Contacts of the helix formed by residues 385 - 399 (chain P) 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 SER 385 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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379P ALA* 3.6 12.2 - - - +
383P ASP 3.6 1.7 + - - -
384P LEU* 1.3 78.3 - - - +
386P VAL* 1.3 71.4 + - - +
387P ASP* 3.1 28.9 + - - -
388P GLU* 3.9 6.3 - - - +
389P SER* 2.9 21.1 + - - -
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Residues in contact with VAL 386 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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375P MET* 6.2 6.5 - - + -
376P LYS* 6.4 2.2 - - - -
379P ALA* 5.1 5.6 - - + -
385P SER* 1.3 80.8 + - - +
387P ASP* 1.3 57.8 + - + +
389P SER* 4.0 2.2 - - - -
390P GLU* 3.1 48.6 + - - +
408P ARG* 5.3 1.8 - - - +
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Residues in contact with ASP 387 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385P SER* 3.1 15.7 + - - -
386P VAL* 1.3 77.5 - - - +
388P GLU* 1.3 76.4 + - - +
389P SER 2.7 14.8 + - - -
390P GLU* 3.1 6.5 + - - -
391P ALA* 2.9 27.8 + - - +
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Residues in contact with GLU 388 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384P LEU* 3.0 52.0 - - + -
385P SER* 3.9 9.1 + - - +
387P ASP* 1.3 94.4 - - - +
389P SER* 1.3 53.9 + - - +
391P ALA* 4.1 4.4 - - - +
392P PHE* 2.1 45.4 + - + -
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Residues in contact with SER 389 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378P MET* 5.9 2.9 - - - -
379P ALA* 4.1 12.0 - - - -
382P LEU* 4.4 17.5 - - - +
384P LEU* 3.8 12.7 + - - +
385P SER 2.9 22.8 + - - -
386P VAL* 4.0 4.3 - - - -
387P ASP 2.7 1.2 + - - -
388P GLU* 1.3 75.0 - - - +
390P GLU* 1.3 69.2 + - - -
391P ALA 3.0 1.3 - - - -
392P PHE* 2.7 19.7 + - - +
393P LEU* 2.8 21.6 + - - +
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Residues in contact with GLU 390 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375P MET* 5.4 3.5 - - + +
386P VAL* 3.1 28.7 + - - +
387P ASP* 3.1 6.7 + - - +
389P SER* 1.3 78.4 - - - +
391P ALA* 1.3 52.3 + - - +
393P LEU* 3.6 7.6 + - - +
394P SER* 2.2 42.4 + - - +
406P VAL* 6.3 4.3 - - + -
408P ARG* 2.2 54.3 + - - +
349Q HIS* 3.8 11.3 + - - +
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Residues in contact with ALA 391 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387P ASP 2.9 17.1 + - - +
388P GLU* 4.1 5.6 - - - +
389P SER 2.8 0.6 + - - -
390P GLU* 1.3 76.1 - - - +
392P PHE* 1.3 65.6 + - + +
394P SER* 3.2 5.9 + - - -
395P ASN* 3.0 34.6 + - - -
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Residues in contact with PHE 392 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355P LYS* 4.7 10.5 - - + -
356P ASN* 4.3 23.3 - - + -
359P VAL* 3.4 37.5 - - + -
360P GLU* 5.4 3.8 - - + -
363P ILE* 5.9 4.9 - - + -
382P LEU* 6.5 1.3 - - + -
384P LEU* 2.7 32.1 - - + -
388P GLU* 2.1 35.6 + - + +
389P SER* 2.7 12.4 + - - +
391P ALA* 1.3 77.8 - - + +
393P LEU* 1.3 62.0 + - + +
395P ASN* 3.6 6.1 + - + +
396P LEU* 3.1 29.0 + - + +
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Residues in contact with LEU 393 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363P ILE* 4.7 15.5 - - + -
382P LEU* 5.7 6.7 - - + -
389P SER* 2.8 24.7 + - - +
390P GLU* 3.8 7.0 - - - +
392P PHE* 1.3 76.3 - - + +
394P SER* 1.3 59.4 + - - +
396P LEU* 3.1 8.3 + - - +
397P VAL* 2.9 37.2 + - + +
402P ILE* 4.9 8.5 - - + -
404P ALA* 6.1 2.7 - - + -
406P VAL* 6.1 5.8 - - + -
413P ILE* 5.5 11.4 - - + -
415P PHE* 5.6 4.7 - - + -
341Q PRO* 5.6 2.0 - - + -
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Residues in contact with SER 394 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390P GLU* 2.2 29.8 + - - +
391P ALA* 3.6 6.6 - - - -
393P LEU* 1.3 77.3 - - - +
395P ASN* 1.3 53.3 + - - +
397P VAL* 3.2 2.4 + - - +
398P VAL* 2.7 40.6 + - - +
337Q ARG* 5.9 2.0 - - - -
341Q PRO* 4.5 23.5 - - - +
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Residues in contact with ASN 395 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391P ALA* 3.0 21.5 + - - +
392P PHE* 3.9 6.3 - - + +
394P SER* 1.3 76.9 - - - +
396P LEU* 1.3 57.7 - - + +
398P VAL* 3.8 6.2 - - - +
399P ASN* 3.0 31.9 + - - +
337Q ARG* 6.3 1.1 - - - +
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Residues in contact with LEU 396 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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359P VAL 5.9 0.2 - - - -
360P GLU* 4.2 41.1 - - + +
363P ILE* 3.7 34.1 - - + -
364P ARG* 5.7 0.4 - - + -
392P PHE* 3.1 16.5 + - + +
393P LEU 3.1 10.2 + - - +
395P ASN* 1.3 79.2 - - + +
397P VAL* 1.3 50.6 + - - +
399P ASN* 3.6 3.1 - - + -
400P LYS* 2.5 14.9 + - - -
401P THR* 2.4 63.3 + - - +
402P ILE* 4.0 20.2 - - + -
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Residues in contact with VAL 397 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393P LEU* 2.9 19.3 + - + +
394P SER 3.8 2.9 - - - +
396P LEU* 1.3 74.3 - - - +
398P VAL* 1.3 68.8 + - - +
400P LYS* 3.1 14.1 + - - +
401P THR 4.5 0.9 - - - +
402P ILE* 3.8 32.5 - - + +
404P ALA* 4.4 17.5 - - + +
340Q GLU* 5.4 5.6 - - + -
341Q PRO* 4.3 28.5 - - + -
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Residues in contact with VAL 398 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394P SER* 2.7 23.0 + - - +
395P ASN* 3.8 7.9 - - - +
397P VAL* 1.3 77.7 - - - +
399P ASN* 1.3 62.7 + - - +
400P LYS* 4.1 2.6 - - - +
337Q ARG* 3.2 55.9 - - + +
340Q GLU* 6.1 2.5 - - + -
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Residues in contact with ASN 399 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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395P ASN 3.0 15.6 + - - +
396P LEU* 4.4 3.1 - - + +
398P VAL* 1.3 76.7 - - - +
400P LYS* 1.3 77.7 + - - +
401P THR* 5.0 4.7 - - - -
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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