Contacts of the helix formed by residues 460 - 479 (chain A) in PDB entry 1ACL
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 ALA 460 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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454A LYS* 6.2 0.9 - - - +
459A THR* 1.3 74.1 - - - +
461A GLU* 1.3 68.1 + - + +
463A GLU* 3.0 14.2 + - + +
464A ALA* 3.0 20.8 + - - +
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Residues in contact with GLU 461 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459A THR* 3.2 7.9 + - - +
460A ALA* 1.3 80.4 - - + +
462A GLU* 1.3 57.1 + - - +
464A ALA* 3.3 8.2 + - - +
465A LEU* 2.8 22.2 + - - +
507A THR* 3.5 29.8 - - + +
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Residues in contact with GLU 462 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425A HIS* 2.7 40.0 + - + +
427A ALA* 3.4 0.5 - - - -
428A SER* 2.8 44.2 + - - -
446A PHE* 3.5 19.7 - - + -
451A PRO* 3.9 1.6 - - + -
458A TYR* 3.2 22.3 - - + -
459A THR* 2.8 29.5 + - - +
461A GLU* 1.3 75.4 - - - +
463A GLU* 1.4 68.1 + - - +
465A LEU* 4.1 2.2 - - - +
466A SER* 2.8 24.9 + - - -
507A THR* 4.4 0.9 - - + -
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Residues in contact with GLU 463 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451A PRO* 3.2 22.1 - - - +
452A LEU* 3.2 27.3 - - + +
454A LYS* 2.9 34.1 + - - +
459A THR 3.2 6.0 + - - +
460A ALA* 3.0 19.3 + - - +
462A GLU* 1.4 76.2 - - - +
464A ALA* 1.3 67.2 + - - +
466A SER* 3.1 2.9 + - - -
467A ARG* 2.9 50.7 + - - +
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Residues in contact with ALA 464 (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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460A ALA 3.0 11.7 + - - +
461A GLU* 3.4 12.3 - - - +
463A GLU* 1.3 80.8 - - - +
465A LEU* 1.3 62.6 + - - +
467A ARG* 2.9 18.7 + - - +
468A ARG* 2.9 19.4 + - + +
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Residues in contact with LEU 465 (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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423A PHE* 4.0 11.2 - - + -
425A HIS* 3.9 23.1 - - + -
446A PHE* 4.1 9.6 - - + -
461A GLU 2.8 19.4 + - - +
462A GLU 3.1 4.4 + - - +
464A ALA* 1.3 72.2 - - - +
466A SER* 1.4 58.6 + - - +
468A ARG* 3.4 20.4 + - - +
469A ILE* 2.9 46.8 + - + +
505A LEU* 4.3 5.2 - - + -
506A ASN* 3.4 33.9 - - - +
507A THR* 3.7 30.7 - - + +
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Residues in contact with SER 466 (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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446A PHE* 3.0 27.6 + - - -
449A GLY* 3.4 20.3 - - - -
451A PRO* 3.7 21.3 - - - +
452A LEU* 3.7 8.0 - - - +
462A GLU 2.8 12.3 + - - -
463A GLU* 3.3 9.4 - - - -
465A LEU* 1.4 76.4 - - - +
467A ARG* 1.3 65.1 + - - +
469A ILE* 3.7 1.7 - - - +
470A MET* 2.9 29.2 + - - +
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Residues in contact with ARG 467 (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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23A LEU* 4.7 10.5 - - - +
137A TYR* 6.1 1.4 - - - -
138A THR* 4.7 15.9 + - + +
139A GLU* 5.1 0.7 - - - +
452A LEU* 3.2 33.4 - - + +
463A GLU* 2.9 38.4 + - - +
464A ALA* 2.9 8.9 + - - +
466A SER* 1.3 79.5 - - - +
468A ARG* 1.4 63.1 + - - +
470A MET* 3.3 15.2 + - + +
471A HIS* 2.9 25.5 + - - +
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Residues in contact with ARG 468 (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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464A ALA* 2.9 19.1 + - + +
465A LEU* 3.6 15.9 - - + +
467A ARG* 1.4 76.3 - - - +
469A ILE* 1.3 64.1 + - + +
471A HIS* 3.6 5.3 - - - +
472A TYR* 2.9 48.0 + - + -
504A ASP 4.3 0.6 + - - -
505A LEU* 3.3 28.3 - - - +
506A ASN 2.8 27.9 + - - -
507A THR* 4.9 1.6 - - - +
508A GLU 3.5 15.0 + - - +
509A PRO* 5.0 0.8 - - - +
510A MET* 3.3 36.1 - - - +
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Residues in contact with ILE 469 (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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423A PHE* 4.8 11.9 - - + -
443A GLU* 6.2 1.8 - - + -
446A PHE* 4.6 6.3 - - + +
447A VAL* 3.5 43.3 - - + +
465A LEU* 2.9 35.3 + - + +
466A SER* 3.7 5.6 - - - +
468A ARG* 1.3 81.3 - - - +
470A MET* 1.4 67.2 + - - +
472A TYR* 2.9 19.3 + - - +
473A TRP* 2.9 28.7 + - + -
505A LEU* 3.3 40.8 - - + -
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Residues in contact with MET 470 (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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134A TYR 4.4 1.6 - - - +
135A LEU* 3.4 33.0 - - + +
138A THR* 3.6 31.9 - - + +
139A GLU* 3.7 7.2 - - + +
446A PHE 3.9 4.5 - - - +
447A VAL 3.3 18.6 - - - +
448A PHE 4.3 0.9 - - - -
449A GLY* 3.6 25.8 - - - -
452A LEU* 3.7 21.1 - - + -
466A SER 2.9 25.5 + - - +
467A ARG* 4.0 12.3 - - + +
469A ILE* 1.4 73.1 - - - +
471A HIS* 1.3 56.7 + - - +
473A TRP* 3.5 6.5 - - - +
474A ALA* 2.9 29.8 + - - +
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Residues in contact with HIS 471 (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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139A GLU* 3.2 25.8 + - - +
467A ARG 2.9 17.7 + - - +
468A ARG* 3.6 6.1 - - - +
470A MET* 1.3 73.3 - - - +
472A TYR* 1.3 64.2 + + + +
473A TRP 2.9 1.7 + - - -
474A ALA 3.0 0.5 + - - -
475A THR* 2.6 60.9 + - + -
482A PRO 4.9 3.4 - - - -
483A ASN* 5.9 0.4 - - - -
484A GLU* 3.8 27.0 - - + +
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Residues in contact with TYR 472 (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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320A LEU* 4.7 0.6 - - - +
468A ARG* 2.9 62.9 + - + -
469A ILE* 2.9 9.7 + - - +
471A HIS* 1.3 81.7 - + - +
473A TRP* 1.3 64.4 + + + +
476A PHE* 2.8 30.5 + - - +
482A PRO* 3.4 27.7 - - + +
483A ASN* 4.5 15.7 - - + -
490A SER 4.3 1.9 + - - -
492A TRP* 3.5 43.5 - + + -
503A ILE* 4.9 0.2 - - + -
505A LEU* 4.0 10.1 - - + -
510A MET* 3.3 25.8 - - + +
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Residues in contact with TRP 473 (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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112A MET* 4.8 9.9 - - + -
135A LEU* 5.7 1.3 - - + -
197A PHE* 4.1 8.3 - + - -
223A ILE* 3.5 32.2 - - + +
225A GLN* 2.8 33.0 - - - +
320A LEU* 3.8 15.9 - - + -
421A TYR* 3.6 34.5 - + - -
443A GLU* 6.0 0.4 - - + -
447A VAL* 3.7 25.6 - - + +
469A ILE* 2.9 40.8 + - + +
470A MET* 3.5 8.1 - - - +
471A HIS 2.9 0.6 + - - -
472A TYR* 1.3 82.3 - + + +
474A ALA* 1.4 59.7 + - - +
476A PHE* 3.0 8.6 + - - +
477A ALA* 2.8 27.4 + - - +
492A TRP* 4.0 14.8 - + - -
505A LEU* 3.9 22.2 - - + -
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Residues in contact with ALA 474 (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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110A THR* 5.1 0.9 - - - +
112A MET* 4.4 8.7 - - + +
139A GLU* 3.3 42.8 - - + +
141A VAL* 3.9 16.6 - - + +
470A MET 2.9 10.4 + - - +
473A TRP* 1.4 68.8 - - - +
475A THR* 1.3 69.0 + - - +
477A ALA* 2.9 23.4 + - - +
478A LYS* 3.4 11.4 + - + +
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Residues in contact with THR 475 (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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139A GLU* 4.5 0.9 + - - -
471A HIS* 2.6 49.5 + - - +
474A ALA* 1.3 73.6 - - - +
476A PHE* 1.3 60.1 + - - -
478A LYS* 4.4 7.1 - - - +
479A THR* 3.1 29.3 + - - +
481A ASN 2.9 16.8 - - - +
482A PRO 3.4 22.0 - - - +
483A ASN 4.0 1.1 - - - -
484A GLU* 3.9 25.0 - - + +
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Residues in contact with PHE 476 (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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195A THR* 4.8 0.4 - - + -
221A ARG* 3.3 19.4 - - + -
222A ALA 3.5 17.9 - - - -
223A ILE* 4.0 19.7 - - + -
318A GLN* 3.6 24.2 - - + -
319A ILE 3.5 22.2 - - - -
320A LEU* 3.6 20.9 - - + -
419A TYR* 3.9 14.6 - + - -
472A TYR 2.8 25.8 + - - +
473A TRP* 3.0 3.1 + - - +
475A THR* 1.3 75.3 - - - +
477A ALA* 1.3 63.4 + - - +
478A LYS 2.8 1.3 + - - -
480A GLY 2.8 53.5 + - - -
481A ASN* 3.2 16.5 + - - -
482A PRO* 3.7 7.4 - - + -
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Residues in contact with ALA 477 (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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110A THR* 3.0 23.8 - - + +
112A MET* 3.5 30.7 - - + -
141A VAL* 5.9 0.2 - - + -
193A THR* 3.5 2.3 - - - +
195A THR* 3.2 28.0 + - + +
221A ARG* 2.7 21.0 + - - +
223A ILE* 5.3 0.2 - - + -
473A TRP 2.8 7.8 + - - +
474A ALA* 2.9 11.1 + - - +
476A PHE* 1.3 78.2 - - + +
478A LYS* 1.4 51.4 + - - +
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Residues in contact with LYS 478 (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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110A THR* 3.5 25.8 - - + +
141A VAL* 6.5 0.9 - - + -
193A THR* 3.9 8.9 - - + +
221A ARG* 2.9 18.2 + - - +
474A ALA* 3.7 13.7 - - + +
475A THR* 3.8 6.1 - - - +
476A PHE 2.8 2.2 + - - -
477A ALA* 1.4 74.6 - - - +
479A THR* 1.3 86.1 + - - +
480A GLY 3.1 1.1 - - - -
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Residues in contact with THR 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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221A ARG* 3.7 2.5 + - - -
475A THR* 3.1 24.8 + - + +
478A LYS* 1.3 88.8 - - - +
480A GLY* 1.3 59.1 + - - +
481A ASN* 2.9 33.7 - - + +
483A ASN 5.0 0.7 - - - +
484A GLU* 6.0 1.6 - - - -
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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
------------------------------------------------------------
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