Contacts of the helix formed by residues 400 - 420 (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 LEU 400 (chain Q).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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398Q SER* 2.8 5.4 + - - +
399Q SER* 1.3 76.2 - - - +
401Q ILE* 1.3 72.5 + - + +
402Q LYS 3.0 1.1 - - - +
403Q LYS* 3.0 11.6 + - + +
404Q ILE* 3.0 36.5 + - + +
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Residues in contact with ILE 401 (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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398Q SER* 4.0 23.6 - - - +
400Q LEU* 1.3 81.7 - - + +
402Q LYS* 1.3 58.2 + - - +
404Q ILE* 3.4 12.6 + - + +
405Q GLU* 3.0 51.0 + - + +
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Residues in contact with LYS 402 (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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398Q SER 3.3 13.0 + - - +
399Q SER* 4.5 9.0 - - - -
400Q LEU 3.0 0.6 - - - -
401Q ILE* 1.3 80.2 - - - +
403Q LYS* 1.3 56.8 + - - +
405Q GLU* 3.2 10.7 + - - +
406Q GLU* 2.8 62.3 + - - +
409Q ARG* 4.4 17.6 - - - +
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Residues in contact with LYS 403 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399Q SER 4.8 4.2 - - - +
400Q LEU* 3.0 21.6 + - + +
402Q LYS* 1.3 80.1 - - - +
404Q ILE* 1.3 56.5 + - + +
406Q GLU* 2.5 42.8 + - - +
407Q ASN* 2.8 55.0 + - - +
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Residues in contact with ILE 404 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400Q LEU* 3.0 28.6 + - + +
401Q ILE* 3.7 14.8 - - + +
403Q LYS* 1.3 74.3 - - + +
405Q GLU* 1.3 71.1 + - + +
406Q GLU 3.0 2.3 + - - -
407Q ASN* 3.3 15.7 + - + +
408Q GLU* 3.3 14.9 + - - +
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Residues in contact with GLU 405 (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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401Q ILE* 3.0 34.7 + - + +
402Q LYS* 3.8 14.6 - - - +
404Q ILE* 1.3 82.0 - - + +
406Q GLU* 1.3 58.8 - - - +
408Q GLU* 3.4 31.3 - - - +
409Q ARG* 3.5 11.9 + - - +
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Residues in contact with GLU 406 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402Q LYS* 2.8 41.2 + - - +
403Q LYS* 2.5 38.4 + - - +
405Q GLU* 1.3 76.3 - - - +
407Q ASN* 1.3 64.0 + - - +
409Q ARG* 3.5 26.9 + - - +
410Q LYS* 3.2 21.3 + - - +
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Residues in contact with ASN 407 (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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403Q LYS* 2.8 48.8 + - - +
404Q ILE* 3.3 9.4 + - + +
406Q GLU* 1.3 76.2 - - - +
408Q GLU* 1.3 64.6 - - - +
410Q LYS* 3.3 17.7 + - - +
411Q ASP* 3.4 13.2 - - - +
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Residues in contact with GLU 408 (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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404Q ILE* 3.3 9.5 + - + +
405Q GLU* 3.4 26.4 - - - +
407Q ASN* 1.3 78.5 - - - +
409Q ARG* 1.3 71.9 + - - +
411Q ASP* 3.2 21.5 + - - +
412Q THR* 3.3 15.1 + - - -
437Q SER 4.5 12.2 - - - +
436R ALA* 3.8 20.2 - - - +
437R SER* 4.7 12.0 - - - +
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Residues in contact with ARG 409 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402Q LYS* 4.4 16.8 - - - +
405Q GLU 3.5 15.3 + - - +
406Q GLU* 3.8 28.4 + - - +
407Q ASN 3.2 0.6 - - - -
408Q GLU* 1.3 84.6 - - + +
410Q LYS* 1.3 66.5 + - - +
412Q THR* 3.3 7.1 + - - +
413Q LEU* 2.9 50.1 + - + +
429Q GLU* 3.7 15.0 + - - -
432Q CYS* 4.6 9.0 - - + +
433Q ILE* 3.6 49.8 - - - +
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Residues in contact with LYS 410 (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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406Q GLU 3.2 11.8 + - - +
407Q ASN* 3.4 12.8 - - - +
408Q GLU 3.2 0.2 - - - -
409Q ARG* 1.3 79.3 - - - +
411Q ASP* 1.3 63.7 + - - +
413Q LEU* 3.2 24.4 + - + +
414Q ASN* 2.4 51.7 + - - +
417Q GLN* 5.5 2.0 - - - -
48U LYS* 4.8 18.7 - - - +
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Residues in contact with ASP 411 (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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407Q ASN 3.4 15.5 + - - +
408Q GLU* 3.2 14.8 + - - +
410Q LYS* 1.3 79.1 - - - +
412Q THR* 1.3 64.8 + - - +
414Q ASN* 3.1 23.0 + - - +
415Q THR* 3.2 14.9 + - - -
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Residues in contact with THR 412 (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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408Q GLU* 3.3 9.7 + - - -
409Q ARG* 3.3 12.1 + - - -
411Q ASP* 1.3 78.1 - - - +
413Q LEU* 1.3 63.0 + - - +
415Q THR* 3.2 7.8 + - - -
416Q LEU* 2.9 45.4 + - + +
432Q CYS* 4.7 4.5 - - + -
437R SER* 3.0 35.6 + - - +
439R ILE* 4.6 10.1 - - + -
442R CYS* 4.2 15.0 - - - -
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Residues in contact with LEU 413 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409Q ARG* 2.9 42.5 + - + +
410Q LYS* 3.4 28.9 - - + +
412Q THR* 1.3 77.6 - - - +
414Q ASN* 1.3 60.0 + - - +
416Q LEU* 3.5 4.6 + - - +
417Q GLN* 2.9 42.1 + - - +
425Q PRO 5.6 0.7 - - - +
428Q ILE* 4.4 2.7 - - + -
429Q GLU* 3.8 34.3 - - + +
432Q CYS* 3.1 43.3 - - + -
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Residues in contact with ASN 414 (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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410Q LYS* 2.4 47.7 + - - +
411Q ASP* 3.1 13.6 + - - +
413Q LEU* 1.3 76.4 - - - +
415Q THR* 1.3 64.2 + - - +
417Q GLN* 3.6 13.9 + - - +
418Q ASN* 3.3 19.4 + - - +
60U ASN* 4.0 20.4 + - - +
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Residues in contact with THR 415 (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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411Q ASP 3.2 9.9 + - - -
412Q THR* 3.2 11.1 + - - -
414Q ASN* 1.3 79.2 - - - +
416Q LEU* 1.3 64.3 + - - +
418Q ASN* 3.0 17.9 + - - +
419Q MSE 3.0 43.9 + - + +
439R ILE* 3.6 17.2 - - + +
60U ASN* 4.9 8.0 + - - +
6V LYS* 6.5 0.9 - - - -
68V HIS* 5.3 3.6 - - + +
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Residues in contact with LEU 416 (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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412Q THR* 2.9 27.1 + - + +
413Q LEU 3.8 1.3 - - - +
415Q THR* 1.3 76.0 - - - +
417Q GLN* 1.3 56.9 + - - +
419Q MSE 3.1 7.8 + - - -
420Q PHE* 2.9 35.5 + - + +
428Q ILE* 3.6 20.6 - - + -
432Q CYS* 3.1 34.1 - - - -
439R ILE* 4.2 9.2 - - + -
442R CYS* 3.6 24.2 - - + -
443R VAL* 3.9 25.8 - - + -
446R LEU* 3.9 19.1 - - + -
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Residues in contact with GLN 417 (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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410Q LYS* 5.5 1.9 - - - -
413Q LEU* 2.9 35.7 + - - +
414Q ASN* 3.8 13.9 + - - +
415Q THR 3.3 0.2 - - - -
416Q LEU* 1.3 76.5 - - - +
418Q ASN* 1.3 60.7 + - - +
420Q PHE 3.3 1.4 - - - +
421Q PRO* 3.2 24.8 - - - +
425Q PRO* 4.0 32.2 - - + +
428Q ILE* 3.7 25.1 - - + +
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Residues in contact with ASN 418 (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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414Q ASN 3.3 10.2 + - - +
415Q THR* 3.0 12.4 + - - +
417Q GLN* 1.3 79.1 - - - +
419Q MSE 1.3 64.7 + - - +
421Q PRO* 3.4 14.3 - - - +
60U ASN* 3.8 30.6 + - + +
62U GLN* 2.3 42.2 + - - +
46V ALA 5.6 1.0 + - - -
68V HIS* 3.0 26.5 + - + -
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Residues in contact with MSE 419 (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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415Q THR* 3.0 39.1 + - + +
416Q LEU* 3.6 8.1 - - - +
418Q ASN* 1.3 76.9 - - - +
420Q PHE* 1.3 70.3 + - + +
421Q PRO* 3.3 2.8 - - - +
439R ILE* 3.4 9.4 - - + -
443R VAL* 3.8 26.2 - - - -
44V ILE* 3.9 14.2 - - + +
46V ALA 3.8 2.9 + - - -
47V GLY* 2.7 33.3 + - - -
68V HIS* 3.6 41.7 - - + +
69V LEU 4.7 3.6 - - - +
70V VAL* 3.4 28.5 - - + -
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Residues in contact with PHE 420 (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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416Q LEU* 2.9 17.9 + - + +
417Q GLN* 3.3 8.2 - - - +
419Q MSE 1.3 92.0 - - + +
421Q PRO* 1.3 64.8 - - - +
422Q ASP 3.3 2.7 - - - -
423Q MSE 3.1 42.2 + - + +
428Q ILE* 4.2 7.6 - - + +
443R VAL* 4.4 17.3 - - + -
446R LEU* 3.6 42.6 - - + -
447R LEU* 3.8 31.0 - - + -
44V ILE* 4.4 9.6 - - + -
47V GLY* 3.5 33.0 - - - -
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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