Contacts of the helix formed by residues 390 - 400 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275H PHE* 6.2 0.4 - + - -
278H VAL* 3.2 54.4 + - + +
282H ARG* 4.1 0.8 - - - +
284H GLY 5.9 0.2 - - - -
285H LEU 2.9 18.9 + - - +
286H GLY* 4.1 2.0 - - - +
287H SER 3.7 21.8 - - - +
288H ILE* 4.4 14.4 - - + -
312H ILE* 3.4 31.0 - - + -
313H TYR* 4.1 22.9 - + - +
315H LEU* 5.3 1.9 - - - +
389H THR* 1.3 76.0 - - - +
391H ARG* 1.3 85.9 + - + +
393H MET* 3.7 4.4 - - - +
394H GLN* 3.6 42.4 + - - +
447H GLN* 4.0 24.5 - - - -
486H HIS* 4.5 6.1 - + - -
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Residues in contact with ARG 391 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389H THR* 3.1 7.0 + - - +
390H TRP* 1.3 108.7 - - + +
392H ASP* 1.3 66.3 + - - +
393H MET 3.1 1.1 - - - -
394H GLN* 3.0 8.1 + - - +
395H HIS* 3.0 29.3 + - + -
444H VAL* 3.8 19.4 + - + +
445H ALA 2.5 30.9 + - - -
446H PRO* 3.3 2.6 - - - +
447H GLN* 2.9 47.4 - - - +
485H GLU* 2.7 50.0 + - - +
486H HIS* 5.5 2.9 - - + -
539H TRP* 6.0 1.1 - - + -
573H THR* 3.6 10.7 - - - +
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Residues in contact with ASP 392 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387H ASN 4.1 0.3 - - - +
388H LEU* 3.6 16.0 - - + +
389H THR* 2.9 36.6 + - - +
391H ARG* 1.3 75.7 - - - +
393H MET* 1.3 62.9 + - - +
395H HIS* 3.1 10.1 + - - +
396H LEU* 3.0 27.6 + - - +
441H TRP* 2.9 31.7 + - - +
443H THR* 2.7 25.1 + - - -
444H VAL* 2.9 24.8 + - - +
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Residues in contact with MET 393 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288H ILE* 3.8 24.0 - - + -
315H LEU* 4.3 15.3 - - + -
378H ILE* 3.7 39.7 - - + +
381H THR* 3.9 19.1 - - + -
382H LEU* 3.8 14.8 - - + -
388H LEU* 3.7 27.5 - - + +
389H THR 3.0 9.9 + - - +
390H TRP* 3.7 10.8 - - - +
391H ARG 3.1 0.2 - - - -
392H ASP* 1.3 78.1 - - - +
394H GLN* 1.3 61.9 + - + +
396H LEU* 3.3 8.2 + - - +
397H VAL* 3.1 27.5 + - + +
434H MET* 4.0 10.8 - - - -
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Residues in contact with GLN 394 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312H ILE 3.1 22.2 + - - +
313H TYR 4.4 4.4 + - - -
314H THR 4.1 10.3 + - - +
315H LEU* 3.7 27.5 - - + +
337H LEU* 3.8 20.4 - - + +
390H TRP* 3.6 27.9 + - - +
391H ARG* 3.0 9.0 + - - +
393H MET* 1.3 73.4 - - - +
395H HIS* 1.3 65.7 + - - +
397H VAL* 3.2 2.9 + - - +
398H VAL* 3.0 28.1 + - - +
486H HIS* 2.6 29.9 + - - -
536H THR* 5.7 0.2 - - - +
539H TRP* 3.8 17.4 - - + -
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Residues in contact with HIS 395 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391H ARG* 3.0 28.3 + - + -
392H ASP 3.3 7.6 - - - +
394H GLN* 1.3 77.4 - - - +
396H LEU* 1.3 62.5 + - - +
398H VAL* 3.3 2.6 + - - +
399H GLN* 3.0 32.4 + - - +
441H TRP* 3.7 20.8 - + + -
444H VAL* 3.6 28.2 - - + +
483H ARG* 5.7 4.6 + - - -
484H LEU 5.3 0.2 - - - -
485H GLU* 2.6 35.5 + - + -
539H TRP* 3.2 37.0 + + - +
540H ASP* 4.5 12.1 + - - -
573H THR* 5.8 2.5 - - + -
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Residues in contact with LEU 396 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381H THR* 3.5 30.3 - - + -
388H LEU* 3.7 22.2 - - + -
392H ASP 3.0 16.7 + - - +
393H MET* 3.6 10.1 - - - +
394H GLN 3.2 0.2 - - - -
395H HIS* 1.3 77.0 - - - +
397H VAL* 1.3 56.1 + - - +
399H GLN 3.4 0.5 + - - -
400H THR* 2.6 37.2 + - - +
434H MET* 3.8 13.2 - - + +
437H LEU* 3.4 35.2 - - + +
438H ALA* 3.8 10.5 - - + +
441H TRP* 3.6 29.4 - - + -
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Residues in contact with VAL 397 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315H LEU* 3.8 20.0 - - + -
317H ILE* 5.6 1.6 - - + -
337H LEU* 4.1 19.7 - - + +
338H ALA* 3.4 32.1 - - + -
378H ILE* 5.1 3.8 - - + -
393H MET* 3.1 16.8 + - + +
394H GLN 3.6 6.5 - - - +
396H LEU* 1.3 76.3 - - - +
398H VAL* 1.3 63.9 + - - +
400H THR* 4.0 0.7 - - - -
401H SER* 2.5 35.2 + - - +
429H LEU* 3.6 9.4 - - + -
434H MET* 3.8 23.3 - - + -
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Residues in contact with VAL 398 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337H LEU* 3.8 25.8 - - + -
394H GLN 3.0 15.3 + - - +
395H HIS 3.3 7.2 + - - +
397H VAL* 1.3 77.9 - - - +
399H GLN* 1.3 61.3 + - + +
400H THR 3.6 0.2 + - - -
401H SER 4.3 3.8 + - - +
418H ARG* 3.7 32.7 - - - +
426H TYR* 3.7 42.7 - - + +
539H TRP* 3.8 34.1 - - + -
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Residues in contact with GLN 399 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395H HIS* 3.0 20.9 + - + +
398H VAL* 1.3 78.3 - - + +
400H THR* 1.3 61.7 + - + +
401H SER 4.8 1.6 - - - +
402H LYS* 5.3 2.4 - - - -
418H ARG* 3.6 32.3 + - - +
437H LEU* 3.7 19.8 - - + +
441H TRP* 2.8 44.6 - - - -
539H TRP* 6.4 0.2 - - - +
540H ASP* 5.2 3.4 - - - +
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Residues in contact with THR 400 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396H LEU 2.6 22.2 + - - +
397H VAL* 3.9 1.2 + - - -
399H GLN* 1.3 80.4 - - - +
401H SER* 1.3 62.4 + - - +
402H LYS* 3.0 30.6 + - - +
429H LEU* 5.7 0.2 - - - +
430H ASP* 3.7 7.9 + - - +
433H ALA* 3.8 35.4 - - + +
434H MET* 3.2 23.9 - - - +
437H LEU* 3.7 23.8 - - + -
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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