Contacts of the helix formed by residues 466 - 486 (chain D) in PDB entry 1C2O
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 THR 466 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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435D SER* 3.9 12.3 - - - +
465D TYR* 1.3 80.8 - - - +
467D THR* 1.3 54.5 + - - +
468D GLU* 3.3 26.1 + - - +
469D GLU* 2.8 41.2 + - - +
470D ARG* 2.7 35.2 + - - +
515D LEU* 5.5 0.7 - - - +
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Residues in contact with THR 467 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466D THR* 1.3 73.1 - - - +
468D GLU* 1.3 61.0 + - - +
470D ARG* 3.0 44.4 + - - +
471D ILE* 2.7 51.9 + - + +
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Residues in contact with GLU 468 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466D THR* 3.3 19.7 + - - +
467D THR* 1.3 90.6 + - - +
469D GLU* 1.3 51.3 + - - +
471D ILE* 3.0 16.5 + - + +
472D PHE* 2.5 38.9 + - - +
515D LEU* 4.2 25.3 - - + +
516D LYS* 6.2 2.2 - - - +
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Residues in contact with GLU 469 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432D HIS* 2.7 33.2 + - + +
434D ALA* 3.4 5.5 - - - -
435D SER* 2.4 47.8 + - - -
453D PHE* 3.6 15.9 - - + -
458D PRO* 4.0 3.5 - - - +
465D TYR* 3.5 16.9 - - + +
466D THR* 2.8 43.3 + - + +
468D GLU* 1.3 74.3 - - + +
470D ARG* 1.3 51.5 + - - +
472D PHE* 3.1 10.0 - - - +
473D ALA* 2.7 35.3 + - - +
515D LEU* 4.6 1.8 - - + +
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Residues in contact with ARG 470 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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458D PRO* 4.0 21.4 + - - +
459D LEU* 4.4 21.8 + - + +
461D PRO* 5.7 10.9 - - - +
465D TYR* 5.9 0.4 + - + -
466D THR 2.7 15.6 + - - +
467D THR* 3.1 43.7 + - - +
469D GLU* 1.3 70.0 - - - +
471D ILE* 1.3 68.6 + - - +
473D ALA* 3.1 5.2 + - - +
474D GLN* 2.9 45.3 + - + +
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Residues in contact with ILE 471 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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467D THR* 2.7 42.4 + - + +
468D GLU* 3.4 12.3 - - + +
470D ARG* 1.3 73.9 - - + +
472D PHE* 1.4 64.7 - - - +
474D GLN* 3.0 19.4 + - + +
475D ARG* 2.9 26.7 + - + +
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Residues in contact with PHE 472 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430D PHE* 3.9 17.7 - + - -
432D HIS* 3.3 37.2 - + + -
453D PHE* 4.2 7.2 - + - -
468D GLU 2.5 21.2 + - - +
469D GLU* 3.1 6.7 - - - +
471D ILE* 1.4 72.4 - - - +
473D ALA* 1.3 64.7 + - - +
475D ARG* 2.7 38.4 + - + +
476D LEU* 2.8 43.6 + - + -
513D LEU* 3.9 7.2 - - + -
514D ASN* 3.5 34.8 - - - -
515D LEU* 3.4 22.4 - - + -
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Residues in contact with ALA 473 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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453D PHE* 4.1 11.2 - - + +
458D PRO* 3.8 28.0 - - + -
459D LEU* 4.0 11.2 - - + -
469D GLU 2.7 16.9 + - - +
470D ARG* 3.1 11.4 - - - +
472D PHE* 1.3 72.7 - - - +
474D GLN* 1.3 53.1 + - - +
476D LEU* 2.9 14.9 + - - +
477D MET* 2.6 40.4 + - - +
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Residues in contact with GLN 474 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141D VAL* 5.7 6.8 - - + +
142D GLU* 4.5 3.4 - - - +
459D LEU* 4.3 22.7 - - + +
470D ARG* 2.9 39.3 + - - +
471D ILE* 3.3 15.2 - - + +
473D ALA* 1.3 74.7 - - - +
475D ARG* 1.3 63.9 + - - +
477D MET* 3.7 11.1 - - - +
478D LYS* 2.9 30.5 + - + +
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Residues in contact with ARG 475 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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471D ILE* 2.9 15.7 + - + +
472D PHE* 2.7 35.9 + - + +
474D GLN* 1.3 76.7 - - - +
476D LEU* 1.3 60.2 + - - +
478D LYS* 3.0 11.5 - - + +
479D TYR* 2.7 62.9 + - + +
512D SER 4.6 3.2 + - - -
513D LEU* 4.9 1.6 - - - +
514D ASN 2.9 36.3 + - - +
515D LEU* 3.8 13.9 + - - +
516D LYS 3.5 9.6 + - - -
517D PRO* 4.1 7.0 - - - +
518D LEU* 3.9 11.3 - - - +
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Residues in contact with LEU 476 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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430D PHE* 4.0 13.5 - - + -
453D PHE* 3.5 28.5 - - + -
454D ILE* 3.8 31.9 - - + -
472D PHE* 2.8 51.2 + - + +
473D ALA* 3.3 5.4 - - - +
475D ARG* 1.3 75.3 - - - +
477D MET* 1.3 63.3 + - - +
479D TYR* 2.9 18.0 + - + +
480D TRP* 3.1 24.7 + - + -
513D LEU* 3.3 31.6 - - + -
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Residues in contact with MET 477 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137D PHE* 3.8 6.1 - - - +
138D LEU* 3.2 58.3 - - + +
141D VAL* 4.6 6.1 - - + -
142D GLU* 4.1 15.0 - - + +
453D PHE 4.4 2.2 - - - +
454D ILE 4.0 12.1 + - - +
455D PHE 4.1 3.6 - - - +
456D GLY* 3.9 4.9 - - - -
459D LEU* 3.5 35.0 - - - -
473D ALA 2.6 35.6 + - - +
474D GLN* 3.7 8.3 - - - +
476D LEU* 1.3 72.9 - - - +
478D LYS* 1.3 52.1 + - - +
480D TRP* 3.4 3.7 + - - +
481D THR* 2.4 41.7 + - - +
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Residues in contact with LYS 478 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142D GLU* 3.5 26.9 + - - +
474D GLN* 2.9 16.3 + - + +
475D ARG* 3.0 17.5 - - + +
477D MET* 1.3 75.5 - - - +
479D TYR* 1.3 59.2 + - + +
481D THR* 2.9 14.0 + - - -
482D ASN* 2.9 57.8 + - - +
485D ARG* 4.2 5.6 - - - +
489D PRO 5.4 0.6 + - - -
491D ASP* 4.8 11.5 - - - +
492D PRO* 4.7 7.4 - - - -
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Residues in contact with TYR 479 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327D LEU* 5.5 0.9 - - + -
475D ARG* 2.7 69.8 + - + -
476D LEU* 2.9 12.9 + - + +
478D LYS* 1.3 77.4 - - + +
480D TRP* 1.3 61.9 + + + +
482D ASN 3.3 0.5 + - - -
483D PHE* 2.7 34.4 + - - +
489D PRO* 3.3 47.0 - - + +
490D ASN* 5.6 4.9 - - - -
498D PRO 6.1 0.9 - - - -
500D TRP* 4.2 15.3 - + + -
513D LEU* 3.8 25.6 - - + -
518D LEU* 3.7 25.5 + - + +
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Residues in contact with TRP 480 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115D LEU* 5.1 8.5 - - + +
138D LEU* 5.2 5.4 - - + -
198D THR* 5.6 0.9 - - + +
200D PHE* 4.0 21.3 - + - -
226D VAL* 3.2 33.6 - - + +
228D GLN* 3.5 14.3 + - - -
327D LEU* 3.7 19.1 - - + -
428D TYR* 3.9 37.9 - + - -
430D PHE* 6.2 0.9 - + - -
454D ILE* 3.2 43.3 - - + -
476D LEU* 3.1 45.9 + - + +
477D MET* 3.8 4.9 - - - +
479D TYR* 1.3 86.6 - - + +
481D THR* 1.3 51.7 + - - +
483D PHE* 2.9 8.9 + - - +
484D ALA* 2.6 37.2 + - - +
500D TRP* 5.2 2.7 - + - -
513D LEU* 4.7 6.7 - - + -
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Residues in contact with THR 481 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113D PRO* 5.4 0.5 - - - +
115D LEU* 4.6 9.3 - - + +
138D LEU* 4.3 13.5 - - + -
142D GLU* 3.2 30.4 + - + -
144D ALA* 4.6 9.6 - - + -
477D MET 2.4 32.6 + - - +
478D LYS* 2.9 17.2 + - - -
480D TRP* 1.3 72.3 - - - +
482D ASN* 1.3 49.9 + - - +
484D ALA* 3.0 10.4 - - - +
485D ARG* 2.6 62.4 + - - +
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Residues in contact with ASN 482 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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478D LYS* 2.9 52.0 + - - +
479D TYR 3.4 3.8 - - - +
481D THR* 1.3 74.5 + - - +
483D PHE* 1.4 61.9 + - - +
485D ARG* 3.9 16.5 + - - +
486D THR* 2.7 44.4 + - - +
488D ASP 3.4 10.1 - - - +
489D PRO 3.8 10.2 + - - +
490D ASN 3.7 19.1 + - - +
492D PRO* 3.8 17.7 - - - +
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Residues in contact with PHE 483 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198D THR* 4.7 2.5 - - + -
224D ARG* 3.1 31.9 - - + -
225D ALA 3.4 20.2 - - - -
226D VAL* 4.0 15.9 - - + -
325D GLN* 3.4 48.0 - - + -
326D VAL 3.5 8.1 - - - -
327D LEU* 3.6 24.9 - - + -
426D TYR* 4.7 6.5 - + - -
479D TYR 2.7 21.2 + - - +
480D TRP 3.6 4.5 - - - +
482D ASN* 1.4 73.6 - - - +
484D ALA* 1.3 63.5 + - - +
487D GLY* 2.9 39.2 + - - -
488D ASP 3.6 9.1 + - - +
489D PRO* 4.0 18.4 - - + -
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Residues in contact with ALA 484 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113D PRO* 4.8 10.8 - - + -
114D VAL 5.6 0.2 - - - +
115D LEU* 3.3 32.8 - - + -
196D SER* 4.4 2.3 + - - +
198D THR* 3.7 15.6 + - + +
224D ARG* 2.6 37.6 + - - -
480D TRP 2.6 17.6 + - - +
481D THR* 3.0 17.0 - - - +
483D PHE* 1.3 72.8 - - - +
485D ARG* 1.3 48.4 + - - +
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Residues in contact with ARG 485 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113D PRO* 4.3 28.6 - - + +
142D GLU* 3.1 45.3 + - - -
144D ALA* 5.9 0.8 - - - +
196D SER* 5.0 1.1 + - - -
224D ARG* 3.5 12.2 + - - +
478D LYS* 4.2 10.7 - - - +
481D THR* 2.6 46.6 + - - +
482D ASN* 3.9 19.0 + - - +
484D ALA* 1.3 76.9 - - - +
486D THR* 1.3 68.9 + - + +
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Residues in contact with THR 486 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224D ARG* 4.4 3.6 + - - -
325D GLN* 3.5 8.9 - - - +
482D ASN* 2.7 29.8 + - - +
485D ARG* 1.3 84.9 - - + +
487D GLY* 1.3 69.1 + - - +
488D ASP* 2.7 28.8 + - - +
490D ASN 5.4 2.7 - - - +
492D PRO* 5.9 4.7 - - + -
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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