Contacts of the helix formed by residues 439 - 452 (chain B) in PDB entry 3OEH
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 ALA 439 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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190B ARG* 3.1 29.4 - - - +
191B TRP* 6.3 1.1 - - - -
438B LEU* 1.3 78.0 - - - +
440B THR* 1.3 68.0 + - - +
441B GLU* 3.3 29.8 - - + +
442B GLU* 3.0 26.8 + - - +
443B GLN* 3.3 13.1 + - - +
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Residues in contact with THR 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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149B GLN* 3.0 35.7 + - - -
191B TRP* 6.2 0.8 - - - -
382B VAL* 3.7 30.2 - - + +
385B LEU* 4.8 8.4 - - + +
439B ALA* 1.3 72.5 - - - +
441B GLU* 1.3 65.7 + - - +
443B GLN* 2.9 26.6 + - - +
444B VAL* 3.2 26.6 + - + +
485B ILE* 4.4 12.3 - - + +
486B ARG* 5.9 1.6 - - - -
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Residues in contact with GLU 441 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439B ALA* 3.6 18.0 - - + +
440B THR* 1.3 86.2 + - - +
442B GLU* 1.3 61.6 + - + +
444B VAL* 4.3 1.0 - - - +
445B PRO* 3.1 26.5 - - - +
482B LEU* 3.4 40.8 - - + +
485B ILE* 4.2 20.3 - - + +
486B ARG* 3.0 48.8 + - - +
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Residues in contact with GLU 442 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190B ARG* 3.4 12.3 + - - -
438B LEU* 3.4 27.4 - - + +
439B ALA* 3.0 33.5 + - + +
440B THR 3.2 1.0 - - - -
441B GLU* 1.3 81.3 - - + +
443B GLN* 1.3 62.6 + - - +
445B PRO* 3.7 4.2 - - - +
446B LEU* 3.4 22.2 - - - +
471B LEU* 3.5 30.5 - - + +
475B LYS* 3.2 34.6 + - - -
482B LEU* 5.4 6.1 - - + -
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Residues in contact with GLN 443 (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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151B GLY* 3.3 27.7 + - - -
152B LEU 3.7 1.2 - - - +
153B LYS* 3.9 30.0 - - + +
156B ASP* 3.8 16.9 + - - +
385B LEU* 3.6 26.1 - - + +
438B LEU* 3.3 29.5 + - + +
439B ALA 3.3 10.0 + - - +
440B THR* 2.9 11.7 + - - +
442B GLU* 1.3 79.1 - - - +
444B VAL* 1.3 67.8 + - - +
445B PRO* 3.3 0.4 - - - -
446B LEU* 2.9 21.0 + - - +
447B ILE* 3.2 18.9 + - + +
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Residues in contact with VAL 444 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384B ALA* 3.7 40.6 - - + +
385B LEU* 4.0 8.3 - - + +
388B VAL* 3.3 18.5 - - + +
440B THR* 3.2 22.9 + - + +
441B GLU 4.3 0.9 - - - +
443B GLN* 1.3 72.3 - - - +
445B PRO* 1.4 73.0 - - + +
447B ILE* 3.4 1.7 + - - -
448B TYR* 2.9 26.3 + - - +
485B ILE* 3.7 31.6 - - + -
491B LEU* 4.6 12.1 - - + -
499B LEU* 4.8 3.8 - - + -
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Residues in contact with PRO 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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441B GLU 3.1 23.3 - - - +
442B GLU* 3.7 5.2 - - - +
443B GLN 3.3 4.7 - - - -
444B VAL* 1.4 95.5 - - + +
446B LEU* 1.3 59.4 + - - +
448B TYR* 3.7 1.8 - - + +
449B ALA* 3.0 28.1 + - - +
470B PHE* 3.8 18.7 - - + -
474B LEU* 4.2 10.3 - - + -
482B LEU* 4.3 15.5 - - + -
485B ILE* 4.6 3.8 - - + -
499B LEU* 3.7 32.3 - - + +
503B THR* 5.2 0.3 + - - -
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Residues in contact with LEU 446 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B LYS* 3.7 24.9 - - + +
429B LEU* 3.3 28.1 - - + +
438B LEU* 4.6 3.4 - - + -
442B GLU 3.4 17.7 - - - +
443B GLN* 2.9 8.3 + - - +
445B PRO* 1.3 77.7 - - - +
447B ILE* 1.3 60.7 + - + +
449B ALA* 3.5 6.1 + - - +
450B GLY 3.2 19.2 + - - -
466B PHE* 4.8 3.6 - - + -
467B GLU* 3.7 42.8 - - + +
470B PHE* 3.8 25.4 - - + -
471B LEU* 4.2 19.3 - - + -
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Residues in contact with ILE 447 (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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153B LYS* 4.8 10.5 - - + +
157B ALA* 4.2 16.8 - - + -
385B LEU* 3.8 28.5 - - + -
388B VAL* 3.4 36.2 - - + +
389B ALA* 4.3 1.1 - - + +
392B LEU* 4.0 19.1 - - + -
429B LEU* 4.1 14.4 - - + -
430B LEU* 5.0 8.1 - - + -
443B GLN* 3.2 19.1 + - + +
446B LEU* 1.3 77.4 - - + +
448B TYR* 1.3 60.5 + - - +
450B GLY 3.8 0.4 - - - -
451B VAL* 2.9 36.8 + - + +
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Residues in contact with TYR 448 (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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388B VAL* 3.9 11.9 - - + +
444B VAL 2.9 17.4 + - - +
445B PRO 3.7 5.2 - - - +
446B LEU 3.3 0.2 - - - -
447B ILE* 1.3 78.1 - - - +
449B ALA* 1.3 59.3 + - - +
452B ASN* 3.0 69.4 + - - +
454B HIS* 3.7 21.9 + + - -
496B LEU* 3.7 45.1 + - + +
499B LEU* 3.7 25.8 - - + -
500B LYS* 3.3 49.1 - - - +
503B THR* 4.4 5.6 - - - -
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Residues in contact with ALA 449 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429B LEU* 5.9 0.2 - - + -
445B PRO 3.0 17.7 + - - +
446B LEU 3.7 5.6 - - - +
448B TYR* 1.3 75.5 - - - +
450B GLY* 1.3 56.1 + - - +
454B HIS* 3.0 38.2 + - + +
455B LEU* 3.4 15.7 - - + +
466B PHE* 4.1 23.3 - - + -
470B PHE* 4.5 1.6 - - + -
503B THR* 3.9 21.8 - - + -
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Residues in contact with GLY 450 (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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422B ARG* 4.1 8.8 - - - -
425B ARG* 6.2 0.7 - - - -
426B LEU* 3.8 23.7 - - - +
429B LEU* 4.0 5.4 - - - -
446B LEU 3.2 12.3 + - - -
447B ILE 3.6 1.5 + - - -
448B TYR 3.1 0.6 - - - -
449B ALA* 1.3 76.9 - - - +
451B VAL* 1.3 66.4 + - - +
453B GLY* 2.8 17.7 + - - -
455B LEU* 4.3 11.4 - - - +
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Residues in contact with VAL 451 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388B VAL* 3.1 28.0 - - - +
390B GLY 5.4 7.2 - - - +
392B LEU* 3.9 24.7 - - + -
422B ARG* 2.9 25.8 + - - -
426B LEU* 4.0 7.0 - - + +
447B ILE* 2.9 29.4 + - + +
450B GLY* 1.3 69.9 - - - +
452B ASN* 1.3 69.6 + - - +
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Residues in contact with ASN 452 (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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388B VAL* 5.6 1.2 - - - +
422B ARG* 4.0 8.9 + - - +
448B TYR* 3.0 58.2 + - + +
451B VAL* 1.3 88.8 - - - +
453B GLY* 1.3 59.8 + - - +
454B HIS* 3.4 24.9 + - + +
500B LYS* 6.1 0.2 - - - -
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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