Contacts of the helix formed by residues 481 - 500 (chain C) in PDB entry 4QGC
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 481 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479C GLN* 3.9 3.1 - - - +
480C GLU* 1.3 82.3 - - + +
482C TRP* 1.3 65.5 + - - +
483C ALA* 4.7 2.0 - - + +
484C GLU* 3.2 28.2 + - + +
485C ASP* 3.0 21.1 + - - +
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Residues in contact with TRP 482 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479C GLN 5.2 0.7 - - - -
480C GLU 3.7 4.0 + - - -
481C ALA* 1.3 72.5 - - - +
483C ALA* 1.3 74.0 + - + +
485C ASP* 3.0 8.5 + - + +
486C VAL* 2.9 43.7 + - + +
489C ARG* 4.8 2.5 - - - -
513C THR* 4.5 2.2 - - - -
514C GLY* 3.2 32.1 - - - -
515C TRP* 3.1 29.8 - + - -
516C ARG* 3.8 9.5 + - - -
517C PRO* 3.5 44.4 - - + -
1003C SO4 2.9 33.1 + - - -
482D TRP* 6.2 1.1 - + - -
515D TRP* 3.5 34.8 - + - -
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Residues in contact with ALA 483 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481C ALA* 3.4 2.1 - - + +
482C TRP* 1.3 92.6 - - + +
484C GLU* 1.3 57.3 + - + +
486C VAL* 3.6 2.0 + - - +
487C ASP* 3.0 34.0 + - - +
482D TRP* 6.0 6.1 - - + -
515D TRP* 4.3 14.2 - - + +
516D ARG* 3.4 26.5 - - - +
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Residues in contact with GLU 484 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479C GLN* 4.4 14.9 - - + +
481C ALA* 3.2 27.3 + - + +
482C TRP 3.1 0.8 - - - -
483C ALA* 1.3 78.9 - - + +
485C ASP* 1.3 57.2 + - - +
487C ASP* 3.4 6.7 + - - +
488C LEU* 3.0 27.0 + - - +
516D ARG* 3.5 23.3 + - - +
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Residues in contact with ASP 485 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455C ARG* 2.8 41.4 + - - -
478C VAL* 3.3 8.6 - - + +
479C GLN* 2.8 41.9 + - + +
481C ALA 3.0 11.2 + - - +
482C TRP* 3.0 12.1 + - + +
484C GLU* 1.3 74.2 - - - +
486C VAL* 1.3 65.0 + - - +
488C LEU* 3.5 3.7 + - - +
489C ARG* 3.2 41.6 + - - +
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Residues in contact with VAL 486 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431C LEU* 4.0 7.6 - - + -
482C TRP* 2.9 54.4 + - + +
483C ALA 3.8 5.2 - - - +
485C ASP* 1.3 76.8 - - - +
487C ASP* 1.3 57.6 + - - +
489C ARG* 3.2 21.5 + - - +
490C VAL* 2.9 34.0 + - + +
513C THR* 3.9 19.1 - - + -
526C ARG* 3.9 15.7 - - - +
1003C SO4 4.5 0.2 - - - +
515D TRP* 3.8 20.9 - - + -
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Residues in contact with ASP 487 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483C ALA 3.0 9.8 + - - +
484C GLU* 3.7 8.7 - - - +
486C VAL* 1.3 76.9 - - - +
488C LEU* 1.3 57.0 + - - +
490C VAL* 3.9 6.7 - - - +
491C ASN* 2.9 32.6 + - - +
526C ARG* 4.5 6.2 + - - -
515D TRP* 3.1 24.7 + - - -
516D ARG* 2.7 36.8 + - - +
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Residues in contact with LEU 488 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455C ARG* 4.5 7.4 - - - +
474C CYS* 5.5 1.3 - - - -
476C ASP* 3.6 37.5 - - + +
477C PRO 4.2 4.0 - - - +
479C GLN* 3.6 33.7 - - + +
484C GLU 3.0 17.4 + - - +
485C ASP 3.6 6.1 - - - +
486C VAL 3.2 0.4 - - - -
487C ASP* 1.3 77.7 - - - +
489C ARG* 1.3 62.0 + - - +
491C ASN* 3.9 6.4 - - + +
492C PHE* 3.1 23.4 + - + +
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Residues in contact with ARG 489 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431C LEU* 3.7 36.1 - - + +
432C THR 5.3 2.6 + - - +
433C LYS* 5.7 2.2 - - - +
453C VAL* 3.9 30.7 + - + +
454C THR* 6.1 1.1 - - - +
455C ARG* 3.7 25.4 - - - +
474C CYS* 4.2 17.5 - - - -
482C TRP* 4.4 2.0 - - - +
485C ASP* 3.2 31.0 + - - +
486C VAL* 3.2 26.8 + - - +
488C LEU* 1.3 77.7 - - - +
490C VAL* 1.3 65.1 + - - +
492C PHE* 3.4 8.8 + - - +
493C ALA* 3.2 20.3 + - - +
1003C SO4 2.8 44.1 + - - -
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Residues in contact with VAL 490 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429C ILE* 4.3 6.5 - - + +
431C LEU* 4.3 9.9 - - + -
486C VAL* 2.9 33.2 + - + +
487C ASP* 3.9 6.3 - - - +
489C ARG* 1.3 74.8 - - - +
491C ASN* 1.3 61.3 + - - +
493C ALA* 3.0 9.4 + - - +
494C MET* 2.9 47.6 + - + +
511C VAL* 3.9 37.0 - - + -
526C ARG* 4.2 10.5 - - - +
528C VAL* 5.6 1.8 - - + -
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Residues in contact with ASN 491 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487C ASP 2.9 18.2 + - - +
488C LEU* 3.9 8.2 - - + +
490C VAL* 1.3 76.8 - - - +
492C PHE* 1.3 63.0 + - - +
494C MET* 3.2 15.3 + - - +
495C ASN* 3.0 44.0 + - - +
498C LYS* 5.9 0.7 + - - -
531C PRO* 5.4 6.2 - - - +
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Residues in contact with PHE 492 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102C PRO* 3.6 34.3 - - + -
103C ILE* 3.7 27.6 - - + -
453C VAL* 4.5 4.5 - - + -
472C VAL* 3.9 32.8 - - + -
473C LEU 3.9 18.6 - - - -
474C CYS* 4.1 18.2 - - + -
475C LYS 6.0 0.2 - - - -
476C ASP* 4.7 15.9 - - - +
488C LEU* 3.1 15.2 + - + +
489C ARG* 3.5 10.1 - - - +
491C ASN* 1.3 77.8 - - - +
493C ALA* 1.3 61.3 + - - +
495C ASN* 3.4 8.2 + - + +
496C VAL* 3.1 34.8 + - + +
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Residues in contact with ALA 493 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429C ILE* 3.7 27.1 - - + -
451C ILE* 3.8 20.2 - - + +
453C VAL* 3.6 27.6 - - + -
472C VAL* 5.3 0.4 - - - -
489C ARG 3.2 2.9 + - - +
490C VAL 3.0 9.5 + - - +
492C PHE* 1.3 76.2 - - - +
494C MET* 1.3 60.9 + - - +
496C VAL* 3.4 5.5 + - - +
497C GLY* 2.9 26.0 + - - -
503C PHE* 4.0 0.7 - - - -
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Residues in contact with MET 494 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429C ILE* 4.3 4.3 - - + -
490C VAL* 2.9 33.1 + - + +
491C ASN* 3.3 22.7 - - - +
493C ALA* 1.3 76.8 - - - +
495C ASN* 1.3 57.4 + - - +
497C GLY 3.2 1.2 + - - -
498C LYS* 2.9 40.9 + - - +
503C PHE* 3.5 22.7 - - - -
509C VAL* 3.6 31.2 - - + -
528C VAL* 3.6 23.6 - - + -
529C PRO 4.0 8.5 - - - +
530C VAL* 4.3 3.6 - - - -
531C PRO* 4.0 20.4 - - + -
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Residues in contact with ASN 495 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103C ILE* 3.9 28.3 - - + +
491C ASN* 3.0 37.3 + - - +
492C PHE* 3.8 7.7 - - - +
494C MET* 1.3 76.9 - - - +
496C VAL* 1.3 61.3 + - - +
498C LYS* 3.9 20.3 + - - +
499C ALA* 3.0 30.3 + - - +
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Residues in contact with VAL 496 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103C ILE* 3.8 37.7 - - + +
451C ILE* 5.1 4.9 - - + -
470C PHE* 3.8 22.4 - - + -
472C VAL* 3.7 32.5 - - + -
492C PHE* 3.1 30.2 + - + +
493C ALA* 3.7 6.7 - - - +
495C ASN* 1.3 75.7 - - - +
497C GLY* 1.3 58.1 + - - +
499C ALA* 3.3 1.6 + - - +
500C ARG* 2.9 33.1 + - + +
502C PHE* 5.5 0.2 - - + -
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Residues in contact with GLY 497 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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451C ILE* 4.2 2.0 - - - +
493C ALA 2.9 11.8 + - - -
494C MET 3.2 0.4 + - - -
496C VAL* 1.3 77.8 - - - +
498C LYS* 1.3 55.8 + - - +
500C ARG 3.6 0.2 + - - -
501C GLY 3.1 5.5 + - - -
502C PHE* 2.8 43.8 + - - +
503C PHE* 3.5 31.5 + - - -
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Residues in contact with LYS 498 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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491C ASN* 5.9 0.8 + - - -
494C MET* 2.9 27.5 + - - +
495C ASN* 4.0 22.3 + - - +
497C GLY* 1.3 73.7 - - - +
499C ALA* 1.3 64.8 + - - +
501C GLY* 3.4 10.7 + - - -
503C PHE* 3.6 27.7 - - + +
504C LYS* 4.2 4.7 - - - -
505C LYS* 4.5 8.1 - - + +
530C VAL* 4.4 8.3 - - + +
531C PRO* 3.1 32.6 + - - +
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Residues in contact with ALA 499 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103C ILE* 4.1 18.6 - - + -
104C LEU* 4.3 16.8 - - + +
495C ASN 3.0 18.6 + - - +
496C VAL 3.3 4.2 + - - +
498C LYS* 1.3 77.7 - - - +
500C ARG* 1.3 65.2 + - + +
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Residues in contact with ARG 500 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103C ILE 5.0 3.6 + - - +
104C LEU* 3.0 47.8 + - - +
106C ARG* 3.3 20.7 - - - +
470C PHE* 3.8 33.7 - - + -
496C VAL* 2.9 21.8 + - + +
497C GLY 4.2 0.7 - - - +
499C ALA* 1.3 80.4 - - + +
501C GLY* 1.3 60.8 + - - +
502C PHE* 3.3 28.8 + - + -
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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