Contacts of the helix formed by residues 380 - 395 (chain C) 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 ASN 380 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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375C TYR* 3.2 19.4 + - - +
378C MET* 3.2 23.5 + - - +
379C LYS* 1.3 72.3 - - - +
381C THR* 1.3 59.0 + - - +
382C SER* 4.0 6.2 + - - -
383C ALA* 3.3 31.5 + - + +
384C ALA 3.3 16.8 + - - -
296O TYR 4.5 5.3 - - - +
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Residues in contact with THR 381 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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375C TYR 5.0 0.4 - - - -
376C MET* 3.9 10.5 - - - +
379C LYS 3.1 4.1 + - - +
380C ASN* 1.3 70.8 + - - +
382C SER* 1.3 58.3 + - - +
383C ALA 3.3 1.6 - - - -
384C ALA* 2.9 8.5 + - - +
385C ILE* 2.8 34.0 + - - +
408C THR* 3.0 23.6 + - - -
412C LEU* 3.7 31.5 - - + +
296O TYR* 4.0 28.8 + - + +
300O LEU* 4.2 4.3 - - + -
95R LEU* 3.9 18.2 - - + -
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Residues in contact with SER 382 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380C ASN* 3.6 4.0 - - - -
381C THR* 1.3 77.2 - - - +
383C ALA* 1.3 65.2 + - - +
385C ILE* 3.3 11.1 + - - +
386C GLN* 3.0 28.6 + - - +
279O ASP 5.0 0.5 + - - +
281O LEU 5.1 0.7 + - - -
282O ILE* 4.0 20.4 - - - +
296O TYR 3.8 17.2 + - - -
297O GLY* 4.2 12.6 - - - -
299O SER* 4.5 9.4 + - - -
300O LEU* 4.9 10.3 - - - +
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Residues in contact with ALA 383 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375C TYR* 3.5 30.8 - - + -
380C ASN* 3.3 37.0 + - - +
382C SER* 1.3 77.0 + - - +
384C ALA* 1.3 51.4 + - - +
386C GLN* 3.3 12.2 + - - +
387C ALA* 2.7 35.0 + - - +
282O ILE* 6.0 0.4 - - - +
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Residues in contact with ALA 384 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372C GLY 3.8 17.9 - - - +
375C TYR* 3.8 9.2 - - + -
376C MET* 4.0 14.1 - - - +
380C ASN 3.3 7.7 + - - +
381C THR* 2.9 20.2 + - - +
383C ALA* 1.3 80.1 - - - +
385C ILE* 1.3 50.3 - - - +
387C ALA* 3.1 5.2 + - - +
388C TYR* 2.7 52.5 + - + -
408C THR* 4.4 1.1 - - - +
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Residues in contact with ILE 385 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381C THR 2.8 17.6 + - - +
382C SER* 3.7 8.3 - - - +
383C ALA 3.3 0.2 - - - -
384C ALA* 1.3 71.9 - - - +
386C GLN* 1.3 55.6 + - - +
387C ALA 3.2 0.2 + - - -
388C TYR 3.2 1.6 + - - -
389C ARG* 2.7 36.4 + - - +
405C LEU* 3.6 23.0 - - + +
408C THR* 3.8 11.7 - - + +
409C TYR* 3.8 14.6 - - + +
412C LEU* 3.6 31.0 - - + -
278O PHE 4.9 1.3 - - - +
279O ASP* 3.6 42.2 - - - +
300O LEU* 3.7 23.3 - - + -
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Residues in contact with GLN 386 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382C SER* 3.0 13.8 + - - +
383C ALA* 3.5 12.3 - - - +
385C ILE* 1.3 73.5 - - - +
387C ALA* 1.3 63.5 + - - +
389C ARG* 3.0 8.3 + - - +
390C HIS* 2.9 24.5 + - - +
279O ASP 3.4 14.9 + - - +
280O ARG* 2.6 48.7 + - - +
281O LEU 3.9 1.4 + - - -
282O ILE* 3.2 39.2 - - + +
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Residues in contact with ALA 387 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368C TRP* 3.8 22.2 - - - +
371C MET* 4.2 5.2 - - + -
372C GLY* 3.7 24.9 - - - +
375C TYR* 3.8 16.4 - - + -
383C ALA 2.7 15.2 + - - +
384C ALA 3.2 9.4 - - - +
385C ILE 3.1 0.2 - - - -
386C GLN* 1.3 75.3 - - - +
388C TYR* 1.3 63.9 - - - +
390C HIS* 3.0 20.3 + - - +
391C ALA 3.4 3.8 + - - -
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Residues in contact with TYR 388 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368C TRP 4.6 2.2 - - - -
369C THR* 3.7 23.1 - - - -
372C GLY* 3.5 8.3 + - - -
373C HIS* 3.0 50.6 + + - -
376C MET* 4.0 7.1 - - - +
384C ALA* 2.7 44.7 + - + +
387C ALA* 1.3 71.9 - - - +
389C ARG* 1.3 57.3 - - - +
391C ALA* 2.9 27.0 + - - +
392C ILE* 3.0 12.8 + - - +
401C ALA* 3.7 12.5 - - - +
404C GLY* 3.6 21.6 + - - -
405C LEU* 3.5 21.3 - - + -
407C GLN* 5.9 0.2 - - - +
408C THR* 3.6 29.7 + - + -
131R LEU* 3.9 8.5 - - - +
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Residues in contact with ARG 389 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A LEU* 3.6 13.3 + - - +
385C ILE 2.7 19.0 + - - +
386C GLN* 3.0 6.7 + - - +
388C TYR* 1.3 77.4 - - - +
390C HIS* 1.3 56.4 + - - +
392C ILE* 3.0 31.2 + - - +
393C GLU* 2.8 41.8 + - - +
402C TRP* 4.7 5.3 - - - -
405C LEU* 4.0 7.1 - - + +
420C TYR* 4.5 12.5 + - - -
421C TYR* 4.4 8.9 - - - -
272O HIS 4.8 1.2 + - - -
275O LEU 3.9 1.2 - - - -
276O HIS* 3.3 57.7 + - - +
279O ASP* 2.5 45.0 + - + +
280O ARG* 3.9 10.1 - - + -
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Residues in contact with HIS 390 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A ARG* 3.1 44.5 + - - -
141C LEU* 4.0 13.3 - - + +
368C TRP* 3.2 53.3 + + + -
386C GLN 2.9 10.5 + - - +
387C ALA 3.0 10.9 + - - +
389C ARG* 1.3 73.8 - - - +
391C ALA* 1.3 65.0 + - - +
393C GLU* 3.1 8.1 + - - +
394C VAL* 3.0 30.7 + - + +
249O ASP* 5.1 2.4 + - - -
280O ARG* 3.3 26.1 + - - -
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Residues in contact with ALA 391 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365C LEU* 3.7 9.8 - - + +
368C TRP* 3.6 28.1 - - + +
369C THR 4.2 6.5 - - - +
387C ALA 3.4 2.6 + - - -
388C TYR 2.9 11.2 + - - +
390C HIS* 1.3 77.6 - - - +
392C ILE* 1.3 57.3 + - - +
394C VAL 3.6 0.2 + - - -
395C ASN* 2.9 32.0 + - - +
398C ASP* 3.9 10.9 - - - +
401C ALA* 3.4 20.6 - - + -
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Residues in contact with ILE 392 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A LEU* 3.9 11.7 - - + +
38A GLN* 4.1 1.0 - - - +
388C TYR 3.0 15.1 + - - +
389C ARG* 3.0 39.7 + - - +
391C ALA* 1.3 72.2 - - - +
393C GLU* 1.3 63.8 + - - +
394C VAL 3.2 0.4 - - - -
395C ASN 3.0 27.6 - - - +
396C LYS* 3.3 5.4 + - - -
398C ASP 3.3 26.0 - - - +
401C ALA* 3.9 7.6 - - + -
402C TRP* 3.5 58.6 - - + +
405C LEU* 4.6 4.0 - - + -
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Residues in contact with GLU 393 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A LEU 3.9 8.3 - - - -
38A GLN* 3.4 5.9 - - - -
39A LEU* 3.4 38.2 + - + +
40A ARG* 2.8 44.1 + - - +
389C ARG* 2.8 28.8 + - - +
390C HIS* 3.1 10.4 + - - +
392C ILE* 1.3 71.8 - - - +
394C VAL* 1.3 59.5 + - - +
248O PRO 3.8 7.4 - - - +
276O HIS* 3.7 19.5 - - + +
280O ARG* 2.7 45.2 + - - +
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Residues in contact with VAL 394 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A GLN* 3.0 23.2 - - - +
40A ARG* 4.0 25.5 - - - +
42A LEU* 3.7 31.0 - - + +
142C GLU* 3.9 14.8 - - - +
362C PRO 5.6 3.1 - - - +
363C ARG* 5.9 1.3 - - - -
365C LEU* 3.6 32.5 - - + -
368C TRP* 4.2 7.0 - - - +
390C HIS* 3.0 22.5 + - - +
391C ALA 3.8 1.6 - - - +
393C GLU* 1.3 77.0 - - - +
395C ASN* 1.3 66.8 + - - +
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Residues in contact with ASN 395 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A GLN* 3.9 5.5 + - - -
42A LEU* 4.8 7.1 - - - +
53A GLY* 5.6 1.2 - - - -
54A ALA* 4.7 4.7 + - - +
55A ALA* 3.8 25.5 + - - +
56A GLY 4.9 2.0 - - - +
57A LEU 5.5 1.0 - - - +
365C LEU* 3.4 30.6 - - + +
391C ALA 2.9 15.7 + - - +
392C ILE* 3.0 19.0 - - - +
394C VAL* 1.3 89.5 + - - +
396C LYS* 1.3 60.5 + - - +
397C ARG* 3.0 21.4 - - - +
398C ASP* 3.4 17.2 + - - +
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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
------------------------------------------------------------
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