Contacts of the helix formed by residues 379 - 397 (chain B) in PDB entry 3E0D
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 THR 379 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325B ARG* 5.0 3.6 - - - +
377B GLU* 3.2 16.2 + - - +
378B TRP* 1.3 76.0 - - - +
380B ALA* 1.3 71.8 + - - +
381B GLU* 3.7 26.0 + - + +
382B ALA* 3.4 25.8 + - + +
383B ILE* 3.1 25.1 + - - +
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Residues in contact with ALA 380 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325B ARG* 3.0 37.2 - - + +
326B ILE* 4.0 6.4 - - - +
330B PHE* 3.4 35.6 - - + -
379B THR* 1.3 80.3 + - - +
381B GLU* 1.3 67.0 + - - +
383B ILE* 3.4 5.9 + - - +
384B LEU 3.2 16.6 + - - -
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Residues in contact with GLU 381 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330B PHE* 3.4 28.5 - - + -
379B THR* 3.4 19.1 + - + +
380B ALA* 1.3 79.4 - - - +
382B ALA* 1.3 63.5 + - - +
384B LEU* 3.3 6.9 + - - +
385B HIS* 3.1 22.3 + - - +
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Residues in contact with ALA 382 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377B GLU 4.8 3.1 - - - +
378B TRP* 3.6 29.8 - - + -
379B THR* 3.4 28.1 + - + +
380B ALA 3.3 0.6 - - - -
381B GLU* 1.3 78.2 - - - +
383B ILE* 1.3 63.4 + - - +
385B HIS* 3.3 7.3 + - - +
386B ARG* 3.1 18.0 + - - +
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Residues in contact with ILE 383 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318B LEU* 3.7 31.0 - - + -
322B TYR* 3.8 25.6 - - + -
325B ARG* 3.7 33.4 - - + +
326B ILE* 3.7 16.2 - - + -
378B TRP* 4.3 19.5 - - + +
379B THR 3.1 15.6 + - - +
380B ALA 3.7 7.2 - - - +
381B GLU 3.3 0.2 - - - -
382B ALA* 1.3 76.6 - - - +
384B LEU* 1.3 66.8 + - - +
386B ARG 3.3 1.8 + - - +
387B ALA* 3.0 22.3 + - - +
431B LEU* 3.7 8.1 - - + +
444B LEU* 4.4 11.7 - - + -
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Residues in contact with LEU 384 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315B PHE* 4.1 28.3 - - + -
318B LEU* 5.0 7.2 - - + -
326B ILE* 4.8 2.5 - - + -
330B PHE* 3.5 32.1 - - + -
331B TYR* 4.5 11.9 - - + -
334B VAL* 3.7 30.1 - - + -
354B LEU* 5.9 1.8 - - + -
362B TRP* 5.2 2.9 - - + -
380B ALA 3.2 6.9 + - - +
381B GLU* 3.5 10.3 - - - +
383B ILE* 1.3 80.3 - - - +
385B HIS* 1.3 51.2 + - - +
387B ALA* 3.3 3.2 + - + +
388B LEU* 2.7 55.5 + - + +
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Residues in contact with HIS 385 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366B ARG* 4.0 42.1 + - + +
381B GLU 3.1 10.7 + - - +
382B ALA* 3.6 9.6 - - - +
383B ILE 3.3 0.2 - - - -
384B LEU* 1.3 78.9 - - - +
386B ARG* 1.3 54.7 + - - +
388B LEU* 3.2 11.2 + - + +
389B TYR* 2.7 50.3 + + + +
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Residues in contact with ARG 386 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378B TRP* 4.0 35.3 - - + -
382B ALA 3.1 10.9 + - - +
383B ILE 3.8 6.1 - - - +
385B HIS* 1.3 78.4 + - - +
387B ALA* 1.3 56.7 + - - +
389B TYR* 3.2 11.8 + - - +
390B GLU* 2.8 54.4 + - - +
429B GLY 2.9 28.3 + - - -
431B LEU* 3.6 21.1 - - + -
443B PRO* 4.2 7.7 - - - +
444B LEU* 4.2 13.9 - - + +
448B LEU 3.0 23.4 + - - -
449B LEU* 4.9 4.1 - - - +
450B PHE* 3.5 13.0 - - - +
451B GLU* 5.5 2.8 + - - -
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Residues in contact with ALA 387 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314B THR* 4.4 13.5 - - + -
315B PHE* 5.5 2.2 - - + -
318B LEU* 3.8 23.1 - - + -
383B ILE 3.0 16.8 + - - +
384B LEU* 3.7 5.2 - - + +
386B ARG* 1.3 76.0 - - - +
388B LEU* 1.3 58.5 + - + +
390B GLU* 3.4 5.8 + - - +
391B LEU* 3.0 37.7 + - + +
431B LEU* 3.4 17.8 - - + +
432B VAL* 4.0 3.0 - - - +
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Residues in contact with LEU 388 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311B ARG* 4.0 12.2 + - - +
315B PHE* 4.0 19.7 - - + -
362B TRP* 3.5 66.9 - - + +
384B LEU* 2.7 47.4 + - + +
385B HIS* 3.7 9.9 - - + +
387B ALA* 1.3 69.8 - - - +
389B TYR* 1.3 64.3 + - - +
391B LEU* 3.6 5.7 + - - +
392B SER* 3.1 22.7 + - - -
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Residues in contact with TYR 389 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385B HIS* 2.7 36.0 + + + +
386B ARG* 3.2 13.2 + - - +
388B LEU* 1.3 69.4 - - - +
390B GLU* 1.3 72.6 + - + +
392B SER* 3.0 22.7 + - - -
393B VAL* 3.0 36.5 + - + +
396B ARG* 5.8 2.0 + - - -
450B PHE* 4.6 5.2 - + + -
451B GLU* 3.5 27.2 + - - +
456B PRO* 4.0 21.7 - - - +
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Residues in contact with GLU 390 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386B ARG* 2.8 46.8 + - - +
387B ALA 3.8 4.0 - - - +
389B TYR* 1.3 76.3 - - + +
391B LEU* 1.3 57.8 + - - +
393B VAL* 3.1 2.9 + - - +
394B ILE* 2.8 34.8 + - - +
430B SER* 2.7 24.4 + - - -
431B LEU* 2.8 28.6 + - - +
432B VAL* 3.0 14.2 + - + +
450B PHE* 3.2 45.3 - - + +
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Residues in contact with LEU 391 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307B ALA 5.5 0.2 - - - +
310B LEU* 4.0 26.7 - - + -
311B ARG* 3.9 42.6 - - + +
314B THR* 3.7 34.3 - - + +
315B PHE* 4.3 16.2 - - + -
387B ALA 3.0 26.0 + - - +
388B LEU* 3.8 7.6 - - - +
390B GLU* 1.3 76.1 - - - +
392B SER* 1.3 57.1 + - - +
394B ILE* 3.8 4.6 - - + +
395B GLU* 2.9 36.7 + - + +
432B VAL* 3.7 12.8 - - + +
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Residues in contact with SER 392 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311B ARG* 4.1 0.8 - - - +
359B GLU* 3.3 30.8 + - - +
388B LEU 3.1 15.1 + - - -
389B TYR* 3.0 20.3 + - - -
391B LEU* 1.3 76.9 - - - +
393B VAL* 1.3 58.0 + - - +
395B GLU* 3.9 1.6 - - - +
396B ARG* 3.1 33.6 + - - +
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Residues in contact with VAL 393 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389B TYR* 3.0 46.8 + - + +
390B GLU 3.1 4.2 + - - +
392B SER* 1.3 73.7 - - - +
394B ILE* 1.3 67.0 + - - +
396B ARG* 3.4 17.1 + - - +
397B MET* 3.1 35.1 + - - +
450B PHE* 3.8 22.2 - - + -
454B LEU* 5.2 0.7 - - + +
456B PRO* 3.4 35.7 - - + -
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Residues in contact with ILE 394 (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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310B LEU* 3.7 24.7 - - + -
390B GLU 2.8 25.2 + - - +
391B LEU* 3.8 5.4 - - - +
393B VAL* 1.3 73.7 - - - +
395B GLU* 1.3 64.5 + - + +
397B MET* 3.4 4.5 + - - +
398B GLY 3.2 15.6 + - - -
399B PHE* 3.5 12.6 + - + +
400B PRO* 4.0 14.6 - - + -
403B PHE* 3.7 31.6 - - + -
432B VAL* 4.2 22.4 - - + -
450B PHE* 4.0 12.8 - - + -
454B LEU* 3.5 26.9 - - + -
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Residues in contact with GLU 395 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307B ALA* 3.6 34.2 - - + +
310B LEU* 6.1 1.3 - - + -
311B ARG* 2.6 50.4 + - + +
359B GLU* 4.4 10.2 - - - +
391B LEU* 2.9 19.9 + - + +
392B SER 3.9 3.8 - - - +
394B ILE* 1.3 78.2 - - + +
396B ARG* 1.3 63.6 + - - +
398B GLY* 3.1 15.7 + - - +
400B PRO* 4.7 8.6 - - + +
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Residues in contact with ARG 396 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359B GLU* 6.0 1.1 - - - +
389B TYR* 5.8 1.8 + - - -
392B SER* 3.1 20.3 + - - +
393B VAL* 3.9 26.1 - - - +
395B GLU* 1.3 80.4 - - - +
397B MET* 1.3 71.4 + - - +
398B GLY 3.9 0.3 + - - -
456B PRO* 3.0 32.9 + - - +
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Residues in contact with MET 397 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A GLU* 5.6 1.9 - - - +
393B VAL* 3.1 33.1 + - - +
394B ILE* 4.0 4.0 - - - +
396B ARG* 1.3 93.1 - - - +
398B GLY* 1.9 45.2 + - - +
399B PHE* 3.9 25.0 - - + -
454B LEU* 4.0 25.8 - - + -
455B ASN 3.6 16.2 - - - +
456B PRO* 4.1 4.5 - - - +
458B ARG 2.8 30.7 - - - +
459B VAL* 3.6 35.8 - - + +
460B SER 3.8 7.2 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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