Contacts of the helix formed by residues 452 - 463 (chain V) in PDB entry 1UW9
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 452 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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422V VAL* 3.9 16.2 - - - +
448V ALA 3.1 15.7 + - - -
449V CYS 3.4 10.1 - - - +
450V LYS 3.6 0.8 - - - -
451V TRP* 1.3 94.7 - - - +
453V PRO* 1.3 61.3 - - - +
454V GLU* 3.7 9.7 + - - +
455V LEU* 3.1 26.6 + - - +
456V ALA 3.0 22.0 + - - -
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Residues in contact with PRO 453 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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411V TRP* 3.5 17.8 - - + -
449V CYS 5.0 0.7 - - - +
451V TRP 3.5 10.5 - - - +
452V SER* 1.3 84.7 - - - +
454V GLU* 1.3 69.5 + - - +
456V ALA* 3.7 8.2 - - + +
457V ALA* 3.0 23.7 + - - +
2W MET* 3.7 33.0 - - + -
135W ALA 5.9 2.2 - - - +
136W ASN* 6.5 1.1 - - - -
139W SER* 4.9 1.8 - - - +
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Residues in contact with GLU 454 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409V HIS* 2.9 23.6 + - - -
411V TRP* 3.7 19.1 - - + -
415V PRO* 3.6 40.2 - - + +
418V ALA* 4.3 1.8 - - + -
419V ALA* 3.6 10.4 - - - +
452V SER* 3.9 7.9 + - - +
453V PRO* 1.3 94.0 - - - +
455V LEU* 1.3 61.4 + - - +
457V ALA 3.5 0.2 + - - -
458V ALA 3.2 7.3 + - - -
2W MET* 4.0 0.9 - - - +
4W TRP* 3.7 26.3 - - + -
139W SER* 2.7 33.6 + - - -
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Residues in contact with LEU 455 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384V VAL* 3.7 29.4 - - + -
419V ALA* 3.8 15.6 - - - +
422V VAL* 3.8 13.9 - - + -
423V ALA* 4.2 12.1 - - + +
445V ILE* 3.9 15.7 - - + +
448V ALA* 3.5 33.0 - - + -
449V CYS* 3.9 11.2 - - - +
452V SER* 3.1 20.4 + - - +
454V GLU* 1.3 77.8 - - - +
456V ALA* 1.3 59.2 + - - +
458V ALA* 3.1 1.6 + - - +
459V CYS* 2.8 46.4 + - - -
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Residues in contact with ALA 456 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449V CYS* 3.7 30.0 - - + +
452V SER 3.0 17.8 + - - +
453V PRO* 3.7 9.0 - - + +
455V LEU* 1.3 75.7 - - - +
457V ALA* 1.3 63.0 + - - +
459V CYS* 3.4 2.5 + - - +
460V GLU* 3.0 27.2 + - + +
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Residues in contact with ALA 457 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409V HIS* 3.8 14.4 - - + -
410V PRO* 4.2 8.7 - - + -
411V TRP* 3.8 25.6 - - + +
453V PRO 3.0 17.2 + - - +
454V GLU 3.8 4.7 - - - +
456V ALA* 1.3 77.0 - - - +
458V ALA* 1.3 61.6 + - - +
460V GLU* 3.4 7.3 + - - +
461V VAL* 3.3 28.1 + - - +
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Residues in contact with ALA 458 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384V VAL* 3.9 17.4 - - + +
409V HIS* 3.7 19.6 + - + -
410V PRO* 5.1 0.9 - - - -
419V ALA* 3.9 13.2 - - + -
454V GLU 3.2 10.3 + - - +
455V LEU 3.1 7.7 + - - +
457V ALA* 1.3 77.6 - - - +
459V CYS* 1.3 63.8 + - - +
461V VAL* 3.2 3.6 + - - -
462V TRP* 3.2 44.3 + - + +
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Residues in contact with CYS 459 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384V VAL* 3.9 9.4 - - - -
385V TRP* 2.9 39.8 + - + +
445V ILE* 3.4 32.5 - - - -
449V CYS* 3.5 17.9 - - - -
455V LEU* 2.8 33.6 + - - +
456V ALA* 3.6 4.9 - - - +
458V ALA* 1.3 73.4 - - - +
460V GLU* 1.3 57.7 + - + +
463V LYS* 3.0 20.5 + - - +
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Residues in contact with GLU 460 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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456V ALA 3.0 18.2 + - - +
457V ALA* 3.7 7.9 - - - +
458V ALA 3.2 0.4 - - - -
459V CYS* 1.3 78.8 - - + +
461V VAL* 1.3 64.1 + - + +
463V LYS* 3.8 28.6 + - - +
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Residues in contact with VAL 461 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15O ALA* 4.0 12.6 - - + +
16O GLY* 3.6 36.3 - - - +
17O VAL 5.4 0.9 + - - -
408V GLY 4.8 0.2 - - - +
410V PRO* 3.9 25.6 - - + -
457V ALA 3.3 15.0 + - - +
458V ALA 3.2 6.0 + - - +
460V GLU* 1.3 79.6 - - + +
462V TRP* 1.3 80.0 + - + +
463V LYS 3.9 0.3 + - - -
464V GLU 5.3 0.5 + - - -
465V ILE* 4.6 5.2 - - - +
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Residues in contact with TRP 462 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16O GLY* 5.0 0.7 - - - -
17O VAL* 4.2 3.4 - - + -
66O TRP* 3.4 27.4 - + - -
67O THR* 3.0 24.8 + - + -
383V HIS* 3.5 42.1 - + + +
384V VAL* 4.6 4.5 - - + -
385V TRP* 3.9 3.6 - - + -
404V GLY 3.6 10.5 - - - -
405V GLY* 3.5 31.2 - - - -
408V GLY 3.5 22.0 - - - -
409V HIS* 3.7 22.0 - + - -
410V PRO* 5.4 0.4 - - + -
458V ALA* 3.2 43.6 + - + +
459V CYS 3.9 1.3 - - - -
461V VAL* 1.3 92.0 - - + +
463V LYS* 1.3 66.8 + - - +
464V GLU 3.2 2.7 - - - -
465V ILE* 3.1 22.7 + - + +
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Residues in contact with LYS 463 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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383V HIS* 5.5 0.5 - - - -
385V TRP* 3.5 26.8 - - + +
459V CYS 3.0 17.9 + - - +
460V GLU* 3.8 27.0 + - - +
461V VAL 3.5 2.2 + - - -
462V TRP* 1.3 78.2 - - - +
464V GLU* 1.3 84.7 + - + +
465V ILE 3.5 1.2 + - - +
466V LYS* 5.5 5.0 - - - +
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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