with VAL 471 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467C GLY 3.0 17.7 + - - +
468C LEU* 3.3 5.1 + - - +
470C ARG* 1.3 74.6 - - - +
472C GLU* 1.3 60.2 + - - +
474C ALA* 3.2 13.0 + - + +
475C VAL* 2.9 27.4 + - - +
492C MET 5.2 0.2 - - - +
493C ILE* 5.9 4.8 - - + -
494C ASN 4.9 13.7 - - - +
497C PRO* 5.3 5.4 - - + +
498C ILE* 5.9 4.9 - - + +
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Residues in contact with GLU 472 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C VAL* 4.3 23.3 - - + +
468C LEU 3.0 17.0 + - - +
469C VAL* 4.3 8.1 - - - +
470C ARG 3.2 0.4 - - - -
471C VAL* 1.3 78.0 - - - +
473C ARG* 1.3 57.3 + - - +
475C VAL* 3.2 5.2 + - - +
476C LYS* 3.0 27.5 + - - +
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Residues in contact with ARG 473 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469C VAL 3.9 10.1 + - - +
470C ARG* 3.1 12.0 + - - +
472C GLU* 1.3 77.0 - - - +
474C ALA* 1.3 63.3 + - - +
476C LYS* 3.8 8.1 - - - +
477C GLU* 3.6 17.7 + - - +
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Residues in contact with ALA 474 (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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470C ARG 3.0 12.1 + - - +
471C VAL* 3.3 16.8 - - + +
472C GLU 3.1 0.4 - - - -
473C ARG* 1.3 77.8 - - - +
475C VAL* 1.3 57.8 + - - +
476C LYS 3.4 0.2 + - - -
477C GLU* 3.4 4.5 + - - +
478C ARG* 2.9 29.0 + - + +
492C MET 4.1 9.2 - - - +
493C ILE* 5.5 0.2 - - - -
494C ASN* 5.2 15.5 - - + +
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Residues in contact with VAL 475 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471C VAL 2.9 15.7 + - - +
472C GLU* 3.2 5.3 + - - +
474C ALA* 1.3 73.3 - - - +
476C LYS* 1.3 61.7 + - - +
478C ARG* 3.8 2.8 - - - +
479C LEU* 2.9 28.1 + - - +
492C MET* 3.7 22.9 + - + +
493C ILE* 5.8 1.8 - - + -
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Residues in contact with LYS 476 (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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472C GLU 3.0 15.6 + - - +
473C ARG* 3.8 10.5 - - - +
474C ALA 3.2 0.2 - - - -
475C VAL* 1.3 79.8 - - - +
477C GLU* 1.3 61.7 + - - +
479C LEU* 3.4 14.4 - - - +
480C SER* 3.9 4.3 + - - -
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Residues in contact with GLU 477 (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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473C ARG 3.6 8.3 + - - +
474C ALA* 3.4 7.4 + - - +
476C LYS* 1.3 78.5 - - - +
478C ARG* 1.3 57.7 + - - +
479C LEU 3.1 0.4 - - - -
480C SER* 2.9 23.3 + - - -
481C LEU* 3.0 12.6 + - - +
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Residues in contact with ARG 478 (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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474C ALA 2.9 18.2 + - - +
475C VAL* 3.8 1.3 - - - -
477C GLU* 1.3 74.9 - - - +
479C LEU* 1.3 62.8 + - - +
480C SER 3.3 0.2 - - - -
481C LEU* 3.8 12.6 - - + +
482C GLY* 3.6 11.3 + - - -
487C LEU* 4.3 6.1 - - - +
491C ASP 3.2 28.7 - - - +
492C MET* 3.5 20.6 - - - +
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Residues in contact with LEU 479 (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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61C SER* 5.2 14.1 - - - -
475C VAL 2.9 19.2 + - - +
476C LYS* 3.4 9.9 - - - +
477C GLU 3.1 0.2 - - - -
478C ARG* 1.3 80.2 - - - +
480C SER* 1.3 60.6 + - - +
482C GLY* 3.9 9.0 + - - +
487C LEU* 5.8 2.0 - - - -
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Residues in contact with SER 480 (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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476C LYS 3.9 3.3 + - - -
477C GLU* 2.9 12.0 + - - -
479C LEU* 1.3 76.1 - - - +
481C LEU* 1.3 64.1 + - - +
482C GLY 3.2 9.3 + - - +
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Residues in contact with LEU 481 (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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477C GLU 3.0 13.9 + - - +
478C ARG* 3.8 13.4 - - + +
479C LEU 3.4 0.6 - - - -
480C SER* 1.3 76.0 - - - +
482C GLY* 1.3 62.8 + - - +
483C ASP* 3.7 1.0 + - - -
491C ASP* 5.3 4.2 - - + +
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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