Contacts of the helix formed by residues 424 - 435 (chain Q) 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 Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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422Q ASP 4.1 0.8 + - - -
423Q MSE 1.3 75.5 - - - +
425Q PRO* 1.3 71.1 - - - +
426Q SER* 2.3 43.4 + - - -
427Q LEU* 3.0 27.3 + - + +
428Q ILE* 3.1 13.3 + - - +
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Residues in contact with PRO 425 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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413Q LEU* 5.6 0.5 - - - +
417Q GLN* 4.0 32.1 - - + +
423Q MSE 3.3 9.9 - - - +
424Q ASP* 1.3 89.1 - - - +
426Q SER* 1.3 59.6 + - - +
428Q ILE* 3.3 12.1 + - + +
429Q GLU* 3.0 22.6 + - - +
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Residues in contact with SER 426 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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424Q ASP* 2.3 28.3 + - - -
425Q PRO* 1.3 75.8 - - - +
427Q LEU* 1.3 65.5 + - - +
429Q GLU* 3.3 11.6 + - - +
430Q ASP* 3.2 25.8 + - - +
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Residues in contact with LEU 427 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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423Q MSE 4.0 19.5 - - + -
424Q ASP* 3.0 20.7 + - + +
426Q SER* 1.3 79.7 + - - +
428Q ILE* 1.3 66.2 + - - +
430Q ASP* 3.1 10.4 + - + +
431Q VAL* 3.0 33.5 + - + +
449R LEU* 4.0 28.0 - - + -
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Residues in contact with ILE 428 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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413Q LEU* 4.4 5.2 - - + -
416Q LEU* 3.6 25.6 - - + +
417Q GLN* 3.7 39.3 - - + +
420Q PHE* 4.2 15.5 - - + +
423Q MSE 4.0 25.8 - - + +
424Q ASP 3.1 13.8 + - - +
425Q PRO* 3.3 8.5 + - + +
427Q LEU* 1.3 75.6 - - - +
429Q GLU* 1.3 57.7 + - - +
431Q VAL* 3.2 2.3 + - - +
432Q CYS* 2.8 51.4 + - - -
446R LEU* 4.1 14.8 - - + -
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Residues in contact with GLU 429 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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409Q ARG* 3.7 22.8 + - - +
413Q LEU* 3.8 29.0 - - + +
425Q PRO 3.0 13.9 + - - +
426Q SER* 3.5 13.6 - - - +
427Q LEU 3.1 0.6 - - - -
428Q ILE* 1.3 77.4 - - - +
430Q ASP* 1.3 60.4 + - - +
432Q CYS* 3.4 0.9 + - - +
433Q ILE* 2.9 50.3 + - + +
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Residues in contact with ASP 430 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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426Q SER* 3.2 10.2 + - - +
427Q LEU* 3.1 14.1 + - + +
429Q GLU* 1.3 81.4 - - - +
431Q VAL* 1.3 62.5 + - + +
433Q ILE* 3.6 13.1 + - - +
434Q ALA* 3.2 23.7 + - - +
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Residues in contact with VAL 431 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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427Q LEU* 3.0 21.7 + - + +
428Q ILE 3.4 7.2 - - - +
430Q ASP* 1.3 75.8 - - + +
432Q CYS* 1.3 55.9 + - - +
434Q ALA* 3.3 6.2 + - - +
435Q ALA* 2.8 32.4 + - - +
442R CYS* 4.3 5.2 - - + +
445R ALA* 3.4 32.3 - - + -
446R LEU* 3.7 28.7 - - + +
449R LEU* 4.3 16.8 - - + -
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Residues in contact with CYS 432 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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409Q ARG* 4.6 12.9 - - + +
412Q THR* 4.7 3.6 - - + -
413Q LEU* 3.1 32.3 - - + -
416Q LEU* 3.1 35.4 - - - -
428Q ILE* 2.8 32.7 + - - +
429Q GLU 3.7 1.8 - - - +
431Q VAL* 1.3 73.2 - - - +
433Q ILE* 1.3 64.9 + - - +
435Q ALA* 3.0 26.1 + - - +
442R CYS* 4.0 7.5 - - - -
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Residues in contact with ILE 433 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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409Q ARG* 3.6 40.8 - - - +
429Q GLU* 2.9 39.1 + - + +
430Q ASP* 3.9 13.2 - - - +
432Q CYS* 1.3 78.3 - - - +
434Q ALA* 1.3 61.1 + - - +
435Q ALA 4.0 3.6 - - - +
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Residues in contact with ALA 434 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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430Q ASP 3.2 18.7 + - - +
431Q VAL* 3.8 4.7 - - - +
433Q ILE* 1.3 76.7 - - - +
435Q ALA* 1.3 62.1 + - - +
436Q ALA* 3.8 1.0 + - - -
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Residues in contact with ALA 435 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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431Q VAL* 2.8 13.7 + - + +
432Q CYS 3.0 14.4 + - - +
433Q ILE 4.0 3.3 - - - +
434Q ALA* 1.3 79.6 - - - +
436Q ALA* 1.3 70.9 + - - +
438R ARG 4.9 0.2 - - - +
441R PRO* 4.7 2.2 - - - +
442R CYS* 3.1 45.8 - - - +
445R ALA* 5.6 1.3 - - + -
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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