Contacts of the helix formed by residues 434 - 447 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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219A ARG* 3.6 28.5 - - - -
261B ARG* 3.3 14.9 + - - -
329B GLU* 5.1 1.8 - - - -
430B ALA 4.0 1.2 + - - -
431B ILE 3.0 11.1 + - - -
432B ALA 2.9 5.5 + - - -
433B ASP* 1.3 83.7 - - - +
435B SER* 1.3 63.5 + - - -
436B LEU 3.3 0.6 + - - -
437B LEU 3.6 4.9 + - - -
438B ASP* 3.6 5.7 + - - +
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Residues in contact with SER 435 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A ARG* 3.8 11.6 + - - -
322B GLN* 6.0 0.7 - - - +
325B GLU* 6.5 0.4 - - - -
326B LEU* 3.8 14.2 - - - +
329B GLU* 2.8 35.6 + - - -
431B ILE 4.5 1.4 + - - -
434B GLY* 1.3 71.3 - - - -
436B LEU* 1.3 64.1 + - - +
437B LEU 3.2 0.7 - - - -
438B ASP* 3.4 11.7 + - - +
439B LEU* 3.1 23.4 + - - +
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Residues in contact with LEU 436 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326B LEU* 3.7 32.3 - - + +
330B LEU* 4.4 6.7 - - + -
375B LEU* 6.0 0.4 - - + -
416B LEU* 4.1 24.5 - - + +
419B CYS* 3.9 9.2 - - + -
420B TYR* 3.3 47.1 - - + +
423B LEU* 3.8 19.1 - - + -
431B ILE 5.0 1.3 + - - +
432B ALA* 3.4 12.8 - - - +
434B GLY 3.3 0.8 - - - -
435B SER* 1.3 79.4 - - - +
437B LEU* 1.3 60.5 + - - +
439B LEU* 3.6 3.1 + - + +
440B LEU* 3.2 25.7 + - + +
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Residues in contact with LEU 437 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261B ARG* 4.8 2.9 - - - +
275B ARG* 3.9 17.9 - - + +
278B TYR* 3.6 21.3 - - + +
420B TYR* 4.1 16.4 - - + +
432B ALA 3.2 14.8 + - - +
433B ASP* 3.7 44.0 - - - +
434B GLY 3.9 0.2 - - - +
435B SER 3.2 0.6 - - - -
436B LEU* 1.3 75.0 - - - +
438B ASP* 1.3 55.4 + - - +
440B LEU* 2.9 8.8 + - - +
441B ARG* 2.8 68.5 + - + +
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Residues in contact with ASP 438 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257B PRO* 3.5 30.5 - - + +
261B ARG* 2.9 40.3 + - - +
322B GLN* 5.6 3.6 - - - +
434B GLY 3.6 6.2 + - - +
435B SER* 3.4 14.2 + - - +
437B LEU* 1.3 78.1 - - - +
439B LEU* 1.3 61.4 + - - +
441B ARG* 3.3 10.6 + - - +
442B GLN* 3.0 30.3 + - - +
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Residues in contact with LEU 439 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319B TYR* 3.9 27.4 - - + +
322B GLN* 3.5 33.2 - - + +
323B ILE* 3.6 33.7 - - + -
326B LEU* 4.0 18.2 - - + -
412B PHE* 5.5 0.2 - - + -
416B LEU* 4.1 20.4 - - + -
435B SER 3.1 16.1 + - - +
436B LEU* 3.8 5.6 - - + +
437B LEU 3.1 0.6 - - - -
438B ASP* 1.3 73.8 - - - +
440B LEU* 1.3 61.5 + - - +
442B GLN* 2.9 15.5 + - - +
443B VAL* 2.8 31.8 + - + +
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Residues in contact with LEU 440 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278B TYR* 3.6 39.3 - - + +
413B LEU* 3.8 26.7 - - + -
416B LEU* 3.8 23.6 - - + +
417B GLU* 4.2 10.1 - - + -
420B TYR* 4.0 26.7 - - + -
436B LEU* 3.2 22.1 + - + +
437B LEU* 2.9 9.5 + - - +
439B LEU* 1.3 77.9 - - - +
441B ARG* 1.3 61.1 + - - +
443B VAL* 3.3 3.2 + - - +
444B PHE* 3.1 35.0 + - + -
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Residues in contact with ARG 441 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256B VAL* 4.7 3.4 - - + +
257B PRO* 4.4 9.6 + - + -
260B LEU* 3.5 47.0 - - + +
261B ARG* 4.2 7.7 - - - +
264B ASP* 2.6 32.6 + - - -
275B ARG* 4.3 1.8 - - - +
276B LEU* 3.3 28.2 + - - +
277B PRO 4.5 1.1 + - - -
278B TYR* 3.7 23.6 - - + +
280B VAL 5.0 2.9 + - - -
437B LEU* 2.8 49.6 + - + +
438B ASP* 3.5 19.1 + - - +
440B LEU* 1.3 76.0 - - - +
442B GLN* 1.3 61.7 + - - +
444B PHE* 3.7 1.7 + - - +
445B THR* 3.1 27.0 + - - -
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Residues in contact with GLN 442 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253B TRP* 2.9 61.9 + - + +
254B LYS* 4.7 1.6 - - - +
256B VAL* 5.4 0.4 - - - -
257B PRO* 3.6 19.3 - - + +
319B TYR* 3.5 5.3 + - + +
322B GLN* 2.8 26.5 + - - +
438B ASP 3.0 15.3 + - - +
439B LEU* 2.9 25.2 + - - +
441B ARG* 1.3 75.2 - - - +
443B VAL* 1.3 58.0 + - - +
445B THR 2.9 1.7 + - - -
446B PHE* 2.7 52.9 + - + -
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Residues in contact with VAL 443 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319B TYR* 3.2 29.4 - - + +
409B ILE* 3.7 23.0 - - + +
412B PHE* 3.8 20.4 - - + -
413B LEU* 3.4 28.3 - - + -
416B LEU* 4.0 17.9 - - + -
439B LEU* 2.8 18.9 + - + +
440B LEU* 3.7 7.6 - - - +
442B GLN* 1.3 75.2 - - - +
444B PHE* 1.3 57.3 + - - +
445B THR 3.1 0.9 + - - -
447B GLY* 2.9 28.6 + - - -
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Residues in contact with PHE 444 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278B TYR* 3.2 52.7 - + - +
279B ASN* 3.3 35.9 - - + +
281B SER* 3.3 15.0 + - - +
284B ARG* 3.4 11.6 + - - -
409B ILE* 5.9 2.7 - - + -
413B LEU* 3.5 42.0 - - + -
417B GLU* 3.9 7.6 - - - -
440B LEU* 3.1 27.9 + - + +
441B ARG 4.3 2.2 - - - +
443B VAL* 1.3 75.5 - - - +
445B THR* 1.3 59.6 + - - +
447B GLY 4.9 0.2 - - - -
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Residues in contact with THR 445 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256B VAL* 4.2 20.5 - - + +
260B LEU* 5.1 3.5 - - - +
281B SER* 3.8 16.9 - - - -
283B ILE* 3.9 17.9 + - - +
284B ARG* 4.5 19.5 + - - +
285B PHE* 4.5 11.3 + - + +
441B ARG 3.1 17.7 + - - -
442B GLN 2.9 4.2 + - - -
444B PHE* 1.3 81.3 + - - +
446B PHE* 1.3 86.6 + - + +
447B GLY 3.8 0.2 - - - -
450B LEU 4.4 2.1 - - - +
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Residues in contact with PHE 446 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248B ILE* 4.3 11.4 - - + -
252B VAL* 3.6 23.6 - - + -
253B TRP* 3.4 50.7 - + + -
256B VAL* 3.4 34.5 - - + -
285B PHE* 4.2 9.9 - + + -
319B TYR* 3.8 2.9 - - - +
442B GLN* 2.7 35.2 + - + +
445B THR* 1.3 86.7 - - + +
447B GLY* 1.3 59.4 + - - +
449B SER* 3.7 3.3 + - - -
450B LEU* 2.6 63.7 + - + +
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Residues in contact with GLY 447 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319B TYR* 3.1 26.2 + - - -
409B ILE* 3.8 21.5 - - - -
412B PHE* 5.9 0.7 - - - -
443B VAL* 2.9 20.9 + - - -
444B PHE 4.9 0.4 - - - -
445B THR 3.8 0.4 - - - -
446B PHE* 1.3 83.8 - - - +
448B LEU* 1.3 63.1 + - - -
449B SER* 4.3 1.1 - - - -
450B LEU 4.1 1.2 + - - -
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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