Contacts of the helix formed by residues 434 - 447 (chain A) in PDB entry 1JQO
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 GLY 434 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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261A ARG* 2.9 22.3 + - - -
329A GLU* 4.9 0.7 - - - -
430A ALA 3.3 4.0 + - - -
431A ILE 3.6 4.7 + - - -
432A ALA 2.8 6.5 + - - -
433A ASP* 1.3 76.6 - - - +
435A SER* 1.3 66.4 + - - -
436A LEU 3.1 1.2 + - - -
437A LEU 3.2 7.6 + - - -
438A ASP* 3.3 6.1 + - - -
219B ARG* 3.5 25.1 - - - -
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Residues in contact with SER 435 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322A GLN* 6.4 0.2 - - - -
326A LEU* 3.8 17.0 - - - -
329A GLU* 2.4 36.0 + - - -
431A ILE 4.8 0.6 + - - -
434A GLY* 1.3 72.5 - - - -
436A LEU* 1.3 62.2 + - - +
438A ASP* 3.1 13.6 + - - +
439A LEU* 3.0 23.7 + - - +
192B ARG* 4.2 5.0 + - - -
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Residues in contact with LEU 436 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326A LEU* 4.1 28.9 - - + +
329A GLU* 5.4 0.4 + - - -
330A LEU* 4.6 11.4 - - + -
375A LEU* 5.9 0.7 - - + -
416A LEU* 4.7 16.8 - - + +
419A CYS* 4.1 11.0 - - + -
420A TYR* 3.5 46.7 - - + +
423A LEU* 3.6 22.0 - - + -
431A ILE 4.7 2.6 + - - +
432A ALA* 3.0 14.8 - - - +
435A SER* 1.3 80.4 - - - +
437A LEU* 1.3 58.8 + - - +
439A LEU* 3.4 2.9 + - + +
440A LEU* 3.1 30.0 + - + +
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Residues in contact with LEU 437 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261A ARG* 4.1 5.2 - - - +
275A ARG* 3.8 18.4 - - + +
276A LEU 5.7 0.9 - - - +
278A TYR* 4.2 23.3 - - + +
420A TYR* 3.4 28.5 - - + +
432A ALA 3.1 3.7 + - - +
433A ASP* 3.4 44.9 - - - +
434A GLY 3.2 1.3 + - - +
436A LEU* 1.3 79.7 - - - +
438A ASP* 1.3 61.6 + - - +
440A LEU* 3.5 6.9 + - + +
441A ARG* 3.1 53.9 + - - +
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Residues in contact with ASP 438 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257A PRO* 4.2 29.8 - - + +
261A ARG* 3.3 29.3 + - - +
322A GLN* 6.1 2.5 - - - +
434A GLY 3.3 10.9 + - - +
435A SER* 3.1 14.7 + - - +
437A LEU* 1.3 75.8 - - - +
439A LEU* 1.3 65.6 + - - +
441A ARG* 3.2 11.4 + - - +
442A GLN* 3.0 28.4 + - + +
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Residues in contact with LEU 439 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319A TYR* 3.5 34.5 - - + -
322A GLN* 3.9 17.5 - - + -
323A ILE* 3.4 30.1 - - + -
326A LEU* 3.7 21.3 - - + -
412A PHE* 5.1 0.2 - - + -
416A LEU* 3.7 17.9 - - + -
435A SER 3.0 14.7 + - - +
436A LEU* 3.8 5.8 - - + +
438A ASP* 1.3 75.3 - - - +
440A LEU* 1.3 63.8 + - - +
442A GLN* 3.0 26.6 + - - +
443A VAL* 3.1 18.1 + - + +
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Residues in contact with LEU 440 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278A TYR* 3.7 51.6 - - + -
413A LEU* 4.1 16.6 - - + -
416A LEU* 4.0 26.9 - - + -
417A GLU* 4.1 8.5 - - + +
420A TYR* 4.0 29.2 - - + -
436A LEU* 3.1 24.1 + - + +
437A LEU* 3.6 8.5 - - - +
438A ASP 3.2 0.2 - - - -
439A LEU* 1.3 77.4 - - + +
441A ARG* 1.3 62.7 + - - +
443A VAL* 3.3 11.5 + - - +
444A PHE* 3.2 23.0 + - - -
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Residues in contact with ARG 441 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256A VAL* 5.7 0.9 - - + -
257A PRO* 4.8 5.8 + - + -
260A LEU* 3.5 48.2 - - + +
261A ARG* 4.3 11.1 - - - +
264A ASP* 3.0 38.0 + - - -
275A ARG* 4.4 3.2 - - - +
276A LEU* 3.0 35.5 + - - +
277A PRO 5.0 0.6 + - - -
278A TYR* 3.9 26.6 - - + +
280A VAL 5.8 1.8 - - - +
437A LEU* 3.1 36.8 + - - +
438A ASP* 3.5 12.7 + - - +
439A LEU 3.2 0.2 - - - -
440A LEU* 1.3 77.9 - - - +
442A GLN* 1.3 63.3 + - - +
444A PHE* 3.1 4.9 + - - +
445A THR* 2.9 25.6 + - - +
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Residues in contact with GLN 442 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253A TRP* 3.1 67.6 + - + +
254A LYS* 4.6 3.4 - - - +
256A VAL* 5.9 0.7 - - - -
257A PRO* 3.4 19.5 - - + +
319A TYR* 3.7 4.5 - - + -
322A GLN* 3.6 24.2 + - - +
438A ASP* 3.0 18.1 + - - +
439A LEU* 3.0 13.0 + - - +
441A ARG* 1.3 75.5 - - - +
443A VAL* 1.3 55.2 + - - +
445A THR* 2.9 1.9 + - - -
446A PHE* 2.6 52.3 + - + -
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Residues in contact with VAL 443 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319A TYR* 3.2 27.6 + - + +
409A ILE* 3.8 22.6 - - + +
412A PHE* 3.8 26.0 - - + -
413A LEU* 3.6 25.1 - - + -
416A LEU* 3.9 16.6 - - + -
439A LEU* 3.1 16.7 + - + +
440A LEU* 3.6 6.5 - - - +
441A ARG 3.2 0.2 - - - -
442A GLN* 1.3 74.3 - - - +
444A PHE* 1.3 57.9 + - - +
447A GLY* 2.8 29.4 + - - -
448A LEU* 6.0 0.4 - - + -
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Residues in contact with PHE 444 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278A TYR* 3.3 44.9 - + - +
279A ASN* 3.2 41.7 - - + +
280A VAL 5.1 1.1 - - - +
281A SER* 4.3 4.7 - - - -
284A ARG* 2.8 39.7 + - - +
409A ILE* 5.9 2.7 - - + -
413A LEU* 3.8 34.5 - - + -
417A GLU* 5.3 4.0 - - - -
440A LEU 3.2 22.3 + - - -
441A ARG 3.1 7.2 + - - +
443A VAL* 1.3 78.5 - - - +
445A THR* 1.3 59.8 + - - +
447A GLY* 4.5 0.6 + - - -
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Residues in contact with THR 445 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256A VAL* 3.8 24.9 - - + +
260A LEU* 5.1 3.3 - - - +
281A SER* 3.8 13.4 + - - -
283A ILE* 3.3 25.4 + - - +
284A ARG* 3.9 16.2 + - - +
285A PHE* 4.3 15.7 + - + +
441A ARG 2.9 14.5 + - - -
442A GLN* 2.9 4.2 + - - -
444A PHE* 1.3 79.9 - - - +
446A PHE* 1.3 83.0 + - + +
450A LEU 4.5 2.1 - - - +
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Residues in contact with PHE 446 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248A ILE* 4.2 18.6 - - + -
252A VAL* 3.6 24.9 - - + -
253A TRP* 3.5 52.0 - + + -
256A VAL* 3.3 33.9 - - + -
285A PHE* 4.2 9.9 - + - -
319A TYR* 4.1 2.9 - - - +
442A GLN* 2.6 34.5 + - + +
445A THR* 1.3 88.2 - - + +
447A GLY* 1.3 64.0 + - - +
449A SER 3.0 23.0 - - - +
450A LEU* 3.3 24.8 - - + +
451A VAL* 5.1 0.6 - - + -
452A LYS* 5.7 2.5 + - - +
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Residues in contact with GLY 447 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315A ALA* 4.4 1.2 - - - +
319A TYR* 2.7 32.9 + - - -
409A ILE* 4.7 13.9 - - - -
443A VAL* 2.8 31.9 + - - -
444A PHE 4.5 0.4 - - - -
445A THR 3.7 0.6 - - - -
446A PHE* 1.3 78.7 - - - +
448A LEU* 1.3 62.9 + - - -
452A LYS* 5.5 4.5 - - - -
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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