Contacts of the helix formed by residues 456 - 476 (chain T) in PDB entry 1BGX
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 LEU 456 (chain T).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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451T LEU* 5.1 1.8 - - + -
452T ASP 3.4 20.3 + - - +
453T VAL 4.5 1.2 + - - +
455T TYR* 1.3 79.5 - - + +
457T ARG* 1.3 55.5 + - - +
459T LEU* 3.7 17.2 + - + +
460T SER* 3.3 23.6 + - - -
546T ILE* 5.8 7.9 - - + -
549T LEU* 4.0 43.3 - - + +
550T PRO* 4.3 22.4 - - + -
594T ILE* 6.1 3.1 - - + +
597T ALA* 4.0 25.6 - - - +
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Residues in contact with ARG 457 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453T VAL 3.8 14.5 + - - +
454T ALA* 3.3 40.8 + - - +
456T LEU* 1.3 74.3 - - - +
458T ALA* 1.3 74.2 + - - +
459T LEU 3.3 0.2 - - - -
460T SER* 3.4 19.6 + - - -
461T LEU* 3.6 16.7 + - - +
550T PRO* 5.9 0.6 - - + +
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Residues in contact with ALA 458 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454T ALA 3.8 13.5 - - - +
455T TYR* 3.2 15.2 + - + +
457T ARG* 1.3 84.5 - - + +
459T LEU* 1.3 62.4 - - - +
460T SER 3.2 0.4 - - - -
461T LEU* 3.5 18.2 - - + +
462T GLU* 3.3 23.2 + - - +
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Residues in contact with LEU 459 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455T TYR* 2.9 42.4 + - + +
456T LEU* 4.0 18.4 - - + +
458T ALA* 1.3 75.0 - - - +
460T SER* 1.3 59.9 - - - +
461T LEU 3.2 0.7 - - - -
462T GLU* 3.6 27.4 - - - +
463T VAL* 3.0 51.2 + - + +
541T LEU* 5.6 7.9 - - + -
593T ARG* 3.9 35.0 - - + +
594T ILE* 4.9 9.4 - - + -
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Residues in contact with SER 460 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53L ASN* 4.0 19.6 + - - +
456T LEU 3.3 15.4 + - - -
457T ARG* 3.4 14.6 - - - -
458T ALA 3.2 0.4 - - - -
459T LEU* 1.3 79.1 - - - +
461T LEU* 1.3 56.2 - - - +
463T VAL* 5.0 1.8 - - - +
464T ALA* 3.3 20.8 + - - +
546T ILE* 4.8 13.3 - - - +
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Residues in contact with LEU 461 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457T ARG* 3.8 15.9 - - - +
458T ALA* 3.5 22.2 - - + +
460T SER* 1.3 76.2 - - - +
462T GLU* 1.3 65.2 + - + +
463T VAL 3.5 0.7 - - - -
464T ALA* 3.7 8.0 - - - +
465T GLU* 3.3 32.8 + - - +
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Residues in contact with GLU 462 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455T TYR* 5.0 5.7 + - - -
458T ALA 3.3 18.7 + - - +
459T LEU* 3.3 24.0 + - + +
461T LEU* 1.3 78.4 - - + +
463T VAL* 1.3 65.0 + - - +
465T GLU* 3.4 26.2 + - - +
466T GLU* 3.7 10.8 - - - +
593T ARG* 3.1 31.9 + - - +
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Residues in contact with VAL 463 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459T LEU* 3.0 38.4 + - + +
460T SER* 5.0 2.0 - - - +
462T GLU* 1.3 72.5 - - + +
464T ALA* 1.3 65.1 + - - +
465T GLU 3.1 2.0 - - - -
466T GLU* 3.0 34.5 + - + +
467T ILE* 3.1 30.2 + - + +
538T LEU* 4.9 9.6 - - + +
539T THR* 5.5 1.6 - - + -
541T LEU* 4.5 28.3 - - + -
546T ILE* 6.1 2.2 - - + -
590T LEU* 6.0 2.2 - - + -
593T ARG* 4.9 7.2 - - - +
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Residues in contact with ALA 464 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53L ASN* 3.8 16.2 - - + +
460T SER 3.3 21.6 + - - +
461T LEU* 3.7 11.2 - - - +
462T GLU 3.3 0.6 - - - -
463T VAL* 1.3 79.1 - - - +
465T GLU* 1.3 60.5 + - + +
467T ILE* 3.6 15.3 + - - +
468T ALA* 3.2 22.3 + - - +
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Residues in contact with GLU 465 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461T LEU* 3.3 25.1 - - - +
462T GLU* 3.6 15.7 - - - +
463T VAL 3.1 1.0 - - - -
464T ALA* 1.3 76.5 - - + +
466T GLU* 1.3 63.9 + - + +
467T ILE 3.1 0.2 - - - -
468T ALA* 3.3 6.4 + - - +
469T ARG* 3.2 59.6 + - - +
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Residues in contact with GLU 466 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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462T GLU* 3.7 11.0 - - - +
463T VAL* 3.0 29.6 + - + +
465T GLU* 1.3 75.8 - - + +
467T ILE* 1.3 60.3 + - + +
469T ARG* 4.0 17.2 - - - +
470T LEU* 3.5 28.7 + - + +
538T LEU* 3.8 34.3 - - + +
590T LEU* 5.3 0.4 - - - -
593T ARG* 3.1 41.6 + - - -
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Residues in contact with ILE 467 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49L TYR* 3.5 24.5 - - - +
53L ASN* 4.6 7.0 - - + -
54L LEU* 3.7 16.6 - - + +
463T VAL* 3.1 28.9 - - + +
464T ALA* 3.6 16.6 - - - +
466T GLU* 1.3 76.2 - - + +
468T ALA* 1.3 59.3 + - - +
469T ARG 3.2 0.5 + - - -
470T LEU 3.2 2.1 + - - -
471T GLU* 3.0 46.0 + - - +
535T TYR* 3.1 28.7 + - + +
539T THR* 3.6 22.2 - - + -
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Residues in contact with ALA 468 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60L VAL* 5.7 2.5 - - + +
464T ALA 3.2 13.7 + - - +
465T GLU* 3.3 7.4 + - - +
467T ILE* 1.3 78.6 - - - +
469T ARG* 1.3 60.9 + - + +
471T GLU* 3.8 12.9 - - - +
472T ALA* 3.3 22.9 + - - +
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Residues in contact with ARG 469 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465T GLU* 3.2 54.3 + - - +
466T GLU* 4.0 16.5 - - - +
467T ILE 3.2 0.6 - - - -
468T ALA* 1.3 78.2 - - + +
470T LEU* 1.3 69.3 + - + +
471T GLU 3.2 0.4 - - - -
472T ALA* 3.5 7.1 + - - +
473T GLU* 3.3 22.2 + - - +
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Residues in contact with LEU 470 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466T GLU* 3.5 16.4 + - + +
467T ILE 3.2 1.6 + - - -
469T ARG* 1.3 83.6 - - + +
471T GLU* 1.3 60.7 + - - +
472T ALA 3.3 0.7 - - - -
473T GLU* 3.7 11.0 + - + +
474T VAL* 3.6 21.5 - - - +
531T LYS* 3.8 47.0 - - + +
534T GLN* 5.6 4.3 - - + -
535T TYR* 3.8 35.1 - - + +
538T LEU* 3.9 21.3 - - + -
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Residues in contact with GLU 471 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54L LEU* 3.3 33.4 - - - +
57L GLY 3.5 13.0 - - - +
58L VAL 3.6 14.6 - - - +
60L VAL* 3.4 25.2 - - + +
467T ILE* 3.0 29.4 + - - +
468T ALA* 3.8 10.7 + - - +
470T LEU* 1.3 77.4 - - - +
472T ALA* 1.3 62.1 + - - +
473T GLU 3.3 0.2 - - - -
474T VAL* 3.8 4.4 + - - +
475T PHE* 3.5 28.6 + - + +
535T TYR* 2.7 27.7 + - + +
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Residues in contact with ALA 472 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60L VAL* 5.8 3.8 - - + -
468T ALA 3.3 16.7 + - - +
469T ARG* 3.5 8.3 + - - +
470T LEU 3.3 0.2 - - - -
471T GLU* 1.3 79.7 - - - +
473T GLU* 1.3 55.5 + - - +
474T VAL 3.5 0.2 - - - -
475T PHE* 3.7 9.6 - - - +
476T ARG* 3.1 27.0 + - - +
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Residues in contact with GLU 473 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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469T ARG 3.3 12.4 + - - +
470T LEU* 3.7 17.1 - - + +
471T GLU 3.3 0.2 - - - -
472T ALA* 1.3 76.2 - - - +
474T VAL* 1.3 64.7 + - + +
476T ARG* 3.4 37.9 + - - +
477T LEU* 3.5 27.2 + - + +
531T LYS* 4.0 36.7 - - + -
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Residues in contact with VAL 474 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57L GLY* 6.5 0.7 - - - -
470T LEU 3.6 17.4 + - - +
471T GLU* 3.8 4.9 + - - +
473T GLU* 1.3 76.0 - - - +
475T PHE* 1.3 60.9 + - + +
477T LEU* 2.8 23.6 + - - +
478T ALA* 4.8 1.4 - - - +
482T PHE* 4.7 24.2 - - + -
528T ILE* 4.0 29.0 - - + +
531T LYS* 4.0 26.2 - - + +
532T ILE* 5.1 12.1 - - + -
535T TYR* 5.1 6.3 - - + -
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Residues in contact with PHE 475 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59L PRO* 4.0 34.8 - - + -
60L VAL* 3.9 30.1 - - + -
61L ARG* 4.8 2.7 - - - -
471T GLU* 3.5 19.9 + - + +
472T ALA* 3.7 10.1 - - - +
473T GLU 3.2 0.4 - - - -
474T VAL* 1.3 80.3 - - + +
476T ARG* 1.3 61.2 + - - +
477T LEU 3.7 4.8 - - - +
479T GLY 3.9 13.9 - - - +
480T HIS 5.8 0.2 - - - -
481T PRO* 3.8 41.7 - - + +
482T PHE* 4.2 14.4 - + - -
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Residues in contact with ARG 476 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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472T ALA 3.1 18.5 + - - +
473T GLU* 3.4 30.5 + - - +
474T VAL 3.3 0.2 - - - -
475T PHE* 1.3 78.6 - - - +
477T LEU* 1.3 86.4 + - + +
479T GLY* 4.5 5.0 + - - -
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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
------------------------------------------------------------
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