Contacts of the helix formed by residues 452 - 463 (chain K) 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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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422K VAL* 3.9 20.0 - - - +
448K ALA 3.0 15.6 + - - -
449K CYS* 3.4 10.6 + - - +
451K TRP* 1.3 90.9 - - - +
453K PRO* 1.3 59.4 - - - +
454K GLU* 3.7 9.5 + - - +
455K LEU* 3.1 27.0 + - - +
456K ALA 3.0 22.7 + - - -
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Residues in contact with PRO 453 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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411K TRP* 3.4 28.8 - - + -
449K CYS 4.9 0.9 - - - +
451K TRP 3.5 11.0 - - - +
452K SER* 1.3 84.4 - - - +
454K GLU* 1.3 74.9 + - - +
456K ALA* 3.7 8.6 - - + +
457K ALA* 3.1 18.2 + - - +
2P MET* 4.0 21.3 - - - -
135P ALA 6.0 1.3 - - - +
139P SER* 4.8 3.8 - - - +
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Residues in contact with GLU 454 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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409K HIS* 2.9 23.3 + - - -
411K TRP* 3.8 18.4 - - + -
415K PRO* 3.6 42.0 - - + +
418K ALA* 4.2 1.8 - - + -
419K ALA* 3.5 11.1 - - - +
452K SER* 3.9 8.0 + - - +
453K PRO* 1.3 92.4 - - - +
455K LEU* 1.3 61.1 + - - +
457K ALA 3.4 1.2 + - - -
458K ALA 3.2 6.9 + - - -
2P MET* 4.1 1.2 - - - +
4P TRP* 3.8 26.0 - - + -
139P SER* 2.8 32.3 + - - -
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Residues in contact with LEU 455 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384K VAL* 3.6 32.1 - - + -
419K ALA* 3.7 16.0 - - - +
422K VAL* 3.8 14.6 - - + -
423K ALA* 4.1 11.9 - - + +
445K ILE* 3.9 17.0 - - + +
448K ALA* 3.5 31.9 - - + -
449K CYS* 3.9 10.5 - - - +
452K SER* 3.1 20.0 + - - +
454K GLU* 1.3 75.1 - - - +
456K ALA* 1.3 60.5 + - - +
458K ALA* 3.1 1.6 + - - +
459K CYS* 2.8 43.9 + - - -
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Residues in contact with ALA 456 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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449K CYS* 3.7 28.8 - - + +
452K SER 3.0 16.3 + - - +
453K PRO* 3.7 10.3 - - + +
455K LEU* 1.3 76.9 - - - +
457K ALA* 1.3 61.9 + - - +
459K CYS* 3.4 2.6 + - - +
460K GLU* 3.1 28.0 + - - +
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Residues in contact with ALA 457 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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409K HIS* 3.9 10.8 - - + -
410K PRO* 4.2 8.1 - - + -
411K TRP* 3.8 29.6 - - + +
453K PRO 3.1 17.2 + - - +
454K GLU 3.8 4.3 - - - +
455K LEU 3.2 0.2 - - - -
456K ALA* 1.3 73.0 - - - +
458K ALA* 1.3 63.8 + - - +
460K GLU* 3.5 6.6 + - - +
461K VAL* 3.3 28.7 + - - +
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Residues in contact with ALA 458 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384K VAL* 3.9 17.5 - - + -
409K HIS* 3.7 25.0 + - + -
410K PRO* 5.1 0.4 - - - -
419K ALA* 3.8 12.8 - - + -
454K GLU 3.2 8.2 + - - +
455K LEU 3.1 7.8 + - - +
457K ALA* 1.3 74.5 - - - +
459K CYS* 1.3 65.6 + - - +
461K VAL* 3.3 11.7 + - - -
462K TRP* 3.3 35.2 + - + +
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Residues in contact with CYS 459 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384K VAL* 4.0 6.1 - - - -
385K TRP* 2.9 44.0 + - + +
445K ILE* 3.4 25.1 - - - -
449K CYS* 3.4 24.9 - - - -
455K LEU* 2.8 35.9 + - - +
456K ALA 3.6 5.2 - - - +
458K ALA* 1.3 72.8 - - - +
460K GLU* 1.3 56.5 + - - +
463K LYS* 3.0 19.6 + - - +
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Residues in contact with GLU 460 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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456K ALA 3.1 19.7 + - - +
457K ALA* 3.7 7.9 - - - +
458K ALA 3.2 0.2 - - - -
459K CYS* 1.3 79.7 - - + +
461K VAL* 1.3 64.4 + - + +
462K TRP 3.5 0.2 + - - -
463K LYS* 3.8 29.4 + - - +
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Residues in contact with VAL 461 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15E ALA* 4.0 11.2 - - + +
16E GLY* 3.7 34.8 - - - +
17E VAL 5.5 0.7 + - - -
408K GLY 4.8 0.2 - - - +
410K PRO* 3.8 26.0 - - + -
457K ALA 3.3 15.5 + - - +
458K ALA 3.3 7.7 + - - +
460K GLU* 1.3 79.6 - - + +
462K TRP* 1.3 79.4 + - + +
463K LYS 3.8 0.3 + - - -
464K GLU 5.3 0.5 + - - -
465K ILE* 4.6 4.7 - - - +
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Residues in contact with TRP 462 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16E GLY* 5.0 0.7 - - - -
17E VAL* 4.3 3.4 - - + -
66E TRP* 3.4 28.3 - + - -
67E THR* 3.0 24.4 + - + -
383K HIS* 3.5 42.1 - - + +
384K VAL* 4.6 4.7 - - + -
385K TRP* 4.0 4.0 - - + -
404K GLY 3.6 10.5 - - - -
405K GLY* 3.6 30.5 - - - -
408K GLY 3.5 21.5 - - - -
409K HIS* 3.6 23.3 - + - -
458K ALA* 3.3 43.1 + - + +
459K CYS 3.9 0.9 - - - -
461K VAL* 1.3 94.1 - - + +
463K LYS* 1.3 65.9 + - - +
464K GLU 3.2 2.7 - - - -
465K ILE* 3.1 24.1 + - + -
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Residues in contact with LYS 463 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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383K HIS* 5.6 0.3 - - - -
385K TRP* 3.5 26.3 - - + +
459K CYS 3.0 18.2 + - - +
460K GLU* 3.9 27.5 + - - +
461K VAL 3.5 2.0 - - - -
462K TRP* 1.3 77.6 - - - +
464K GLU* 1.3 82.3 + - + +
465K ILE 3.5 1.0 + - - +
466K LYS* 5.6 4.7 - - - +
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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