Contacts of the helix formed by residues 429 - 443 (chain B) in PDB entry 6PUO
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 VAL 429 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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189B ILE* 3.6 39.5 - - + +
190B PHE* 4.0 20.6 - - + +
193B GLY* 3.8 20.2 - - - -
194B LEU* 4.6 4.0 - - + +
419B PHE* 4.0 19.5 - - + -
428B ASP* 1.3 77.1 - - - +
430B ASP* 1.3 67.0 + - - +
431B VAL 3.4 0.2 - - - -
432B ALA* 3.1 5.0 + - - +
433B ILE* 3.1 40.2 + - + +
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Residues in contact with ASP 430 (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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193B GLY* 3.9 10.0 + - - +
196B LYS* 3.3 24.8 + - - +
197B VAL* 3.7 33.0 - - + +
428B ASP* 3.3 20.8 - - - +
429B VAL* 1.3 74.4 - - - +
431B VAL* 1.3 72.8 + - - +
433B ILE* 3.2 6.4 + - - +
434B LEU* 3.0 38.5 + - + +
464B ARG* 3.8 13.8 + - - +
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Residues in contact with VAL 431 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427B GLN* 3.8 29.2 - - + -
428B ASP* 3.9 13.5 - - + +
430B ASP* 1.3 96.3 + - - +
432B ALA* 1.3 60.4 + - + +
434B LEU* 4.1 6.2 - - - +
435B GLN* 2.9 46.2 + - - +
464B ARG* 4.8 8.7 - - - +
466B ASP* 4.9 4.3 - - - +
467B ILE* 4.6 19.7 - - + +
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Residues in contact with ALA 432 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351B VAL* 4.9 6.5 - - + +
417B THR* 5.4 5.2 - - + +
419B PHE* 4.1 21.1 - - + -
428B ASP 3.8 11.7 - - - +
429B VAL 3.1 10.8 + - - +
431B VAL* 1.3 82.8 - - + +
433B ILE* 1.3 58.7 + - + +
435B GLN* 3.8 8.0 - - - +
436B ALA* 2.9 30.4 + - - +
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Residues in contact with ILE 433 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169B LEU* 5.7 4.0 - - + -
171B ILE* 5.5 7.4 - - + -
194B LEU* 5.0 9.9 - - + -
197B VAL* 4.5 24.5 - - + -
326B VAL* 4.1 32.5 - - + +
328B VAL* 5.4 15.0 - - + -
351B VAL* 4.7 17.5 - - + -
429B VAL* 3.1 32.4 + - + +
430B ASP* 3.7 5.8 - - - +
432B ALA* 1.3 76.8 - - + +
434B LEU* 1.3 62.3 + - + +
436B ALA* 3.3 6.7 + - - +
437B LEU* 2.9 29.5 + - + +
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Residues in contact with LEU 434 (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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169B LEU* 4.7 10.3 - - + -
197B VAL* 4.4 22.4 - - + -
201B THR* 5.1 4.3 - - - +
430B ASP* 3.0 22.6 + - + +
431B VAL* 4.1 5.8 - - - +
433B ILE* 1.3 78.2 - - + +
435B GLN* 1.3 57.2 + - - +
437B LEU* 3.3 6.1 + - + +
438B LEU* 2.9 34.0 + - - +
462B TRP* 3.6 41.0 - - + -
464B ARG* 3.7 35.4 - - - +
467B ILE* 4.7 15.7 - - + -
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Residues in contact with GLN 435 (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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431B VAL* 2.9 35.1 + - - +
432B ALA* 3.9 6.3 - - - +
434B LEU* 1.3 73.8 - - - +
436B ALA* 1.3 61.3 + - - +
438B LEU* 3.9 5.2 - - - +
439B LYS* 2.9 31.1 + - - +
442B ARG* 4.9 1.7 + - - -
467B ILE* 5.4 10.0 - - + +
470B SER* 4.9 10.1 + - - -
471B GLU* 5.0 17.6 - - + +
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Residues in contact with ALA 436 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326B VAL* 5.8 0.9 - - + -
349B PRO* 4.6 9.3 - - + +
351B VAL* 3.9 23.8 - - + -
414B GLN 5.5 0.3 - - - +
415B LEU 5.6 0.8 - - - +
417B THR* 4.0 19.7 - - + +
432B ALA 2.9 18.6 + - - +
433B ILE 3.6 4.5 - - - +
435B GLN* 1.3 77.4 - - - +
437B LEU* 1.3 56.7 + - - +
439B LYS* 3.4 13.9 + - - +
440B ALA* 2.9 29.6 + - - +
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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
----------------------------------------------------------
169B LEU* 3.8 28.5 - - + -
324B PRO* 3.8 22.0 - - + -
325B ILE 4.4 7.6 - - - +
326B VAL* 4.9 10.5 - - + +
349B PRO* 3.8 27.1 - - + +
433B ILE* 2.9 17.1 + - + +
434B LEU* 3.7 7.4 - - + +
436B ALA* 1.3 77.7 - - - +
438B LEU* 1.3 57.5 + - - +
440B ALA* 3.4 1.4 + - + +
441B SER* 3.0 28.1 + - - -
458B LEU* 5.6 4.5 - - + -
462B TRP* 3.7 27.6 - - + -
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Residues in contact with LEU 438 (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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434B LEU* 2.9 19.3 + - + +
435B GLN* 3.9 5.6 - - - +
437B LEU* 1.3 76.1 - - - +
439B LYS* 1.3 59.8 + - - +
441B SER* 3.3 3.7 + - - -
442B ARG* 2.9 38.8 + - - +
455B GLN* 3.8 46.0 - - + +
458B LEU* 4.9 13.7 - - + -
459B ALA* 5.4 2.7 - - + -
462B TRP* 4.7 17.3 - - + -
467B ILE* 3.7 18.2 - - + -
471B GLU* 3.3 28.0 - - - +
472B ILE* 4.9 5.2 - - + -
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Residues in contact with LYS 439 (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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413B ARG 4.3 6.3 + - - -
414B GLN* 3.3 41.2 + - - +
416B LEU 4.2 4.0 + - - -
417B THR* 3.2 28.7 + - - +
435B GLN 2.9 17.6 + - - +
436B ALA* 3.8 10.5 - - - +
438B LEU* 1.3 76.2 - - - +
440B ALA* 1.3 61.6 + - - +
442B ARG* 3.3 26.3 + - - +
443B SER* 3.2 23.2 + - - -
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Residues in contact with ALA 440 (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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347B GLY 5.3 1.8 - - - +
349B PRO* 3.7 28.0 - - + -
414B GLN* 5.2 3.8 - - - +
415B LEU* 4.0 29.0 - - + +
436B ALA 2.9 17.2 + - - +
437B LEU* 3.7 2.9 - - + +
439B LYS* 1.3 80.4 - - - +
441B SER* 1.3 60.6 + - - +
442B ARG 3.5 0.2 + - - -
443B SER* 3.7 6.1 + - - -
444B GLN* 3.6 16.5 + - - +
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Residues in contact with SER 441 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437B LEU* 3.0 19.3 + - - -
438B LEU* 3.3 7.2 + - - -
440B ALA* 1.3 76.3 - - - +
442B ARG* 1.3 61.0 + - - +
444B GLN* 3.6 10.2 - - - +
451B ASN* 2.8 22.7 + - - -
454B HIS* 3.7 24.3 + - - -
455B GLN* 4.1 12.2 - - - +
458B LEU* 4.7 12.2 - - - +
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Residues in contact with ARG 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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435B GLN 4.9 1.6 + - - -
438B LEU* 2.9 20.4 + - - +
439B LYS* 3.5 37.8 + - - +
440B ALA 3.2 0.4 - - - -
441B SER* 1.3 79.3 - - - +
443B SER* 1.3 62.0 + - - +
444B GLN 3.1 9.5 + - - +
446B HIS* 4.3 6.9 + - - -
451B ASN* 3.4 15.0 + - - +
452B TRP* 4.9 22.3 - - + +
455B GLN* 3.4 32.8 + - - +
471B GLU* 3.7 22.4 + - - -
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Residues in contact with SER 443 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414B GLN* 3.6 44.8 - - - +
415B LEU* 4.9 4.2 - - - +
439B LYS 3.2 5.1 + - - -
440B ALA* 3.7 9.0 + - - -
441B SER 3.4 0.2 - - - -
442B ARG* 1.3 77.5 - - - +
444B GLN* 1.3 64.7 + - - +
445B ASP* 3.7 1.7 + - - -
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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