Contacts of the helix formed by residues 459 - 480 (chain X) in PDB entry 2W6C
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 459 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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428X SER* 3.5 25.4 - - - +
454X LYS* 5.7 1.1 - - - -
457X ASN 5.6 0.2 - - - +
458X TYR* 1.3 79.0 - - - +
460X ALA* 1.3 62.8 + - - +
461X GLU* 3.3 21.0 + - - +
462X GLU* 3.1 30.4 + - - +
463X GLU* 3.2 17.7 + - - +
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Residues in contact with ALA 460 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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454X LYS* 5.7 3.6 - - - +
458X TYR 3.9 0.2 + - - -
459X THR* 1.3 76.1 - - - +
461X GLU* 1.3 66.9 + - - +
463X GLU* 3.2 14.2 + - - +
464X ALA* 3.0 25.6 + - - +
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Residues in contact with GLU 461 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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459X THR* 3.4 23.0 + - - +
460X ALA* 1.3 85.0 + - - +
462X GLU* 1.3 58.6 + - - +
464X ALA* 3.7 8.0 - - + +
465X LEU* 3.0 27.5 + - - +
507X THR* 3.6 30.3 - - + +
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Residues in contact with GLU 462 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425X HIS* 2.5 42.5 + - + +
427X ALA* 3.4 1.4 - - - -
428X SER* 2.8 42.3 + - - -
446X PHE* 3.7 17.3 - - + -
451X PRO* 3.9 2.6 - - - +
458X TYR* 3.3 25.0 - - + +
459X THR* 3.1 29.8 + - - +
460X ALA 3.1 0.4 - - - -
461X GLU* 1.3 77.3 - - - +
463X GLU* 1.3 64.7 + - - +
465X LEU* 3.3 0.6 + - - -
466X SER* 3.0 22.9 + - - -
507X THR* 4.3 2.9 - - + -
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Residues in contact with GLU 463 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451X PRO* 3.5 26.6 - - - +
452X LEU* 4.0 8.9 - - + +
454X LYS* 2.8 35.9 + - - -
459X THR 3.2 13.3 + - - +
460X ALA* 3.2 13.3 + - - +
462X GLU* 1.3 75.9 - - - +
464X ALA* 1.3 64.5 + - + +
466X SER* 3.4 3.7 + - - -
467X ARG* 3.0 58.7 + - - +
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Residues in contact with ALA 464 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460X ALA 3.0 15.7 + - - +
461X GLU* 3.7 9.6 - - + +
462X GLU 3.1 0.2 - - - -
463X GLU* 1.3 79.3 - - + +
465X LEU* 1.3 65.2 + - - +
467X ARG* 3.0 10.2 + - - +
468X ARG* 3.0 25.1 + - + +
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Residues in contact with LEU 465 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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423X PHE* 4.5 8.1 - - + -
425X HIS* 4.2 13.0 - - + -
446X PHE* 3.9 21.5 - - + -
461X GLU 3.0 17.2 + - - +
462X GLU 3.3 3.1 + - - +
464X ALA* 1.3 72.9 - - - +
466X SER* 1.3 68.9 + - - +
468X ARG* 2.9 34.0 + - - +
469X ILE* 2.8 43.8 + - + +
505X LEU* 4.2 1.8 - - - -
506X ASN* 3.9 35.0 - - - +
507X THR* 4.1 10.5 - - + +
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Residues in contact with SER 466 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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446X PHE* 2.9 33.2 + - - +
449X GLY* 3.2 20.3 - - - -
451X PRO* 3.6 20.5 - - - +
452X LEU* 4.1 3.8 - - - +
462X GLU 3.0 13.2 + - - -
463X GLU 3.6 9.0 - - - -
465X LEU* 1.3 77.9 - - - +
467X ARG* 1.3 62.1 + - - +
469X ILE* 3.3 2.0 + - - +
470X MET* 3.0 27.9 + - - +
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Residues in contact with ARG 467 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23X LEU* 4.6 5.7 - - - +
138X THR* 4.0 19.5 + - + +
139X GLU* 4.6 1.3 - - - +
452X LEU* 3.2 35.3 - - + +
463X GLU* 3.0 45.0 + - - +
464X ALA* 3.0 11.9 + - - +
466X SER* 1.3 75.2 - - - +
468X ARG* 1.3 66.1 + - - +
470X MET* 4.2 9.9 - - + +
471X HIS* 3.1 25.1 + - - +
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Residues in contact with ARG 468 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464X ALA* 3.0 15.4 + - + +
465X LEU* 2.9 21.2 + - - +
467X ARG* 1.3 75.4 - - - +
469X ILE* 1.3 59.8 + - + +
471X HIS* 3.3 4.6 + - - +
472X TYR* 2.9 54.4 + - + -
504X ASP 4.3 2.6 + - - -
505X LEU* 4.1 13.2 - - - +
506X ASN 3.5 25.1 + - - +
507X THR* 5.1 3.2 + - - +
508X GLU 4.9 2.4 + - - -
509X PRO* 6.1 0.4 - - - +
510X MET* 3.1 43.2 - - - +
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Residues in contact with ILE 469 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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423X PHE* 4.2 13.5 - - + -
443X GLU* 6.1 0.7 - - + -
446X PHE* 4.2 16.4 - - + +
447X VAL* 3.8 29.6 - - + -
465X LEU* 2.8 42.2 + - + +
466X SER* 3.8 4.5 - - - +
467X ARG 3.2 0.4 - - - -
468X ARG* 1.3 78.7 - - + +
470X MET* 1.3 57.9 + - - +
472X TYR* 3.1 5.4 + - + -
473X TRP* 2.8 52.2 + - + +
505X LEU* 3.9 28.9 - - + -
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Residues in contact with MET 470 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134X TYR 4.4 5.2 - - - +
135X LEU* 3.3 35.0 - - + +
138X THR* 4.3 12.3 - - + +
139X GLU* 3.2 8.4 - - + +
446X PHE 4.0 3.6 - - - +
447X VAL 3.2 22.2 - - - +
448X PHE 4.2 2.5 - - - -
449X GLY* 3.6 29.4 - - - -
452X LEU* 4.1 25.4 - - + -
466X SER* 3.0 24.7 + - - +
467X ARG* 4.2 10.8 - - + +
469X ILE* 1.3 74.6 - - - +
471X HIS* 1.3 60.0 + - - +
473X TRP* 4.0 5.0 - - - +
474X ALA* 2.8 33.1 + - - +
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Residues in contact with HIS 471 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139X GLU* 2.6 35.0 + - - +
467X ARG 3.1 16.8 + - - +
468X ARG* 4.1 4.0 - - - +
470X MET* 1.3 76.7 - - - +
472X TYR* 1.3 56.9 + + + +
475X THR* 2.6 63.2 + - - -
482X PRO 5.5 2.5 - - - -
484X GLU* 3.4 35.6 + - + +
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Residues in contact with TYR 472 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320X LEU* 5.0 0.4 - - - -
468X ARG* 2.9 38.0 + - + -
469X ILE* 3.4 9.2 - - - +
471X HIS* 1.3 74.7 - + - +
473X TRP* 1.3 75.7 + + + +
476X PHE* 2.8 28.7 + - - +
482X PRO* 3.3 30.4 - - + +
483X ASN* 4.5 13.0 - - - -
490X SER 4.2 7.4 + - - -
492X TRP* 3.6 34.6 - + + +
503X ILE* 4.6 0.2 - - + -
505X LEU* 4.0 14.1 - - + -
510X MET* 2.8 39.6 - - + +
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Residues in contact with TRP 473 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112X MET* 4.1 11.6 - - + +
135X LEU* 5.8 3.1 - - + -
197X PHE* 4.0 10.1 - + - -
223X ILE* 3.5 30.4 - - + +
225X GLN* 2.8 27.4 + - + -
320X LEU* 4.0 9.2 - - + -
421X TYR* 3.5 42.0 - + - -
443X GLU* 5.6 0.9 - - + -
447X VAL* 3.7 34.8 - - + +
469X ILE* 2.8 42.2 + - + +
470X MET* 4.0 6.1 - - - +
472X TYR* 1.3 78.9 - + + +
474X ALA* 1.3 57.4 + - - +
476X PHE* 3.6 6.1 - - - +
477X ALA* 2.8 27.9 + - - +
492X TRP* 4.1 21.8 - + - -
505X LEU* 4.3 11.7 - - + -
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Residues in contact with ALA 474 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110X THR* 4.8 1.7 - - - +
112X MET* 4.4 8.7 - - - -
135X LEU* 5.2 1.3 - - + -
139X GLU* 3.3 34.8 - - + +
141X VAL* 4.1 13.1 - - + +
470X MET 2.8 20.5 + - - +
473X TRP* 1.3 73.9 - - - +
475X THR* 1.3 62.2 + - - +
477X ALA* 3.2 7.4 + - - +
478X LYS* 2.9 29.6 + - - +
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Residues in contact with THR 475 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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471X HIS* 2.6 50.0 + - - -
472X TYR 3.9 0.2 - - - -
474X ALA* 1.3 77.7 - - - +
476X PHE* 1.3 63.3 + - - +
478X LYS* 3.3 6.8 + - + -
479X THR* 2.9 40.0 + - + +
481X ASN 3.2 14.6 - - - +
482X PRO 3.9 14.1 - - - +
483X ASN 3.9 13.5 - - - +
484X GLU* 4.7 9.8 + - - +
485X PRO* 5.9 0.4 - - + -
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Residues in contact with PHE 476 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195X THR* 4.6 2.2 - - + -
221X ARG* 3.1 25.2 + - + -
222X ALA 3.6 18.2 - - - -
223X ILE* 3.7 24.9 - - + -
318X GLN* 3.7 27.8 - - + -
319X ILE* 3.7 10.8 - - - -
320X LEU* 3.7 41.5 - - + -
419X TYR* 4.4 3.8 - + - -
472X TYR 2.8 18.8 + - - +
473X TRP 3.6 1.6 - - - +
475X THR* 1.3 75.4 - - - +
477X ALA* 1.3 65.6 + - - +
480X GLY* 2.7 44.4 + - - -
481X ASN 3.5 9.1 + - - -
482X PRO* 3.8 13.5 - - + -
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Residues in contact with ALA 477 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110X THR* 3.8 15.8 - - + +
112X MET* 4.0 14.8 - - + -
193X THR* 3.6 11.3 - - - +
195X THR* 3.0 36.7 + - + +
221X ARG* 3.0 19.2 + - - -
473X TRP 2.8 20.9 + - - +
474X ALA 3.2 5.3 + - - +
476X PHE* 1.3 77.8 - - - +
478X LYS* 1.3 56.7 + - - +
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Residues in contact with LYS 478 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110X THR* 3.0 26.4 - - - +
141X VAL* 6.1 0.4 - - + -
193X THR* 4.1 7.1 - - - +
221X ARG* 3.3 8.8 + - - -
474X ALA 2.9 16.2 + - - +
475X THR* 3.9 7.4 - - + +
477X ALA* 1.3 76.3 - - - +
479X THR* 1.3 68.8 + - + +
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Residues in contact with THR 479 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221X ARG* 3.5 10.8 + - - +
318X GLN* 5.3 0.7 - - - -
475X THR* 2.9 27.7 + - + +
478X LYS* 1.3 99.9 - - + +
480X GLY* 1.3 59.8 + - - +
481X ASN* 3.0 25.9 + - - +
483X ASN 5.1 1.1 + - - +
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Residues in contact with GLY 480 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221X ARG* 3.1 27.4 - - - -
318X GLN* 3.4 24.1 - - - +
419X TYR* 3.8 12.5 + - - -
476X PHE* 2.7 30.5 + - - -
479X THR* 1.3 71.0 - - - +
481X ASN* 1.3 57.5 + - - +
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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