Contacts of the helix formed by residues 374 - 383 (chain B) in PDB entry 5E9W
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 TYR 374 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291B PHE* 5.2 3.5 - - - -
321B SER* 3.8 16.6 - - - -
322B PHE* 3.6 31.2 - + - -
353B LEU* 4.7 20.3 + - + +
372B LEU* 3.9 10.7 + - + +
373B VAL* 1.3 70.6 - - - +
375B PHE* 1.3 65.5 + - - +
376B PRO* 3.6 33.0 - - + +
377B LEU* 2.9 39.4 + - + +
378B LEU* 3.2 5.7 + - - +
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Residues in contact with PHE 375 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318B THR* 5.4 0.4 - - + -
320B ASN* 6.1 0.2 - - - +
321B SER* 4.2 3.2 + - - +
322B PHE* 5.2 6.3 - - + -
373B VAL* 3.2 11.7 + - + +
374B TYR* 1.3 72.5 - - - +
376B PRO* 1.3 74.1 - - + +
378B LEU* 3.1 27.8 + - + +
379B ASN* 2.9 26.5 + - + +
389B LEU* 3.8 20.6 - - + -
392B LYS* 3.5 48.0 - - + -
468B LEU* 4.3 22.2 - - + -
470B PHE* 3.7 23.1 - + + -
472B PHE* 3.7 22.0 - + - -
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Residues in contact with PRO 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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322B PHE* 4.3 12.1 - - + -
374B TYR* 3.6 39.5 - - + +
375B PHE* 1.3 96.1 - - + +
377B LEU* 1.3 57.9 + - - +
379B ASN* 3.6 8.6 + - + +
380B GLU* 3.2 27.7 + - - +
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Residues in contact with LEU 377 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291B PHE* 3.8 22.7 - - + -
353B LEU* 3.9 42.4 - - + +
354B PHE* 3.9 19.7 - - + -
374B TYR* 2.9 26.7 + - + +
376B PRO* 1.3 77.8 - - - +
378B LEU* 1.3 59.4 + - - +
380B GLU* 3.1 8.5 + - + +
381B MET* 2.9 47.8 + - + +
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Residues in contact with LEU 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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287B CYS* 5.6 7.2 - - + -
291B PHE* 4.1 25.1 - - + -
301B LEU* 3.8 30.1 - - + -
314B PHE* 4.9 4.3 - - + -
318B THR* 5.3 1.1 - - + -
373B VAL* 4.2 18.8 - - + -
374B TYR 3.2 6.7 + - - +
375B PHE* 3.1 35.5 + - + +
377B LEU* 1.3 79.0 - - - +
379B ASN* 1.3 63.0 + - - +
381B MET* 3.9 4.2 - - - +
382B ALA* 3.0 24.3 + - - +
470B PHE* 4.6 17.9 - - + -
472B PHE* 4.2 14.6 - - + -
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Residues in contact with ASN 379 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375B PHE* 2.9 23.3 + - + +
376B PRO* 3.6 10.3 + - + +
378B LEU* 1.3 78.7 - - - +
380B GLU* 1.3 64.8 + - - +
382B ALA* 3.5 8.7 + - - +
383B LYS* 3.5 34.2 + - - +
387B MET 5.2 0.7 - - - +
389B LEU* 3.4 24.7 + - - +
472B PHE* 3.4 27.7 - - + -
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Residues in contact with GLU 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 PRO 3.2 13.7 + - - +
377B LEU* 3.1 14.4 + - + +
379B ASN* 1.3 82.3 + - - +
381B MET* 1.3 63.6 + - + +
383B LYS* 2.4 52.0 + - - +
384B LYS* 4.1 1.4 + - - +
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Residues in contact with MET 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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291B PHE* 4.3 11.2 - - - -
294B TYR* 3.7 28.0 - - + -
297B ALA* 3.9 9.6 - - + -
298B ASP* 3.6 36.2 - - + +
301B LEU* 3.5 18.0 - - + +
354B PHE* 3.9 17.5 - - - -
377B LEU* 2.9 42.9 + - + +
378B LEU* 4.0 2.0 - - - +
380B GLU* 1.3 75.9 - - + +
382B ALA* 1.3 62.3 + - - +
384B LYS* 3.1 24.2 + - - +
385B TYR* 4.1 3.6 - - - -
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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
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301B LEU* 3.8 18.8 - - + +
305B CYS* 5.4 0.7 - - - -
378B LEU 3.0 18.6 + - - +
379B ASN 3.7 6.5 - - - +
380B GLU 3.2 0.4 - - - -
381B MET* 1.3 75.8 - - - +
383B LYS* 1.3 61.5 + - - +
384B LYS 3.1 0.2 - - - -
385B TYR* 3.1 14.9 + - - +
387B MET* 3.3 37.9 + - + +
472B PHE* 4.1 20.4 - - + -
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Residues in contact with LYS 383 (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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379B ASN* 3.5 28.0 + - - +
380B GLU* 2.4 50.7 + - - +
382B ALA* 1.3 73.9 - - - +
384B LYS* 1.3 60.2 + - - +
386B ASN* 2.8 20.9 + - - +
387B MET 3.9 17.9 + - - +
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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