Contacts of the helix formed by residues 395 - 407 (chain K) in PDB entry 5GJQ
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 LEU 395 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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355K SER* 5.3 10.1 - - - +
357K GLU* 5.5 5.4 - - - +
358K VAL* 5.4 3.4 - - + -
391K ARG* 2.6 42.6 - - - +
394K VAL* 1.3 80.1 - - - +
396K ALA* 1.3 74.0 + - + +
397K LYS* 3.3 12.3 - - + +
398K ASP* 2.2 40.5 + - - +
399K PHE* 3.2 9.7 + - - -
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Residues in contact with ALA 396 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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358K VAL* 5.0 14.7 - - + +
363K TYR* 3.5 4.5 + - - +
395K LEU* 1.3 77.5 - - + +
397K LYS* 1.3 54.2 + - + +
399K PHE* 2.8 15.1 + - - +
400K GLU* 2.7 47.0 + - + +
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Residues in contact with LYS 397 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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385K LEU* 4.2 3.1 - - + -
391K ARG* 6.0 2.7 - - - +
395K LEU* 3.3 10.6 - - + +
396K ALA* 1.3 81.8 - - + +
398K ASP* 1.3 62.5 + - - +
400K GLU* 3.3 24.0 - - - +
401K LYS* 2.5 45.8 + - + +
185h LYS* 5.6 8.2 - - - +
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Residues in contact with ASP 398 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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381K GLU 4.9 0.3 - - - -
382K SER* 3.8 15.4 - - - +
385K LEU* 3.2 29.4 - - - +
386K ALA* 3.6 17.9 + - - +
389K GLU* 5.6 0.3 - - - +
391K ARG* 4.2 10.0 + - - -
394K VAL* 2.2 41.7 - - + +
395K LEU* 2.2 36.0 + - - +
397K LYS* 1.3 78.2 - - - +
399K PHE* 1.3 55.4 + - - +
401K LYS* 4.1 1.4 - - - +
402K ALA* 3.2 25.8 + - - +
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Residues in contact with PHE 399 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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349K THR* 4.4 14.6 - - + -
352K MET* 4.5 4.3 - - + -
354K LEU* 3.0 51.6 - - + -
355K SER* 5.3 1.3 - - - -
358K VAL* 4.9 14.8 - - + -
360K LEU* 4.6 15.5 - - + -
363K TYR* 3.1 32.0 - + + +
378K ILE* 4.4 18.2 - - + -
379K CYS* 5.3 4.7 - - - -
382K SER* 4.2 13.7 - - - -
394K VAL* 3.7 11.4 - - + -
395K LEU 3.2 22.2 + - - -
396K ALA* 2.8 6.1 + - - +
398K ASP* 1.3 74.6 - - - +
400K GLU* 1.3 52.4 + - - +
402K ALA* 3.1 4.1 + - - +
403K TYR* 2.4 39.7 + - + +
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Residues in contact with GLU 400 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363K TYR* 3.6 13.2 + - + +
396K ALA* 2.7 27.5 + - + +
397K LYS* 2.8 33.9 + - - +
399K PHE* 1.3 71.4 - - - +
401K LYS* 1.3 51.8 + - + +
403K TYR* 3.0 7.3 + - - +
404K LYS* 2.6 47.3 + - + +
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Residues in contact with LYS 401 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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385K LEU* 3.2 34.9 - - + +
388K ARG* 4.1 21.2 - - - +
397K LYS* 2.5 23.6 + - + +
400K GLU* 1.3 71.8 - - + +
402K ALA* 1.3 50.4 - - - +
404K LYS* 2.9 5.7 + - - +
405K THR* 2.2 52.2 + - - +
143L ARG* 5.0 5.3 - - - +
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Residues in contact with ALA 402 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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378K ILE* 3.2 43.1 - - + +
381K GLU* 4.0 6.9 - - + -
382K SER* 4.3 0.4 - - - +
398K ASP 3.2 17.9 + - - +
399K PHE* 3.1 4.0 + - - +
401K LYS* 1.3 78.1 - - - +
403K TYR* 1.3 55.1 + - - +
405K THR* 3.8 11.4 - - - -
406K VAL* 2.5 40.2 + - - +
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Residues in contact with TYR 403 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341K LYS* 5.8 2.8 - - - +
345K PHE* 3.9 17.4 - + - -
360K LEU* 5.7 0.2 - - + -
363K TYR* 2.5 60.2 + + + +
364K VAL* 4.7 0.2 - - - -
366K ARG* 2.4 57.6 - - - +
368K ASP* 4.0 12.2 + - - +
370K ILE* 5.3 3.7 - - + +
378K ILE* 3.9 15.7 - - + -
399K PHE* 2.4 25.5 + - + +
400K GLU* 3.4 5.4 - - - +
402K ALA* 1.3 71.6 - - - +
404K LYS* 1.3 61.9 + - + +
407K ILE* 2.0 58.2 + - + +
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Residues in contact with LYS 404 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366K ARG* 5.2 13.1 - - - +
400K GLU* 2.6 28.5 + - + +
401K LYS* 3.1 4.3 - - - +
403K TYR* 1.3 78.0 - - + +
405K THR* 1.3 60.0 + - - +
406K VAL 3.5 0.2 - - - -
408K LYS* 4.0 19.6 + - - -
410K ASP* 4.6 19.5 - - - +
177h SER* 4.5 19.7 + - - +
180h GLU* 3.0 37.1 + - - +
181h LYS* 5.7 2.4 - - - +
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Residues in contact with THR 405 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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381K GLU* 3.4 35.2 + - + +
401K LYS* 2.2 39.6 + - - +
402K ALA* 3.6 8.3 - - - +
404K LYS* 1.3 72.3 - - - +
406K VAL* 1.3 61.4 + - + +
408K LYS* 3.0 26.9 - - - +
144L GLU* 5.5 0.2 + - - -
297L ARG* 3.9 29.8 + - + +
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Residues in contact with VAL 406 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370K ILE* 4.2 6.1 - - + -
374K ASP* 4.0 20.6 - - + +
377K SER* 3.0 34.3 - - - +
378K ILE* 2.9 46.4 - - + +
402K ALA 2.5 17.5 + - - +
405K THR* 1.3 77.2 - - + +
407K ILE* 1.3 61.5 + - - +
408K LYS* 2.2 31.7 - - - +
409K LYS* 5.0 2.3 + - - -
292L PRO* 5.5 1.1 - - + -
298L LYS* 4.8 4.0 + - - +
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Residues in contact with ILE 407 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368K ASP* 2.7 38.8 - - + +
370K ILE* 3.4 23.8 - - + -
378K ILE* 4.4 0.4 - - + -
402K ALA 4.0 0.9 - - - +
403K TYR* 2.0 72.2 + - + +
404K LYS* 5.0 0.2 - - - -
406K VAL* 1.3 81.2 - - + +
408K LYS* 1.3 55.7 + - - +
409K LYS* 2.5 62.1 + - + +
410K ASP* 4.5 5.4 - - - +
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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