Contacts of the helix formed by residues 482 - 495 (chain C) in PDB entry 3UK3
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 SER 482 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2B A 5.9 4.5 - - - -
3B T 3.8 27.1 - - - +
471C ARG* 4.0 14.5 - - - +
480C PHE* 3.3 5.5 + - - +
481C ARG* 1.3 90.9 + - - +
483C ASN* 1.3 60.8 + - - +
484C TYR* 3.6 3.0 + - - -
485C TYR* 3.1 24.3 + - - +
486C LEU* 3.0 26.2 + - - +
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Residues in contact with ASN 483 (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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2B A 5.8 3.9 + - - +
3B T 4.9 5.2 + - - +
471C ARG* 4.3 13.7 - - + +
482C SER* 1.3 72.0 - - - +
484C TYR* 1.3 65.5 + - - +
486C LEU* 3.6 18.8 - - - +
487C ASN* 3.0 26.8 + - - +
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Residues in contact with TYR 484 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B A 4.8 1.2 - - + +
3B T 3.4 74.6 + + + +
4B G 3.5 55.4 + + - +
5B C 6.0 1.3 - + - -
482C SER* 3.3 7.9 + - - +
483C ASN* 1.3 81.0 + - - +
485C TYR* 1.3 67.4 + + + +
487C ASN* 3.5 10.0 + - + +
488C ILE* 3.4 45.5 + - + +
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Residues in contact with TYR 485 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A T 3.3 0.3 - - - +
16A C 2.6 55.1 + + + -
17A T 3.5 34.5 - - + -
480C PHE* 3.6 29.4 - + + -
481C ARG* 5.1 7.2 - - + +
482C SER* 3.1 18.9 + - - +
484C TYR* 1.3 83.8 - + + +
486C LEU* 1.3 60.7 + - - +
488C ILE* 3.0 24.2 + - + +
489C HIS* 2.7 30.7 + - + +
510C GLN* 3.1 30.0 + - - -
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Residues in contact with LEU 486 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471C ARG* 3.6 27.8 - - - +
472C GLU 3.6 16.8 - - - +
473C CYS* 3.8 25.6 - - + +
480C PHE* 3.8 26.9 - - + +
482C SER 3.0 17.8 + - - +
483C ASN* 3.3 17.7 + - - +
485C TYR* 1.3 76.2 - - - +
487C ASN* 1.3 62.6 + - - +
489C HIS* 3.1 5.6 + - + +
490C LEU* 3.0 37.5 + - + +
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Residues in contact with ASN 487 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483C ASN* 3.0 21.0 + - - +
484C TYR* 3.5 11.2 + - + +
486C LEU* 1.3 78.1 - - - +
488C ILE* 1.3 65.0 + - - +
490C LEU* 3.6 25.0 + - - +
491C ARG* 4.0 27.0 + - - +
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Residues in contact with ILE 488 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484C TYR* 3.4 46.8 + - + +
485C TYR* 3.0 21.9 + - + +
487C ASN* 1.3 76.7 - - - +
489C HIS* 1.3 66.7 + - - +
491C ARG* 3.2 51.1 + - - +
492C THR 4.2 0.7 + - - -
509C ALA* 4.6 1.3 - - - +
510C GLN* 3.6 39.9 + - + +
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Residues in contact with HIS 489 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A T 4.6 1.5 + - - -
16A C 3.0 28.8 + - - -
473C CYS* 3.7 11.0 - - + -
476C CYS* 4.1 4.5 - - - -
478C LYS* 4.5 2.7 - - + -
480C PHE* 3.2 33.5 - + + -
485C TYR* 2.7 31.8 + - + +
486C LEU* 3.4 11.9 - - + +
488C ILE* 1.3 74.4 - - - +
490C LEU* 1.3 58.7 + - - +
492C THR* 2.8 53.6 + - + +
493C HIS* 3.3 1.9 + + - -
510C GLN* 5.1 2.2 - - - +
968C ZN 2.0 37.1 - - - -
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Residues in contact with LEU 490 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473C CYS* 4.0 27.1 - - + -
474C SER* 4.9 5.6 - - - +
475C TYR* 4.0 17.3 - - + -
486C LEU* 3.0 33.2 + - + +
487C ASN* 3.8 20.9 - - - +
488C ILE 3.3 0.6 - - - -
489C HIS* 1.3 77.5 - - - +
491C ARG* 1.3 56.6 + - - +
493C HIS* 2.9 10.5 + - - +
494C THR* 2.8 38.4 + - + +
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Residues in contact with ARG 491 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487C ASN* 4.0 25.1 + - - +
488C ILE* 3.3 37.0 - - - +
489C HIS 3.0 0.4 + - - -
490C LEU* 1.3 77.2 - - - +
492C THR* 1.3 58.0 + - - +
494C THR* 3.4 8.5 - - - +
495C GLY* 2.9 28.2 + - - -
496C GLU* 3.3 37.6 + - + +
497C LYS* 5.5 1.2 - - - -
498C PRO* 3.7 25.4 - - - +
499C TYR* 4.0 10.5 - - - -
509C ALA* 2.7 49.9 + - + +
510C GLN* 4.9 0.2 - - - +
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Residues in contact with THR 492 (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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14A T 4.5 0.2 + - - -
15A T 2.8 42.7 + - - -
488C ILE 4.2 0.6 + - - -
489C HIS* 2.8 39.1 + - + +
491C ARG* 1.3 79.0 - - - +
493C HIS* 1.3 86.8 + - + +
495C GLY* 4.8 1.0 + - - -
509C ALA* 4.6 0.6 - - - +
510C GLN* 6.1 0.9 - - - -
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Residues in contact with HIS 493 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473C CYS* 3.7 2.2 - - - -
475C TYR* 3.4 52.8 - + + +
476C CYS* 4.0 11.4 - - + -
489C HIS* 3.3 8.0 + + - -
490C LEU* 2.9 6.6 + - - +
492C THR* 1.3 100.1 + - + +
494C THR* 1.3 64.6 + - - +
495C GLY* 3.2 4.3 + - - -
968C ZN 2.1 36.6 - - - -
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Residues in contact with THR 494 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475C TYR* 3.5 28.5 - - + +
490C LEU* 2.8 30.9 + - + +
491C ARG* 3.4 10.0 - - - +
493C HIS* 1.3 72.4 - - - +
495C GLY* 1.3 60.7 + - - +
496C GLU* 3.2 22.9 + - - +
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Residues in contact with GLY 495 (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 ARG 2.9 15.2 + - - -
492C THR 5.3 1.1 - - - -
493C HIS 3.2 4.5 - - - -
494C THR* 1.3 76.8 - - - +
496C GLU* 1.3 63.3 + - - +
497C LYS* 3.4 28.6 + - - +
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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
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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