Contacts of the helix formed by residues 478 - 489 (chain C) in PDB entry 2UZ1
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 TRP 478 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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421C MET* 4.7 2.0 - - + -
449C GLY* 3.3 34.5 - - - -
450C SER* 3.7 3.1 - - - -
453C TYR* 3.6 27.1 - + - -
477C SER* 1.3 67.8 - - - +
479C GLY* 1.3 58.5 + - - +
480C ALA 3.7 0.4 - - - -
481C THR* 2.7 31.7 + - - +
482C LEU* 3.0 17.8 + - - +
496C GLY 3.8 21.6 + - - -
497C THR* 2.7 19.3 + - + +
499C LEU* 3.6 25.6 - - + +
1557C TPP 3.4 48.0 - - + -
25D LEU* 4.0 27.8 - - + +
26D HIS* 5.4 2.9 - - + +
46D ASP* 4.9 4.8 + - - +
47D THR 4.1 11.5 + - - -
48D ARG* 4.1 16.8 - - - -
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Residues in contact with GLY 479 (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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395C LEU* 3.5 7.9 - - - -
477C SER* 3.2 14.3 + - - -
478C TRP* 1.3 70.6 - - - +
480C ALA* 1.3 66.3 + - - +
482C LEU* 3.1 5.5 + - - +
483C HIS* 2.9 25.3 + - - -
546C LEU* 3.9 10.1 - - - -
1557C TPP 2.8 27.0 + - - -
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Residues in contact with ALA 480 (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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394C ALA* 3.4 29.6 - - + -
395C LEU* 3.6 22.1 - - + +
398C LEU* 5.8 2.7 - - + -
478C TRP 3.7 0.2 - - - -
479C GLY* 1.3 72.1 - - - +
481C THR* 1.3 58.3 + - - +
483C HIS* 3.3 4.7 + - - +
484C PHE* 2.9 26.5 + - - +
553C GLU* 4.0 6.0 - - - +
1557C TPP 3.0 17.1 + - - +
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Residues in contact with THR 481 (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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478C TRP* 2.7 34.5 + - - +
480C ALA* 1.3 75.4 - - - +
482C LEU* 1.3 61.9 + - - -
484C PHE* 3.2 9.3 + - - +
485C GLN* 3.0 26.7 + - - +
497C THR* 3.9 4.1 - - - +
1557C TPP 3.3 42.1 - - + +
26D HIS* 3.2 32.8 + - + +
27D GLY* 4.0 4.3 - - - -
28D ALA* 4.1 7.4 - - + +
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Residues in contact with LEU 482 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477C SER* 4.0 15.0 - - - -
478C TRP 3.0 15.5 + - - +
479C GLY* 3.1 10.3 + - - +
481C THR* 1.3 73.3 - - - +
483C HIS* 1.3 67.7 + - + +
485C GLN* 3.1 6.0 + - - +
486C GLN* 3.0 59.8 + - + +
494C VAL* 3.8 12.8 - - + -
497C THR* 3.6 24.6 - - - +
498C ARG* 3.7 39.9 - - + +
546C LEU* 3.9 15.9 - - + -
547C ASP* 5.9 0.4 - - - +
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Residues in contact with HIS 483 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395C LEU* 3.4 16.1 - - + +
479C GLY 2.9 16.5 + - - +
480C ALA 3.4 4.7 - - - +
482C LEU* 1.3 73.5 - - + +
484C PHE* 1.3 60.2 + - - +
486C GLN* 3.2 19.1 + - - +
487C LEU* 2.8 44.1 + - + +
546C LEU* 2.8 30.8 + - + +
547C ASP* 4.0 10.5 + - - -
548C PRO 3.3 26.7 - - - -
549C ILE* 4.3 5.7 - - + +
553C GLU* 2.6 40.9 + - - +
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Residues in contact with PHE 484 (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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480C ALA 2.9 14.5 + - - +
481C THR* 3.3 13.9 - - - +
483C HIS* 1.3 76.5 - - - +
485C GLN* 1.3 61.4 + - + +
487C LEU* 4.9 2.2 - - - -
488C ALA* 2.7 61.1 + - + +
489C VAL* 4.2 4.5 - - + -
553C GLU* 4.7 0.8 + - - -
26D HIS* 5.0 0.4 - - - -
28D ALA* 3.7 34.8 - - + -
31D ASP* 3.8 31.9 - - + -
163D TRP* 4.1 20.4 - + - -
167D MET* 5.5 6.1 - - - -
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Residues in contact with GLN 485 (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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481C THR 3.0 12.0 + - - +
482C LEU* 3.1 6.0 + - - +
484C PHE* 1.3 75.7 - - + +
486C GLN* 1.3 58.5 + - - +
489C VAL* 3.0 17.0 + - - +
490C GLY 2.9 27.4 + - - +
493C ARG 3.6 15.3 - - - +
494C VAL* 3.3 5.3 - - + -
495C THR* 2.9 40.4 + - - +
497C THR* 2.8 31.3 + - - -
26D HIS* 3.3 10.1 - - + +
31D ASP* 2.9 29.6 + - - +
34D PHE* 4.7 1.4 - - - +
35D GLN* 3.6 8.2 - - - +
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Residues in contact with GLN 486 (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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482C LEU* 3.0 40.3 + - - +
483C HIS* 3.8 19.6 + - - +
485C GLN* 1.3 76.1 - - - +
487C LEU* 1.3 73.0 + - + +
490C GLY* 3.5 25.0 + - - +
491C PRO* 3.8 17.7 - - + +
494C VAL* 3.7 19.6 - - + +
498C ARG* 4.6 6.6 + - - -
547C ASP* 5.0 11.3 + - - +
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Residues in contact with LEU 487 (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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483C HIS* 2.8 42.1 + - + +
484C PHE* 4.8 1.8 - - - -
486C GLN* 1.3 89.7 - - + +
488C ALA* 1.3 61.6 + - + +
489C VAL 3.5 0.6 - - - -
549C ILE* 4.3 27.8 - - + -
553C GLU* 4.4 15.9 - - + +
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Residues in contact with ALA 488 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484C PHE* 2.7 51.5 + - + +
487C LEU* 1.3 74.7 - - + +
489C VAL* 1.3 61.9 + - + +
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Residues in contact with VAL 489 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484C PHE* 4.2 10.8 - - + +
485C GLN* 3.0 20.0 + - - +
487C LEU 3.5 0.8 - - - -
488C ALA* 1.3 84.3 - - + +
490C GLY* 1.3 59.2 + - - +
493C ARG* 3.7 27.7 - - + +
31D ASP* 3.3 23.6 - - - +
35D GLN* 3.9 17.5 - - + +
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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
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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