Contacts of the helix formed by residues 424 - 436 (chain R) in PDB entry 1P3Q
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 ASP 424 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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422R ASP 3.8 1.0 + - - -
423R MSE 1.3 73.4 - - - +
425R PRO* 1.3 61.1 - - - +
426R SER* 2.7 42.3 + - - -
427R LEU* 2.5 46.2 + - + +
428R ILE* 3.3 8.2 + - - +
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Residues in contact with PRO 425 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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417R GLN* 3.2 35.9 + - - +
423R MSE 3.0 10.7 - - - +
424R ASP* 1.3 85.6 - - - +
426R SER* 1.3 58.3 + - - +
428R ILE* 3.6 5.3 + - + +
429R GLU* 3.5 23.9 + - - +
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Residues in contact with SER 426 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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424R ASP* 2.7 17.7 + - - -
425R PRO* 1.3 75.8 - - - +
427R LEU* 1.3 60.4 + - - +
428R ILE 3.3 0.4 - - - -
429R GLU* 4.3 7.4 - - - +
430R ASP* 2.8 39.4 + - - +
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Residues in contact with LEU 427 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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423R MSE 4.5 21.5 - - + -
424R ASP* 2.5 33.0 + - + +
426R SER* 1.3 73.3 - - - +
428R ILE* 1.3 61.3 + - - +
430R ASP* 3.6 12.8 - - + +
431R VAL* 3.1 34.6 + - + +
8V LEU* 5.7 0.2 - - + -
34V GLU 3.5 22.9 - - - +
35V GLY* 3.9 24.2 - - - +
36V ILE* 4.4 12.1 - - + -
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Residues in contact with ILE 428 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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416R LEU* 3.7 49.6 - - + +
417R GLN* 2.9 37.5 - - + +
420R PHE* 3.9 11.4 - - + +
423R MSE 3.6 29.2 - - + -
424R ASP 3.8 8.1 - - - +
425R PRO* 3.8 7.0 - - + +
426R SER 3.3 0.2 - - - -
427R LEU* 1.3 75.0 - - - +
429R GLU* 1.3 71.4 + - - +
431R VAL* 2.8 19.4 + - - +
432R CYS* 3.2 11.1 + - - -
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Residues in contact with GLU 429 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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425R PRO 3.5 13.9 + - - +
426R SER* 4.3 7.7 - - - +
428R ILE* 1.3 80.3 - - - +
430R ASP* 1.3 63.4 + - - +
432R CYS* 3.0 9.8 + - - -
433R ILE* 2.6 42.7 - - + +
9V THR* 5.8 4.3 - - + -
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Residues in contact with ASP 430 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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426R SER* 2.8 32.6 + - - +
427R LEU* 3.6 17.0 - - + +
428R ILE 3.1 0.2 - - - -
429R GLU* 1.3 82.2 - - - +
431R VAL* 1.3 62.0 + - - +
433R ILE* 3.8 15.8 + - - +
434R ALA* 4.1 1.9 + - - +
8V LEU* 3.8 35.9 - - + +
9V THR* 3.1 34.4 + - - +
34V GLU* 5.1 7.3 - - - +
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Residues in contact with VAL 431 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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441Q PRO 5.1 0.2 - - - +
442Q CYS* 3.9 23.5 - - - +
444Q ASP 5.1 6.3 - - - -
423R MSE 6.2 1.8 - - - -
427R LEU* 3.1 24.9 - - + +
428R ILE* 2.8 11.7 + - - +
430R ASP* 1.3 72.0 - - + +
432R CYS* 1.3 65.6 + - - +
434R ALA* 3.3 9.7 + - - +
435R ALA* 3.5 11.8 + - - +
8V LEU* 4.9 3.1 - - + -
36V ILE* 6.2 0.7 - - + -
71V LEU* 3.5 32.1 - - + -
73V LEU* 4.8 10.4 - - + +
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Residues in contact with CYS 432 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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442Q CYS* 3.4 24.9 - - - -
416R LEU* 2.9 38.6 - - - -
428R ILE* 3.2 17.5 + - - -
429R GLU* 3.0 11.2 + - - +
431R VAL* 1.3 72.7 - - - +
433R ILE* 1.3 59.9 + - + +
434R ALA 2.4 18.1 + - - -
435R ALA* 2.9 2.3 + - - +
436R ALA* 2.9 28.7 + - + +
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Residues in contact with ILE 433 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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429R GLU* 2.6 49.3 + - + +
430R ASP* 4.0 7.7 - - - +
432R CYS* 1.3 76.1 - - + +
434R ALA* 1.3 60.5 + - - +
436R ALA* 4.8 7.4 - - - +
437R SER* 4.1 14.8 + - - -
439R ILE* 5.3 1.2 - - - +
8V LEU 4.6 15.2 - - - +
9V THR* 5.2 11.7 - - + -
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Residues in contact with ALA 434 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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430R ASP 4.1 7.9 - - - +
431R VAL 3.6 9.6 - - - +
432R CYS 2.4 21.4 + - - -
433R ILE* 1.3 72.4 - - - +
435R ALA* 1.3 59.3 + - - +
436R ALA 3.4 0.4 - - - -
437R SER* 4.1 3.6 - - - -
438R ARG* 3.0 25.1 + - - -
439R ILE* 3.4 21.3 + - + +
440R GLY 4.4 1.6 + - - -
441R PRO* 5.6 0.2 - - - +
8V LEU* 5.5 6.7 - - + +
71V LEU* 4.7 22.7 - - + +
73V LEU* 5.6 5.7 - - + +
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Residues in contact with ALA 435 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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437Q SER* 3.8 10.6 - - - -
441Q PRO* 3.3 33.4 - - + +
442Q CYS* 3.7 15.9 - - - +
431R VAL 3.5 7.9 + - - +
432R CYS 2.9 4.7 + - - +
434R ALA* 1.3 80.8 - - - +
436R ALA* 1.3 57.5 + - - +
437R SER 2.9 10.9 + - - -
438R ARG* 3.1 28.9 + - - +
73V LEU* 4.8 8.9 - - + +
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Residues in contact with ALA 436 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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408Q GLU* 3.8 16.4 - - - +
437Q SER* 5.4 3.4 - - - -
442Q CYS* 4.8 8.5 - - - -
432R CYS* 2.9 18.9 + - + +
433R ILE* 4.8 4.3 - - - +
435R ALA* 1.3 73.5 - - - +
437R SER* 1.3 61.4 + - - +
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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