Contacts of the helix formed by residues 471 - 491 (chain C) in PDB entry 4P3N
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 GLN 471 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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427C TRP 4.8 2.8 + - - -
430C LEU* 3.2 32.1 + - - +
431C PRO* 3.4 20.2 - - + +
467C CYS* 3.2 15.6 - - + +
468C ALA* 2.5 47.0 + - + +
470C GLU* 1.3 79.8 - - + +
472C ILE* 1.3 67.0 + - - +
473C GLU 3.4 1.3 - - - -
474C ASP* 3.1 18.6 + - + +
475C GLU* 3.1 12.2 + - + +
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Residues in contact with ILE 472 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467C CYS* 3.5 26.2 - - - -
468C ALA 3.7 0.8 + - - -
469C MET* 2.9 42.1 + - + +
470C GLU 3.3 0.2 - - - -
471C GLN* 1.3 74.9 - - - +
473C GLU* 1.3 65.6 + - - +
475C GLU* 2.9 5.6 + - + +
476C ILE* 2.9 45.6 + - + +
515C ALA* 4.7 3.8 - - - +
518C GLN* 3.5 18.4 - - + +
519C LEU* 4.6 5.8 - - + -
563C LEU* 4.0 17.9 - - + -
587C VAL* 4.0 21.5 - - + -
589C VAL* 4.2 9.4 - - + -
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Residues in contact with GLU 473 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470C GLU 5.2 0.7 - - - +
471C GLN 3.2 0.8 + - - -
472C ILE* 1.3 79.1 - - - +
474C ASP* 1.3 59.8 + - - +
476C ILE* 4.7 1.3 - - - -
477C LYS* 3.3 8.3 + - - +
518C GLN* 3.5 40.9 + - + +
521C ASN* 3.5 38.1 - - + +
522C SER* 2.6 34.2 + - - +
525C GLU* 4.4 12.9 - - - +
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Residues in contact with ASP 474 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470C GLU 5.4 0.4 + - - +
471C GLN* 3.1 11.8 + - + +
473C GLU* 1.3 79.4 - - - +
475C GLU* 1.3 68.2 + - + +
477C LYS* 3.2 22.8 + - - +
478C GLY* 3.1 17.3 + - - -
525C GLU* 5.8 0.2 - - - -
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Residues in contact with GLU 475 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431C PRO* 3.5 25.0 - - + +
433C ARG* 2.7 45.8 + - - -
465C ILE* 3.3 32.6 - - + +
467C CYS* 4.6 9.0 - - + -
471C GLN 3.1 12.2 + - - +
472C ILE* 2.9 10.8 + - + +
474C ASP* 1.3 79.6 - - + +
476C ILE* 1.3 61.4 + - + +
478C GLY* 2.9 6.3 + - - -
479C CYS* 2.8 31.3 + - - -
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Residues in contact with ILE 476 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465C ILE* 6.5 0.2 - - + -
472C ILE* 2.9 33.7 + - + +
473C GLU* 4.6 0.9 - - - +
475C GLU* 1.3 77.6 - - + +
477C LYS* 1.3 63.8 + - - +
479C CYS* 2.9 16.6 + - - +
480C LEU* 3.0 22.7 + - + +
519C LEU* 3.6 32.5 - - + -
522C SER* 3.9 20.6 - - - +
544C ILE* 4.1 15.7 - - + -
561C ILE* 4.0 27.1 - - + -
563C LEU* 4.3 10.8 - - + -
589C VAL* 4.5 8.5 - - + -
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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 GLU 3.3 13.4 + - - +
474C ASP* 3.2 25.7 + - - +
475C GLU 3.2 0.6 - - - -
476C ILE* 1.3 77.7 - - - +
478C GLY* 1.3 62.0 + - - +
480C LEU* 3.5 10.0 + - - +
481C ASP* 3.2 20.8 + - + +
522C SER* 3.6 6.0 + - - +
525C GLU* 3.8 33.4 + - + +
526C PHE* 5.2 4.4 - - + -
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Residues in contact with GLY 478 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367C ARG* 3.9 5.2 + - - -
474C ASP 3.1 9.4 + - - -
475C GLU* 2.9 8.7 + - - -
477C LYS* 1.3 76.7 - - - +
479C CYS* 1.3 64.2 + - - +
481C ASP* 2.9 9.2 + - - +
482C PHE* 2.9 24.8 + - - +
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Residues in contact with CYS 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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369C PHE* 5.4 2.9 - - - -
465C ILE* 3.8 26.9 - - - -
475C GLU 2.8 21.7 + - - +
476C ILE* 2.9 11.6 + - - +
478C GLY* 1.3 72.2 - - - +
480C LEU* 1.3 61.8 + - - +
482C PHE* 3.3 9.9 - - - +
483C LEU* 3.1 32.3 + - + +
561C ILE* 3.6 34.3 - - + -
589C VAL* 5.2 0.9 - - - -
591C ARG* 4.3 18.2 - - + -
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Residues in contact with LEU 480 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476C ILE* 3.0 30.1 + - + +
477C LYS* 3.8 5.6 - - - +
479C CYS* 1.3 76.1 - - - +
481C ASP* 1.3 65.3 + - - +
483C LEU* 3.5 22.9 + - + +
484C ARG* 3.0 23.0 + - - +
496C LEU* 4.0 20.4 - - + -
522C SER 4.3 7.2 - - - +
523C LEU* 3.8 25.4 - - + -
526C PHE* 3.6 45.3 - - + -
544C ILE* 4.9 3.4 - - + -
561C ILE* 4.1 13.5 - - + -
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Residues in contact with ASP 481 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367C ARG* 2.5 34.5 + - - +
477C LYS* 3.2 13.9 + - + +
478C GLY* 2.9 10.8 + - - +
480C LEU* 1.3 72.0 - - - +
482C PHE* 1.3 66.2 + - - +
484C ARG* 2.8 52.5 + - - +
485C THR* 2.8 18.7 + - - +
526C PHE* 4.3 0.6 - - - -
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Residues in contact with PHE 482 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360C ILE* 4.5 7.6 - - + -
363C GLU* 3.5 31.4 - - + -
364C TYR* 3.5 30.5 - + - -
367C ARG* 3.4 34.4 - - - +
369C PHE* 3.9 17.0 - + - -
478C GLY 2.9 12.2 + - - +
479C CYS* 3.3 14.6 - - - +
481C ASP* 1.3 74.0 - - - +
483C LEU* 1.3 64.7 + - - +
485C THR* 2.4 20.6 + - - -
486C VAL* 3.1 15.3 + - + +
591C ARG* 3.2 30.5 - - - -
593C ILE* 3.5 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
----------------------------------------------------------
479C CYS* 3.1 23.5 + - + +
480C LEU* 3.5 22.9 - - + +
482C PHE* 1.3 76.8 - - + +
484C ARG* 1.3 65.4 + - - +
486C VAL* 3.0 3.8 + - - +
487C TYR* 2.9 47.5 + - + +
494C PHE* 5.3 4.9 - - + -
496C LEU* 4.7 2.7 - - + -
546C ILE* 3.6 38.6 - - + -
559C ALA* 4.4 8.5 - - + -
561C ILE* 4.7 5.8 - - + -
591C ARG* 5.9 3.8 - - + -
592C ALA 4.7 2.2 - - - +
593C ILE* 3.5 36.8 - - + -
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Residues in contact with ARG 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 LEU 3.0 9.3 + - - +
481C ASP* 2.8 51.0 + - - +
483C LEU* 1.3 80.5 - - - +
485C THR* 1.3 63.5 + - + +
487C TYR* 4.3 0.9 - - - +
488C SER* 3.0 32.7 + - - -
494C PHE* 4.4 19.0 - - + -
526C PHE* 3.5 29.8 - - + -
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Residues in contact with THR 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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359C PHE* 5.2 0.4 - - - -
363C GLU* 4.7 13.2 - - - +
367C ARG* 3.0 22.3 + - - +
481C ASP* 2.8 13.4 + - - +
482C PHE* 2.4 21.5 + - - -
484C ARG* 1.3 83.0 - - + +
486C VAL* 1.3 63.8 + - - +
488C SER* 3.3 6.4 + - - -
489C VAL* 3.1 29.1 + - + +
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Residues in contact with VAL 486 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359C PHE* 3.6 26.0 - - + -
360C ILE* 4.6 6.7 - - + -
363C GLU* 4.9 4.5 - - + -
482C PHE* 3.4 37.2 - - + +
483C LEU 3.0 6.2 + - - +
485C THR* 1.3 74.9 - - - +
487C TYR* 1.3 59.5 + - + +
489C VAL* 2.9 21.1 + - - +
490C PHE* 3.1 37.0 + - + -
593C ILE* 4.1 25.4 - - + -
594C LEU* 4.5 6.3 - - + -
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Residues in contact with TYR 487 (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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483C LEU* 2.9 29.0 + - + +
484C ARG 4.3 1.3 - - - +
486C VAL* 1.3 78.8 - - + +
488C SER* 1.3 52.9 + - - +
490C PHE* 2.9 19.1 + + - -
491C GLY 2.7 31.7 + - - -
492C PHE* 2.9 30.4 + + + +
494C PHE* 3.9 24.2 - + + -
546C ILE* 4.0 17.7 - - + -
548C ILE* 3.5 30.5 - - + +
558C CYS* 3.8 6.9 - - - +
559C ALA* 3.3 15.6 - - - +
593C ILE* 2.9 42.5 + - + +
594C LEU* 5.7 0.2 - - - -
600C MET* 4.9 10.3 - - + -
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Residues in contact with SER 488 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484C ARG* 3.0 25.4 + - - -
485C THR* 3.6 8.1 - - - -
486C VAL 3.2 0.4 - - - -
487C TYR* 1.3 76.3 - - - +
489C VAL* 1.3 61.3 + - - +
491C GLY* 3.6 6.5 + - - +
492C PHE 4.5 3.6 + - - -
717C LYS* 3.3 20.4 + - - -
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Residues in contact with VAL 489 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359C PHE* 3.9 27.1 - - + -
485C THR* 3.1 15.5 + - + +
486C VAL 2.9 11.0 + - - +
488C SER* 1.3 79.3 - - - +
490C PHE* 1.3 61.0 + - + +
608C TYR* 4.9 1.0 + - - -
615C TRP* 4.1 16.8 + - + -
714C PHE 5.4 2.7 - - - +
715C ARG* 3.7 36.5 - - + +
717C LYS* 3.4 24.8 + - - +
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Residues in contact with PHE 490 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356C LEU* 3.8 21.5 - - + -
359C PHE* 4.3 9.6 - + - -
486C VAL* 3.1 41.5 + - + -
487C TYR* 2.9 17.8 + + - +
489C VAL* 1.3 77.5 - - - +
491C GLY* 1.3 60.5 + - - +
492C PHE* 3.6 32.7 - + + -
594C LEU* 3.8 17.7 - - + -
600C MET* 4.4 6.7 - - + -
604C LEU* 3.8 24.7 - - + -
607C ASN* 5.1 0.9 + - - -
608C TYR* 3.6 32.9 + - - +
615C TRP* 4.0 23.8 - + - -
616C LEU* 4.4 0.7 - - + -
717C LYS* 4.3 5.7 - - - +
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Residues in contact with GLY 491 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487C TYR 2.7 4.7 + - - -
488C SER* 3.6 4.4 + - - -
489C VAL 3.3 3.4 - - - -
490C PHE* 1.3 79.6 - - - +
492C PHE* 1.3 66.1 + - - +
493C SER 4.0 1.0 + - - -
549C LYS 5.0 0.9 - - - +
717C LYS* 4.1 18.8 - - - -
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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
------------------------------------------------------------
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