Contacts of the helix formed by residues 422 - 438 (chain X) in PDB entry 5G04
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 422 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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764H MET* 5.7 2.9 - - - +
417X TYR* 3.1 27.1 + - - +
420X SER* 3.8 14.7 + - - -
421X ASN* 1.3 73.8 - - - +
423X ILE* 1.3 59.0 + - - +
424X ARG 3.6 1.8 - - - -
425X GLU* 3.7 27.2 + - - -
426X ALA* 3.1 28.3 + - - +
454X ASP* 4.8 1.1 - - - -
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Residues in contact with ILE 423 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421X ASN* 3.2 25.4 + - - +
422X SER* 1.3 68.8 - - - +
424X ARG* 1.3 77.0 + - + +
426X ALA* 3.4 5.6 + - - +
427X MET* 3.1 26.4 + - - +
451X CYS* 5.4 1.2 - - - +
454X ASP* 3.4 42.2 - - - +
455X PRO* 4.1 36.1 - - + +
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Residues in contact with ARG 424 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
757H LEU* 3.8 40.4 - - - +
423X ILE* 1.3 92.1 - - + +
425X GLU* 1.3 59.9 + - - +
427X MET* 3.4 9.5 + - + +
428X VAL* 3.0 36.3 + - + +
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Residues in contact with GLU 425 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
757H LEU* 6.4 0.7 - - - -
761H SER* 3.1 44.7 + - - +
764H MET* 4.0 24.9 - - - +
417X TYR* 3.5 22.2 + - - -
422X SER* 3.6 28.5 + - - +
424X ARG* 1.3 77.2 - - - +
426X ALA* 1.3 61.0 + - - +
428X VAL* 3.4 7.1 + - - +
429X MET* 3.1 38.1 + - + +
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Residues in contact with ALA 426 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414X ILE* 4.0 27.1 - - + +
417X TYR* 4.4 11.4 - - + -
418X LEU* 5.1 2.9 - - + +
422X SER 3.1 18.8 + - - +
423X ILE* 3.5 7.2 - - - +
425X GLU* 1.3 75.2 - - - +
427X MET* 1.3 55.6 + - - +
429X MET* 3.5 13.5 + - - +
430X ALA* 2.9 30.1 + - - +
451X CYS* 4.6 4.7 - - + -
454X ASP* 4.8 7.0 - - + +
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Residues in contact with MET 427 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
757H LEU* 6.2 0.4 - - + -
423X ILE 3.1 13.6 + - - +
424X ARG* 3.5 12.8 - - + +
425X GLU 3.3 0.2 - - - -
426X ALA* 1.3 76.1 - - - +
428X VAL* 1.3 72.2 + - + +
430X ALA* 3.3 7.6 + - - +
431X ASN* 3.0 62.9 + - - +
451X CYS* 4.5 23.7 - - + +
455X PRO* 6.3 2.0 - - + -
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Residues in contact with VAL 428 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
754H HIS* 4.0 10.5 - - - +
757H LEU* 3.7 36.1 - - + +
758H MET* 3.6 36.8 - - + +
761H SER* 5.7 2.2 - - - -
424X ARG* 3.0 23.0 + - + +
425X GLU* 3.8 6.1 - - - +
427X MET* 1.3 90.5 - - + +
429X MET* 1.3 62.1 + - + +
431X ASN* 3.3 8.4 + - - +
432X ASN* 3.0 32.0 + - - +
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Residues in contact with MET 429 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
758H MET* 3.7 25.1 - - + -
761H SER* 4.0 16.2 - - - +
765H ASP* 4.8 6.1 - - - +
400X ILE* 5.9 0.2 - - - -
410X TYR* 5.6 1.7 - - - -
413X LEU* 3.8 32.5 - - + +
414X ILE* 5.3 6.5 - - + -
417X TYR* 3.5 44.4 - - + -
425X GLU* 3.1 36.3 + - + +
426X ALA* 3.8 8.5 - - - +
428X VAL* 1.3 73.4 - - + +
430X ALA* 1.3 59.8 + - - +
432X ASN* 3.4 3.6 + - - +
433X VAL* 3.2 27.1 + - - +
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Residues in contact with ALA 430 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414X ILE* 4.8 6.4 - - + +
426X ALA 2.9 11.8 + - - +
427X MET 3.4 4.9 - - - +
429X MET* 1.3 74.9 - - - +
431X ASN* 1.3 62.4 + - - +
433X VAL* 3.1 14.2 - - + +
434X TYR* 2.9 29.7 + - - +
447X LEU* 5.2 4.3 - - + -
448X ALA* 5.2 8.1 - - + +
451X CYS* 3.2 35.0 - - + -
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Residues in contact with ASN 431 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
754H HIS* 5.8 8.0 - - + +
427X MET* 3.0 45.2 + - - +
428X VAL* 3.3 10.9 + - + +
430X ALA* 1.3 78.4 - - - +
432X ASN* 1.3 56.4 + - - +
434X TYR* 3.4 8.3 - - - +
435X LYS* 2.8 33.8 + - - +
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Residues in contact with ASN 432 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
754H HIS* 4.8 6.5 + - - +
755H LEU* 5.4 6.0 - - - +
758H MET* 3.3 46.5 - - + +
410X TYR* 6.1 0.4 - - - -
428X VAL* 3.0 27.7 + - - +
429X MET 3.7 8.1 - - - +
430X ALA 3.3 0.4 - - - -
431X ASN* 1.3 75.6 - - - +
433X VAL* 1.3 62.8 + - - +
435X LYS* 3.5 7.8 + - - +
436X THR* 3.3 23.2 + - - +
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Residues in contact with VAL 433 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407X LEU* 5.8 2.0 - - - -
410X TYR* 3.5 52.4 - - + -
414X ILE* 6.5 0.9 - - + -
429X MET 3.2 14.1 + - - +
430X ALA* 3.1 28.0 - - - +
432X ASN* 1.3 73.8 - - - +
434X TYR* 1.3 62.3 + - - +
436X THR* 3.2 19.2 - - - +
437X LEU* 3.2 15.4 + - + -
444X LEU* 3.3 19.5 - - + +
447X LEU* 4.2 21.1 - - + -
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Residues in contact with TYR 434 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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430X ALA 2.9 20.6 + - - +
431X ASN* 3.4 11.9 - - - +
432X ASN 3.3 0.2 - - - -
433X VAL* 1.3 76.9 - - - +
435X LYS* 1.3 57.9 + - - +
438X GLY* 2.8 42.6 + - - -
439X ALA* 5.7 2.9 - - - -
441X ALA 6.0 0.2 - - - -
444X LEU* 3.4 45.5 - - + +
445X THR* 4.0 20.3 - - + +
448X ALA* 4.8 11.4 - - + -
464X LEU* 4.9 8.3 - - + +
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Residues in contact with LYS 435 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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431X ASN 2.8 20.6 + - - +
432X ASN* 3.7 9.6 - - - +
434X TYR* 1.3 76.2 - - - +
436X THR* 1.3 63.5 + - - +
438X GLY* 3.7 7.8 + - - -
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Residues in contact with THR 436 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248X THR 4.5 11.7 + - - +
250X ASP* 4.8 1.9 - - - +
405X CYS* 4.0 20.9 - - - -
410X TYR* 4.6 14.1 - - + +
432X ASN 3.3 11.9 + - - +
433X VAL* 3.2 21.5 - - + +
435X LYS* 1.3 81.7 - - - +
437X LEU* 1.3 71.6 + - + +
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Residues in contact with LEU 437 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249X GLY* 4.5 15.0 - - - +
250X ASP* 3.2 25.4 - - - +
251X ASN* 5.6 0.4 - - - +
405X CYS* 5.2 7.0 - - + -
407X LEU* 3.5 34.1 - - + -
410X TYR* 4.9 7.2 - - + -
433X VAL* 3.2 34.0 + - + +
436X THR* 1.3 86.1 - - + +
438X GLY* 1.3 62.2 + - - +
439X ALA 3.9 5.9 + - - +
441X ALA* 3.8 19.1 - - + +
443X THR* 4.2 5.8 - - - +
444X LEU* 3.5 26.2 - - + -
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Residues in contact with GLY 438 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434X TYR* 2.8 29.6 + - - -
435X LYS* 4.1 7.2 - - - -
436X THR 3.5 1.6 - - - -
437X LEU* 1.3 76.4 - - - +
439X ALA* 1.3 64.4 + - - +
441X ALA* 4.1 2.6 + - - +
444X LEU* 3.2 20.1 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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