Contacts of the helix formed by residues 390 - 400 (chain E) in PDB entry 1P8J
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 TRP 390 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275E PHE* 6.2 0.7 - + - -
278E VAL* 3.2 54.2 + - + +
282E ARG* 4.1 1.0 - - - +
284E GLY 5.9 0.2 - - - -
285E LEU 2.8 18.1 + - - +
286E GLY 4.1 2.0 - - - +
287E SER 3.7 22.9 - - - +
288E ILE* 4.4 14.2 - - + +
312E ILE* 3.4 30.1 - - + -
313E TYR* 4.1 21.5 - + - -
315E LEU* 5.4 1.7 - - - +
389E THR* 1.3 76.3 - - - +
391E ARG* 1.3 86.5 + - + +
393E MET* 3.7 4.7 - - - +
394E GLN* 3.6 41.1 + - - +
447E GLN* 4.0 24.0 - - - -
486E HIS* 4.4 5.6 - + - -
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Residues in contact with ARG 391 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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389E THR* 3.0 7.7 + - - +
390E TRP* 1.3 107.6 - - + +
392E ASP* 1.3 67.1 + - - +
393E MET 3.1 2.0 - - - -
394E GLN* 2.9 16.4 + - - +
395E HIS* 3.0 21.3 + - + -
444E VAL* 3.7 19.4 + - + +
445E ALA 2.5 31.5 + - - -
446E PRO* 3.3 2.2 - - - +
447E GLN* 2.9 45.5 - - - +
485E GLU* 2.7 49.0 + - - +
486E HIS* 5.5 3.1 - - + -
539E TRP* 4.8 1.3 - - + -
573E THR* 3.6 9.7 - - - +
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Residues in contact with ASP 392 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387E ASN 4.1 0.3 - - - +
388E LEU* 3.6 15.7 - - + -
389E THR* 2.8 37.5 + - - +
391E ARG* 1.3 75.3 - - - +
393E MET* 1.3 58.0 + - - +
395E HIS* 3.0 10.0 + - - +
396E LEU* 2.9 32.6 + - - +
441E TRP* 3.0 24.8 + - - +
443E THR* 2.7 24.6 + - - -
444E VAL* 2.9 31.2 + - - +
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Residues in contact with MET 393 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288E ILE* 3.8 24.5 - - + -
315E LEU* 4.4 7.0 - - + -
378E ILE* 3.6 46.0 - - + +
381E THR* 3.9 19.3 - - + -
382E LEU* 3.9 14.8 - - + -
388E LEU* 3.8 27.1 - - + +
389E THR 3.0 11.0 + - - +
390E TRP 3.7 11.7 - - - +
391E ARG 3.1 0.2 - - - -
392E ASP* 1.3 78.2 - - - +
394E GLN* 1.3 62.8 + - - +
396E LEU* 3.2 7.2 + - - +
397E VAL* 3.1 26.8 + - + +
434E MET* 4.1 10.8 - - - -
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Residues in contact with GLN 394 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312E ILE 3.1 22.0 + - - +
313E TYR 4.4 4.6 + - - -
314E THR 4.2 10.6 + - - +
315E LEU* 3.7 27.1 - - + +
337E LEU* 3.8 20.0 - - + +
390E TRP* 3.6 26.8 + - - +
391E ARG* 2.9 10.5 + - - +
393E MET* 1.3 73.6 - - - +
395E HIS* 1.3 65.9 + - - +
397E VAL* 3.2 2.8 + - - +
398E VAL* 3.0 27.9 + - - +
486E HIS* 2.6 30.1 + - - -
536E THR* 5.7 0.2 - - - +
539E TRP* 3.8 17.1 - - + -
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Residues in contact with HIS 395 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391E ARG* 3.0 27.0 + - + -
392E ASP 3.0 7.8 + - - +
394E GLN* 1.3 78.0 - - - +
396E LEU* 1.3 62.7 + - - +
398E VAL* 3.2 2.8 + - - +
399E GLN* 3.0 33.2 + - - +
441E TRP* 3.8 19.1 - + + -
444E VAL* 3.5 29.5 - - + +
483E ARG* 5.3 10.1 - - - -
485E GLU* 2.7 34.5 + - + -
539E TRP* 3.1 38.5 + + - +
540E ASP* 4.4 13.0 + - - -
573E THR* 5.8 0.9 - - - -
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Residues in contact with LEU 396 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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381E THR* 3.7 29.6 - - + -
388E LEU* 3.7 22.2 - - + -
392E ASP 2.9 17.0 + - - +
393E MET* 3.6 10.5 - - - +
394E GLN 3.2 0.2 - - - -
395E HIS* 1.3 78.1 - - - +
397E VAL* 1.3 55.8 + - - +
400E THR* 2.7 38.7 + - + +
434E MET* 3.8 12.6 - - + +
437E LEU* 3.6 25.1 - - + +
438E ALA* 3.8 10.5 - - + +
441E TRP* 3.4 39.7 - - + -
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Residues in contact with VAL 397 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315E LEU* 3.8 20.2 - - + -
317E ILE* 5.6 1.1 - - + -
337E LEU* 4.1 19.7 - - + +
338E ALA* 3.4 31.6 - - + -
378E ILE* 5.0 3.6 - - + -
393E MET* 3.1 16.8 + - + +
394E GLN 3.6 7.2 - - - +
395E HIS 3.2 0.2 - - - -
396E LEU* 1.3 75.0 - - - +
398E VAL* 1.3 57.8 + - - +
401E SER* 2.6 41.1 + - - +
429E LEU* 3.7 8.5 - - + -
434E MET* 3.7 24.9 - - + -
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Residues in contact with VAL 398 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337E LEU* 3.9 25.4 - - + -
394E GLN 3.0 15.2 + - - +
395E HIS 3.6 7.2 - - - +
397E VAL* 1.3 79.3 - - - +
399E GLN* 1.3 62.5 + - + +
401E SER 4.1 4.2 + - - +
418E ARG* 3.6 33.2 - - - +
426E TYR* 3.8 42.1 - - + +
539E TRP* 3.9 34.3 - - + -
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Residues in contact with GLN 399 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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395E HIS* 3.0 21.7 + - - +
396E LEU 4.1 0.2 - - - +
398E VAL* 1.3 79.9 - - + +
400E THR* 1.3 60.8 + - - +
401E SER 4.8 1.8 - - - +
402E LYS* 5.4 0.3 + - - -
418E ARG* 3.6 31.8 + - - +
437E LEU* 3.7 20.1 - - + +
441E TRP* 2.8 44.6 - - - -
539E TRP* 6.4 0.2 - - - +
540E ASP* 5.1 3.8 - - - +
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Residues in contact with THR 400 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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396E LEU* 2.7 21.2 + - - +
397E VAL 3.9 0.9 + - - -
399E GLN* 1.3 77.5 - - - +
401E SER* 1.3 65.7 + - - +
402E LYS* 2.8 30.1 + - - +
430E ASP* 3.8 7.1 + - - +
433E ALA* 3.7 35.0 - - + +
434E MET* 3.2 23.7 - - - +
437E LEU* 3.5 28.3 - - + -
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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