Contacts of the helix formed by residues 471 - 485 (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 GLU 471 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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463C TYR* 3.5 15.3 - - - -
469C PHE* 3.9 1.9 - - - +
470C PRO* 1.3 88.5 - - + +
472C ARG* 1.3 66.9 + - - +
473C ARG* 3.1 35.5 - - + +
474C GLU* 3.1 19.9 + - + +
475C ALA 3.7 2.8 + - - -
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Residues in contact with ARG 472 (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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456C SER* 3.6 9.5 + - - +
459C VAL* 3.5 22.5 - - + +
460C ASP* 2.8 31.3 + - - +
463C TYR* 3.5 41.9 + - + -
471C GLU* 1.3 73.9 - - - +
473C ARG* 1.3 62.9 + - - +
475C ALA* 3.0 13.9 + - - +
476C ARG* 3.1 11.9 + - - +
499C GLU* 3.0 38.8 + - - -
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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
----------------------------------------------------------
471C GLU* 3.1 30.4 - - + +
472C ARG* 1.3 76.6 - - - +
474C GLU* 1.3 79.3 + - + +
476C ARG* 3.3 14.5 + - + +
477C LYS* 3.1 32.9 + - - +
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Residues in contact with GLU 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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469C PHE* 3.9 18.1 - - + -
470C PRO* 3.9 29.4 - - + -
471C GLU* 3.1 12.2 + - + +
473C ARG* 1.3 99.9 + - + +
475C ALA* 1.3 57.7 + - - +
477C LYS* 3.3 38.9 + - - +
478C TYR* 3.1 26.3 + - - +
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Residues in contact with ALA 475 (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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459C VAL* 4.0 14.0 - - + +
462C LEU* 3.8 7.0 - - + +
463C TYR* 4.0 24.0 - - + +
469C PHE* 3.7 36.7 - - + -
471C GLU 3.7 1.4 + - - -
472C ARG 3.0 9.4 + - - +
474C GLU* 1.3 74.7 - - - +
476C ARG* 1.3 60.3 + - - +
478C TYR* 3.4 2.3 + - - +
479C ALA* 3.0 27.7 + - - +
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Residues in contact with ARG 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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473A ARG* 4.9 1.4 - - - +
101C SO4 2.7 44.3 + - - -
459C VAL* 3.8 16.7 - - + +
472C ARG* 3.1 11.8 + - - +
473C ARG* 3.4 16.6 - - - +
474C GLU 3.3 0.2 - - - -
475C ALA* 1.3 77.4 - - - +
477C LYS* 1.3 62.2 + - - +
479C ALA* 3.3 3.8 + - - +
480C SER* 3.1 29.2 + - - -
497C PHE* 3.2 43.4 + - + +
499C GLU* 3.9 16.4 + - - +
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Residues in contact with LYS 477 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473C ARG* 3.1 19.7 + - - +
474C GLU* 3.3 41.8 + - - +
476C ARG* 1.3 75.6 - - - +
478C TYR* 1.3 63.9 + - - +
480C SER* 3.4 9.4 + - - -
481C GLY* 3.1 17.8 + - - -
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Residues in contact with TYR 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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462C LEU* 3.7 32.8 - - + -
466C VAL* 5.4 2.5 - - + -
469C PHE* 3.7 27.8 - + + -
474C GLU 3.1 13.1 + - - +
475C ALA 3.6 7.4 - - - +
477C LYS* 1.3 74.3 - - - +
479C ALA* 1.3 63.6 + - - +
481C GLY* 3.0 4.5 + - - -
482C LEU* 2.9 36.2 + - + -
418D SER 4.9 0.6 + - - -
419D VAL* 5.0 19.1 - - + -
421D THR 4.3 5.1 + - - -
423D MET* 3.7 35.7 - - + +
426D VAL* 3.4 33.7 - - + +
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Residues in contact with ALA 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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458C VAL* 4.1 9.2 - - + -
459C VAL* 3.9 11.4 - - + -
462C LEU* 4.0 15.5 - - + -
475C ALA 3.0 14.5 + - - +
476C ARG 3.3 8.7 + - - +
478C TYR* 1.3 77.7 - - - +
480C SER* 1.3 61.5 + - - +
482C LEU* 3.0 19.3 + - - +
483C LEU* 3.1 10.7 + - - +
488C ILE* 4.0 7.0 - - + +
497C PHE* 3.8 24.5 - - + -
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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 ARG* 3.1 19.0 + - - -
477C LYS* 3.5 13.7 - - - -
478C TYR 3.3 0.2 - - - -
479C ALA* 1.3 76.5 - - - +
481C GLY* 1.3 57.0 + - - +
483C LEU* 3.3 5.0 + - - +
484C LYS* 3.0 47.1 + - - +
497C PHE* 3.8 30.7 + - - +
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Residues in contact with GLY 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 LYS 3.1 10.0 + - - -
478C TYR 3.0 9.2 + - - -
480C SER* 1.3 72.2 - - - +
482C LEU* 1.3 65.5 + - - +
484C LYS* 3.3 15.0 + - - +
485C ALA* 3.1 25.3 + - - +
423D MET* 4.1 15.9 - - - +
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Residues in contact with LEU 482 (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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458C VAL* 4.8 4.0 - - + -
462C LEU* 4.4 15.3 - - + -
478C TYR* 2.9 43.5 + - + +
479C ALA* 3.0 10.0 + - - +
481C GLY* 1.3 76.4 - - - +
483C LEU* 1.3 62.3 + - - +
485C ALA* 3.4 3.9 + - - +
486C GLY 3.2 3.3 + - - -
487C LEU* 3.1 43.2 + - + -
488C ILE* 3.5 16.3 + - + -
423D MET* 4.0 14.8 - - + +
426D VAL* 5.7 0.7 - - + -
427D THR* 3.4 27.1 - - - +
430D MET* 4.6 17.9 - - + -
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Residues in contact with LEU 483 (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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479C ALA 3.1 10.5 + - - +
480C SER* 3.5 8.3 - - - +
482C LEU* 1.3 76.3 - - - +
484C LYS* 1.3 65.3 + - + +
486C GLY* 3.1 12.1 + - - -
488C ILE* 3.5 31.9 - - + +
489C ARG* 4.1 1.1 - - - -
490C HIS* 3.6 42.8 - - + +
495C ILE 3.2 26.7 - - - +
497C PHE* 3.7 26.9 - - + +
503C TYR* 4.0 8.7 - - + -
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Residues in contact with LYS 484 (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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480C SER* 3.0 34.3 + - - +
481C GLY* 3.3 15.7 + - - +
483C LEU* 1.3 78.5 - - + +
485C ALA* 1.3 60.7 + - - +
486C GLY 3.6 0.3 + - - -
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Residues in contact with ALA 485 (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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481C GLY 3.1 14.9 + - - +
482C LEU 3.7 4.9 - - - +
483C LEU 3.2 0.2 - - - -
484C LYS* 1.3 80.1 - - - +
486C GLY* 1.3 56.7 + - - +
487C LEU* 3.6 23.0 + - + +
423D MET* 5.1 6.3 - - - -
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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