Contacts of the helix formed by residues 390 - 400 (chain G) 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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275G PHE* 6.1 0.9 - + - -
278G VAL* 3.2 54.3 + - + +
282G ARG* 4.1 1.0 - - - +
285G LEU 2.9 19.8 + - - +
286G GLY 4.1 1.6 - - - +
287G SER 3.7 22.4 - - - +
288G ILE* 4.4 14.4 - - + -
312G ILE* 3.4 29.8 - - + -
313G TYR* 4.0 21.3 - + - +
315G LEU* 5.3 2.4 - - - +
389G THR* 1.3 75.6 - - - +
391G ARG* 1.3 87.7 + - + +
393G MET* 3.8 3.5 + - - +
394G GLN* 3.6 42.3 + - - +
447G GLN* 4.0 23.6 - - - -
486G HIS* 4.4 5.2 - + - -
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Residues in contact with ARG 391 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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389G THR* 3.0 7.7 + - - +
390G TRP* 1.3 109.7 - - + +
392G ASP* 1.3 66.7 + - - +
393G MET 3.1 1.6 - - - -
394G GLN* 3.0 8.9 + - - +
395G HIS* 3.0 29.0 + - + -
444G VAL* 3.7 20.5 + - + +
445G ALA 2.5 31.7 + - - -
446G PRO* 3.3 2.4 - - - +
447G GLN* 2.9 45.7 - - - +
485G GLU* 2.6 51.3 + - - +
486G HIS* 5.4 2.9 - - + -
539G TRP* 4.8 0.8 - - + -
572G GLY 4.7 0.2 + - - -
573G THR* 3.6 8.7 - - - +
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Residues in contact with ASP 392 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388G LEU* 3.6 16.7 - - + +
389G THR* 2.8 37.9 + - - +
391G ARG* 1.3 74.7 - - - +
393G MET* 1.3 63.3 + - - +
395G HIS* 3.0 11.0 + - - +
396G LEU* 2.9 26.8 + - - +
441G TRP* 2.8 32.2 + - - +
443G THR* 2.8 24.2 + - - -
444G VAL* 2.9 24.1 + - - +
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Residues in contact with MET 393 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288G ILE* 3.7 25.4 - - + -
315G LEU* 4.6 6.5 - - + -
378G ILE* 3.6 46.9 - - + +
381G THR* 3.9 21.1 - - + -
382G LEU* 3.8 19.3 - - + -
388G LEU* 3.8 21.0 - - + +
389G THR 3.0 10.8 + - - +
390G TRP* 3.8 9.9 - - - +
391G ARG 3.1 0.2 - - - -
392G ASP* 1.3 77.5 - - - +
394G GLN* 1.3 60.5 + - + +
396G LEU* 3.3 8.2 + - - +
397G VAL* 3.1 26.7 + - + +
434G MET* 4.1 10.1 - - - -
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Residues in contact with GLN 394 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312G ILE 3.1 22.0 + - - +
313G TYR 4.4 4.6 + - - -
314G THR 4.1 11.0 + - - +
315G LEU* 3.7 24.5 - - + +
337G LEU* 3.8 20.0 - - + +
390G TRP* 3.6 28.1 + - - +
391G ARG* 3.0 9.9 + - - +
393G MET* 1.3 74.2 - - - +
395G HIS* 1.3 66.5 + - - +
397G VAL* 3.2 3.5 + - - +
398G VAL* 3.0 29.0 + - - +
486G HIS* 2.6 29.7 + - - -
536G THR* 5.7 0.3 - - - +
539G TRP* 3.8 16.4 - - + -
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Residues in contact with HIS 395 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391G ARG* 3.0 26.9 + - + -
392G ASP 3.0 8.0 + - - +
394G GLN* 1.3 77.4 - - - +
396G LEU* 1.3 63.0 + - - +
398G VAL* 3.2 2.8 + - - +
399G GLN* 3.0 33.3 + - - +
441G TRP* 3.9 20.0 - + + -
444G VAL* 3.5 29.8 - - + +
483G ARG* 6.0 4.5 - - - -
484G LEU 5.3 0.2 - - - -
485G GLU* 2.7 33.8 + - + -
539G TRP* 3.1 37.8 + + - +
540G ASP* 4.5 12.1 + - - -
573G THR* 6.0 1.8 - - + -
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Residues in contact with LEU 396 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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381G THR* 3.6 30.3 - - + -
388G LEU* 3.7 22.0 - - + -
392G ASP 2.9 17.1 + - - +
393G MET* 3.6 9.6 - - - +
394G GLN 3.3 0.2 - - - -
395G HIS* 1.3 76.8 - - - +
397G VAL* 1.3 55.8 + - - +
399G GLN 3.4 0.2 + - - -
400G THR* 2.7 38.0 + - + +
434G MET* 3.8 13.7 - - - +
437G LEU* 3.4 37.2 - - + +
438G ALA* 3.9 9.9 - - + -
441G TRP* 3.6 26.9 - - + -
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Residues in contact with VAL 397 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315G LEU* 3.6 20.2 - - + -
317G ILE* 5.6 0.9 - - + -
337G LEU* 4.0 21.5 - - + +
338G ALA* 3.4 31.9 - - + -
378G ILE* 5.0 3.4 - - + -
393G MET* 3.1 16.8 + - + +
394G GLN 3.2 6.9 + - - +
396G LEU* 1.3 75.2 - - - +
398G VAL* 1.3 59.4 + - - +
400G THR* 4.0 0.7 - - - -
401G SER* 2.5 38.6 + - - +
429G LEU* 3.8 9.4 - - + -
434G MET* 3.7 24.2 - - + -
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Residues in contact with VAL 398 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337G LEU* 3.9 21.5 - - + -
394G GLN 3.0 19.3 + - - +
395G HIS 3.6 7.0 - - - +
397G VAL* 1.3 78.5 - - - +
399G GLN* 1.3 61.8 + - + +
401G SER 4.1 5.9 + - - +
418G ARG* 3.7 34.2 - - - +
426G TYR* 3.8 37.8 - - + +
539G TRP* 3.9 41.1 - - + -
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Residues in contact with GLN 399 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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395G HIS* 3.0 21.4 + - - +
398G VAL* 1.3 79.8 - - + +
400G THR* 1.3 61.6 + - - +
401G SER 4.5 2.6 - - - +
418G ARG* 3.7 31.5 + - - +
437G LEU* 3.5 21.4 - - + +
441G TRP* 2.9 42.6 - - - -
483G ARG* 5.4 6.2 + - - -
539G TRP* 6.5 0.2 - - + -
540G ASP* 5.1 4.0 - - - +
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Residues in contact with THR 400 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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396G LEU* 2.7 21.9 + - + +
397G VAL* 3.9 1.4 + - - -
399G GLN* 1.3 78.8 - - - +
401G SER* 1.3 67.8 + - - +
402G LYS* 3.4 6.6 + - - +
429G LEU* 5.7 0.2 - - - +
430G ASP* 4.0 16.0 + - - +
433G ALA* 3.7 42.7 - - + +
434G MET* 3.3 23.2 - - - +
437G LEU* 3.8 21.8 - - + -
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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