Contacts of the helix formed by residues 373 - 385 (chain B) in PDB entry 2D2O
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 ASN 373 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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371B VAL* 2.9 8.4 + - - +
372B MET* 1.3 66.5 - - - +
374B TYR* 1.3 61.1 + - - +
375B LEU* 3.3 19.6 - - - +
376B PHE* 3.2 34.1 + - - +
377B ARG 3.3 4.3 + - - -
401B ALA* 6.1 1.2 - - - +
405B TYR* 5.1 4.9 + - - -
413B LEU* 3.6 32.1 - - + +
414B TRP 2.9 23.9 + - - +
415B ASN* 2.9 21.0 - - - +
416B LEU* 3.4 12.0 - - - +
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Residues in contact with TYR 374 (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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323B ARG* 5.6 1.6 + - - -
354B GLU* 5.0 4.1 + - + +
355B ILE 4.7 0.6 + - - -
356B TRP* 3.3 88.8 + + + +
372B MET* 2.9 41.1 + - + +
373B ASN* 1.3 70.3 - - - +
375B LEU* 1.3 64.8 + - - +
376B PHE 3.2 0.2 - - - -
377B ARG* 3.3 31.2 + - + +
378B GLU* 3.0 29.4 + - + +
416B LEU* 3.8 16.2 - - + +
419B SER* 2.8 27.9 + - - -
420B HIS* 5.8 0.2 - - - -
421B ASP* 4.4 2.1 + - - -
422B THR* 4.2 6.1 - - + -
1D GLC 6.0 2.2 - - - -
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Residues in contact with LEU 375 (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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98A GLU* 3.6 21.1 - - - +
356B TRP 3.8 16.8 - - - +
357B HIS* 4.1 7.4 - - - +
358B ASP* 4.3 6.1 - - - -
373B ASN* 3.2 11.1 - - - +
374B TYR* 1.3 77.7 - - - +
376B PHE* 1.3 63.8 + - - +
378B GLU* 3.3 9.2 + - + +
379B SER* 3.2 25.6 + - - -
401B ALA* 4.7 17.5 - - + -
404B LEU* 3.7 30.3 - - + -
405B TYR* 3.7 17.3 - - + +
1D GLC 5.0 5.8 - - - +
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Residues in contact with PHE 376 (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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373B ASN* 3.2 29.2 + - - +
375B LEU* 1.3 80.3 - - - +
377B ARG* 1.3 64.2 + - - +
379B SER* 3.4 5.6 + - - -
380B VAL* 3.0 46.8 + - + +
398B LEU* 5.5 7.0 - - + -
401B ALA* 6.1 0.6 - - - +
415B ASN* 3.5 42.8 - - + +
416B LEU 3.4 23.1 - - - -
417B LEU* 4.4 7.4 - - + -
442B PHE* 3.4 31.2 - + - -
443B GLN* 4.1 15.5 - - + -
446B TYR* 3.9 22.2 - + + -
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Residues in contact with ARG 377 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356B TRP* 5.3 1.4 - - - -
373B ASN 3.3 2.9 + - - +
374B TYR* 3.3 36.9 + - + +
375B LEU 3.2 0.4 - - - -
376B PHE* 1.3 81.0 - - - +
378B GLU* 1.3 74.7 + - - +
380B VAL* 3.1 6.2 + - - +
381B ILE* 2.7 57.2 + - + +
416B LEU* 3.6 18.2 - - + +
417B LEU 3.0 31.5 + - - +
418B ASP* 3.7 11.0 - - - +
422B THR* 3.5 30.3 + - - +
423B GLU* 4.3 12.5 + - - +
425B PHE* 5.9 0.4 - - + -
428B SER* 4.5 3.8 + - - -
1D GLC 4.6 9.7 + - - -
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Residues in contact with GLU 378 (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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374B TYR* 3.0 17.7 + - + +
375B LEU* 3.6 12.3 - - + +
376B PHE 3.3 0.2 - - - -
377B ARG* 1.3 100.4 + - + +
379B SER* 1.3 58.2 + - - +
381B ILE* 3.3 8.2 + - - +
382B ARG* 3.0 59.3 + - - +
1D GLC 2.7 44.3 + - - +
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Residues in contact with SER 379 (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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375B LEU 3.2 11.8 + - - -
376B PHE* 3.8 5.6 - - - -
378B GLU* 1.3 79.1 - - - +
380B VAL* 1.3 58.2 + - - +
382B ARG* 3.5 1.8 + - - +
383B PHE* 2.9 32.2 + - - +
389B ILE* 3.9 1.4 - - - +
394B PHE* 3.5 8.9 - - - -
397B GLU* 2.7 39.4 + - - +
398B LEU* 3.7 26.7 - - - +
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Residues in contact with VAL 380 (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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376B PHE* 3.0 47.0 + - + +
377B ARG* 3.5 6.1 - - - +
379B SER* 1.3 75.6 - - - +
381B ILE* 1.3 65.1 + - - +
384B PHE* 3.0 43.7 + - + +
385B ALA 3.7 0.7 + - - -
394B PHE* 4.2 3.4 - - + -
398B LEU* 5.8 0.2 - - + -
417B LEU* 3.9 19.3 - - + -
425B PHE* 3.8 19.6 - - + -
439B ALA* 4.1 3.6 - - + +
442B PHE* 3.8 18.8 - - + -
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Residues in contact with ILE 381 (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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377B ARG* 2.7 56.5 + - + +
378B GLU* 3.5 11.7 - - - +
380B VAL* 1.3 72.3 - - - +
382B ARG* 1.3 66.9 + - - +
385B ALA* 2.9 27.9 + - + +
386B THR* 2.9 30.0 + - + +
423B GLU* 5.1 1.3 - - - +
425B PHE* 3.5 24.7 - - + -
428B SER* 3.6 26.0 - - - +
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Residues in contact with ARG 382 (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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99A THR* 3.8 25.5 + - - +
378B GLU* 3.0 45.8 + - - +
379B SER* 3.9 0.4 - - - +
381B ILE* 1.3 85.1 - - - +
383B PHE* 1.3 57.5 + - - +
386B THR* 3.4 6.1 - - - +
387B GLY* 3.1 6.1 + - - -
388B GLU* 2.8 67.3 + - + +
389B ILE* 3.3 21.0 + - + +
393B ARG* 4.8 1.8 - - - +
397B GLU* 3.0 40.9 + - - -
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Residues in contact with PHE 383 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379B SER 2.9 18.8 + - - +
380B VAL 4.3 0.4 - - - +
382B ARG* 1.3 79.6 - - - +
384B PHE* 1.3 87.8 + + + +
387B GLY* 4.1 10.0 - - - -
389B ILE* 3.6 17.6 - - + +
390B HIS 3.9 0.4 - - - -
391B ALA* 3.4 38.4 - - + -
394B PHE* 3.3 48.5 - + + -
515B ASN* 3.4 11.6 + - - -
517B TYR* 4.3 9.9 - + + -
532B LEU* 5.2 1.6 - - + -
534B ASN* 2.8 52.0 + - + -
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Residues in contact with PHE 384 (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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380B VAL* 3.0 28.7 + - + +
383B PHE* 1.3 103.7 - + - +
385B ALA* 1.3 63.5 + - - +
387B GLY 4.7 0.9 - - - -
394B PHE* 3.8 15.0 - + - -
425B PHE* 4.3 1.8 - - + -
429B CYS* 4.6 1.3 - - - -
435B LYS* 3.6 34.3 - - + +
438B LEU* 3.7 37.9 - - + -
439B ALA* 3.9 18.8 - - + -
442B PHE* 3.8 22.7 - + + -
532B LEU* 3.5 27.6 - - + -
534B ASN* 3.7 19.4 - - - +
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Residues in contact with ALA 385 (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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380B VAL 3.7 0.4 + - - -
381B ILE* 2.9 26.1 + - + +
384B PHE* 1.3 81.5 - - - +
386B THR* 1.3 63.5 + - + +
387B GLY 3.5 0.2 - - - -
425B PHE* 4.0 10.5 - - + -
428B SER* 3.7 42.0 - - - +
429B CYS* 4.0 14.4 - - - -
435B LYS* 4.5 12.3 + - - +
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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