Contacts of the helix formed by residues 471 - 491 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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427A TRP* 4.7 4.4 + - - +
430A LEU* 3.4 29.5 + - - +
431A PRO* 3.8 18.3 - - + +
467A CYS* 3.3 15.8 - - + +
468A ALA* 2.7 43.3 + - + +
469A MET 3.0 0.2 + - - -
470A GLU* 1.3 80.7 - - + +
472A ILE* 1.3 65.6 + - - +
473A GLU 3.4 0.9 - - - -
474A ASP* 3.0 20.9 + - + +
475A GLU* 3.1 13.3 + - + +
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Residues in contact with ILE 472 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467A CYS* 3.9 23.8 - - - -
468A ALA 3.6 2.0 + - - +
469A MET* 2.9 43.0 + - + +
471A GLN* 1.3 75.7 - - - +
473A GLU* 1.3 67.0 + - - +
475A GLU* 2.9 5.3 + - - +
476A ILE* 2.9 42.5 + - + +
515A ALA* 4.6 3.4 - - + +
518A GLN* 3.8 15.7 - - + +
519A LEU* 4.5 4.0 - - + -
563A LEU* 3.7 32.1 - - + -
587A VAL* 3.7 18.2 - - + -
589A VAL* 5.4 2.7 - - + -
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Residues in contact with GLU 473 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470A GLU 5.4 1.3 - - - +
471A GLN 5.3 0.2 - - - -
472A ILE* 1.3 79.8 - - - +
474A ASP* 1.3 61.9 + - - +
476A ILE* 3.8 0.6 + - - -
477A LYS* 3.3 20.4 + - - +
518A GLN* 3.3 39.8 + - + +
521A ASN* 3.3 44.2 + - - +
522A SER* 3.6 13.3 - - - -
525A GLU* 4.3 11.8 - - - +
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Residues in contact with ASP 474 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470A GLU 5.4 0.4 + - - +
471A GLN* 3.0 13.8 + - + +
473A GLU* 1.3 77.3 - - - +
475A GLU* 1.3 72.3 + - - +
477A LYS* 3.0 29.2 + - - +
478A GLY* 3.0 11.1 + - - -
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Residues in contact with GLU 475 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431A PRO* 3.6 21.6 - - + +
433A ARG* 2.8 44.6 + - - -
465A ILE* 3.3 32.5 - - + +
467A CYS* 4.4 9.6 - - + -
471A GLN 3.1 12.9 + - - +
472A ILE* 2.9 10.4 + - - +
474A ASP* 1.3 82.5 - - + +
476A ILE* 1.3 52.7 + - + +
478A GLY* 2.9 5.5 + - - +
479A CYS* 2.7 38.3 + - - -
589A VAL* 5.8 3.1 - - + -
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Residues in contact with ILE 476 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472A ILE* 2.9 27.8 + - + +
473A GLU 3.9 0.9 - - - +
475A GLU* 1.3 75.4 - - + +
477A LYS* 1.3 63.8 + - - +
479A CYS* 3.0 8.5 + - - +
480A LEU* 2.8 31.1 + - + +
519A LEU* 3.6 27.4 - - + +
522A SER* 3.6 25.6 - - - +
523A LEU 5.4 0.2 - - - +
544A ILE* 3.8 23.8 - - + -
561A ILE* 3.7 28.7 - - + -
563A LEU* 4.3 12.6 - - + -
589A VAL* 4.9 6.1 - - + -
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Residues in contact with LYS 477 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473A GLU* 3.3 12.5 + - + +
474A ASP* 3.0 25.0 + - - +
476A ILE* 1.3 81.4 - - - +
478A GLY* 1.3 63.0 + - - +
480A LEU* 3.3 9.3 + - - +
481A ASP* 3.1 21.7 + - + +
522A SER* 4.3 11.2 - - - -
525A GLU* 5.5 17.9 - - + +
526A PHE* 5.2 3.0 - - - -
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Residues in contact with GLY 478 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367A ARG* 4.1 4.4 + - - -
474A ASP 3.0 8.7 + - - -
475A GLU* 2.9 8.2 + - - -
477A LYS* 1.3 75.3 - - - +
479A CYS* 1.3 66.7 + - - +
481A ASP* 2.9 10.3 + - - +
482A PHE* 2.8 23.1 + - - +
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Residues in contact with CYS 479 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369A PHE* 5.7 2.0 - - - -
465A ILE* 3.8 27.1 - - - -
475A GLU 2.7 21.0 + - - -
476A ILE* 3.0 11.2 + - - +
478A GLY* 1.3 69.6 - - - +
480A LEU* 1.3 64.1 + - - +
482A PHE* 3.0 13.0 + - - +
483A LEU* 2.9 26.6 + - + +
561A ILE* 3.7 35.2 - - + -
589A VAL* 4.9 1.1 - - - -
591A ARG* 4.2 18.2 - - - +
593A ILE* 5.0 0.3 - - - +
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Residues in contact with LEU 480 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476A ILE* 2.8 32.0 + - + +
477A LYS* 3.6 7.4 - - - +
479A CYS* 1.3 74.2 - - - +
481A ASP* 1.3 58.9 + - - +
483A LEU* 2.9 19.4 + - + +
484A ARG* 2.8 30.0 + - - +
494A PHE* 6.1 0.2 - - + -
496A LEU* 4.0 32.1 - - + -
522A SER 4.1 10.3 - - - +
523A LEU* 4.3 14.1 - - + -
526A PHE* 3.5 48.2 - - + -
544A ILE* 5.1 2.0 - - + -
561A ILE* 4.3 9.9 - - + -
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Residues in contact with ASP 481 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367A ARG* 2.5 34.0 + - - +
477A LYS* 3.1 14.0 + - + +
478A GLY* 2.9 12.8 + - - +
480A LEU* 1.3 75.5 - - - +
482A PHE* 1.3 61.5 + - - +
484A ARG* 2.4 41.3 + - - +
485A THR* 3.1 25.4 + - - -
526A PHE* 4.2 1.9 - - + -
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Residues in contact with PHE 482 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360A ILE* 4.4 7.4 - - + -
363A GLU* 3.4 33.7 - - + -
364A TYR* 3.6 41.3 - + - -
367A ARG* 3.5 26.9 - - - +
369A PHE* 3.9 21.1 - + - -
478A GLY 2.8 11.9 + - - +
479A CYS* 3.0 14.3 + - - +
481A ASP* 1.3 76.7 - - - +
483A LEU* 1.3 63.7 + - - +
485A THR* 3.0 12.8 + - - -
486A VAL* 3.2 26.5 + - + +
591A ARG* 3.7 17.0 - - - +
593A ILE* 3.3 14.4 - - + -
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Residues in contact with LEU 483 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479A CYS 2.9 14.0 + - - +
480A LEU* 3.2 29.6 - - + +
482A PHE* 1.3 77.6 - - - +
484A ARG* 1.3 62.1 + - - +
486A VAL* 4.2 0.3 - - - +
487A TYR* 3.2 43.1 + - + -
494A PHE* 4.7 6.7 - - + -
496A LEU* 4.8 2.7 - - + -
526A PHE* 6.0 0.2 - - + -
546A ILE* 3.8 27.4 - - + -
559A ALA* 3.5 26.9 - - + -
561A ILE* 4.2 13.7 - - + -
592A ALA 5.1 0.2 - - - +
593A ILE* 3.7 30.5 - - + -
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Residues in contact with ARG 484 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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480A LEU 2.8 17.5 + - - +
481A ASP* 2.4 36.0 + - - +
483A LEU* 1.3 73.4 - - - +
485A THR* 1.3 64.0 + - - +
487A TYR* 4.4 0.9 - - - +
488A SER* 3.1 27.5 + - - -
494A PHE* 4.0 18.9 - - + -
526A PHE* 4.1 37.5 + - + -
528A GLU* 6.0 1.8 - - - -
629C THR* 5.7 10.3 - - - +
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Residues in contact with THR 485 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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359A PHE* 5.4 0.9 - - + -
363A GLU* 4.1 21.5 - - + +
367A ARG* 2.8 32.2 + - - +
481A ASP* 3.1 10.5 + - - -
482A PHE 3.0 6.2 + - - -
484A ARG* 1.3 77.0 + - - +
486A VAL* 1.3 69.1 + - - +
488A SER* 3.0 15.5 + - - -
489A VAL* 3.1 20.3 + - + +
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Residues in contact with VAL 486 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359A PHE* 3.7 26.6 - - + -
360A ILE* 4.3 8.3 - - + -
363A GLU* 4.9 4.5 - - + -
482A PHE* 3.2 38.9 + - + +
483A LEU 4.2 0.7 - - - +
485A THR* 1.3 74.5 - - - +
487A TYR* 1.3 67.5 + - + +
489A VAL* 2.9 17.2 + - - +
490A PHE* 3.2 35.3 + - + -
593A ILE* 4.0 27.1 - - + -
594A LEU* 4.2 7.2 - - + -
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Residues in contact with TYR 487 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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483A LEU* 3.2 36.8 + - + +
484A ARG 4.4 0.9 - - - +
486A VAL* 1.3 81.9 - - + +
488A SER* 1.3 51.9 + - - +
490A PHE* 2.9 20.3 + + - -
491A GLY 2.6 31.4 + - - -
492A PHE* 2.9 30.2 + + + +
494A PHE* 3.8 18.6 - + + -
546A ILE* 4.0 12.1 - - + +
548A ILE* 3.5 37.1 - - + +
558A CYS* 4.0 4.5 - - - +
559A ALA* 3.1 17.2 + - - +
593A ILE* 2.5 39.8 + - + -
594A LEU* 5.1 2.7 - - + -
600A MET* 5.2 2.7 - - - -
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Residues in contact with SER 488 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484A ARG* 3.1 23.2 + - - -
485A THR* 3.0 7.9 + - - -
487A TYR* 1.3 77.0 - - - +
489A VAL* 1.3 60.4 + - - +
491A GLY* 3.3 9.3 + - - +
492A PHE 4.7 2.4 + - - +
494A PHE* 5.9 0.2 - - - -
717A LYS* 3.1 20.3 + - - -
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Residues in contact with VAL 489 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359A PHE* 3.6 29.4 - - + -
485A THR* 3.1 15.1 + - + +
486A VAL 2.9 10.1 + - - +
488A SER* 1.3 76.3 - - - +
490A PHE* 1.3 62.5 + - + +
608A TYR* 5.1 0.9 + - - -
615A TRP* 3.8 29.9 + - + -
714A PHE 5.5 2.0 - - - +
715A ARG* 4.0 26.0 - - + +
717A LYS* 3.3 25.6 - - - +
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Residues in contact with PHE 490 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356A LEU* 3.8 19.5 - - + -
359A PHE* 4.4 11.0 - + - -
486A VAL* 3.2 33.8 + - + -
487A TYR* 2.9 12.4 + + - +
489A VAL* 1.3 79.6 - - + +
491A GLY* 1.3 62.0 + - - +
492A PHE* 3.4 39.2 - + + -
594A LEU* 3.8 18.6 - - + -
600A MET* 4.2 6.5 - - + -
604A LEU* 3.6 21.5 - - + -
607A ASN* 5.2 1.0 + - - -
608A TYR* 3.7 32.8 + - - +
615A TRP* 3.9 25.4 - + - -
616A LEU* 4.2 0.4 - - + -
717A LYS* 4.3 5.1 - - - +
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Residues in contact with GLY 491 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487A TYR 2.6 11.0 + - - -
488A SER* 3.3 10.2 + - - -
489A VAL 3.2 4.0 - - - -
490A PHE* 1.3 77.5 - - - +
492A PHE* 1.3 62.6 + - - -
493A SER 4.0 1.0 + - - -
549A LYS 5.1 0.3 - - - +
717A LYS* 4.0 14.6 - - - -
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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