Contacts of the helix formed by residues 320 - 335 (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 ARG 320 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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291X VAL* 4.1 13.1 - - - +
295X GLU* 4.1 19.2 + - - -
311X TYR* 5.2 0.4 + - - -
315X LEU* 2.9 31.4 + - + +
316X ALA* 4.9 0.4 - - - +
318X GLU* 4.1 18.6 - - + +
319X GLY* 1.3 77.3 - - - +
321X LEU* 1.3 64.0 + - - +
322X GLU 3.4 2.6 + - - +
323X ASP* 3.0 45.9 + - + +
324X VAL* 3.4 17.3 - - - +
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Residues in contact with LEU 321 (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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316X ALA* 5.6 4.7 - - + -
319X GLY* 3.6 8.4 + - - +
320X ARG* 1.3 72.5 - - - +
322X GLU* 1.3 65.3 - - - +
324X VAL* 3.3 12.7 + - + +
325X GLU* 3.2 17.8 + - - +
348X HIS* 3.6 41.4 + - + +
351X TYR* 3.5 46.4 - - + +
352X SER* 4.6 4.3 - - - +
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Residues in contact with GLU 322 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320X ARG* 3.4 0.8 - - - +
321X LEU* 1.3 78.3 - - - +
323X ASP* 1.3 67.6 + - - +
325X GLU* 3.3 7.2 + - - +
326X ASN* 3.1 31.0 + - - +
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Residues in contact with ASP 323 (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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311X TYR* 5.7 0.2 + - - -
315X LEU* 3.7 20.6 - - + +
320X ARG* 3.0 58.5 + - + +
321X LEU 3.3 0.2 - - - -
322X GLU* 1.3 80.0 - - - +
324X VAL* 1.3 53.3 + - - +
326X ASN* 3.4 5.2 + - - +
327X LEU* 2.8 35.7 + - - +
330X ARG* 4.4 6.0 + - - +
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Residues in contact with VAL 324 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312X GLY 4.0 9.0 - - - +
315X LEU* 3.7 24.9 - - + -
316X ALA* 4.5 7.9 - - + +
320X ARG 3.4 17.3 - - - +
321X LEU* 3.3 15.4 + - + +
323X ASP* 1.3 74.6 - - - +
325X GLU* 1.3 57.2 + - - +
327X LEU* 3.3 4.3 + - - +
328X GLY* 2.8 27.4 + - - -
344X VAL* 3.5 34.1 - - + +
347X CYS* 4.7 3.8 - - + -
348X HIS* 3.6 25.8 - - + +
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Residues in contact with GLU 325 (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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321X LEU 3.2 7.0 + - - +
322X GLU* 3.3 9.6 + - - +
324X VAL* 1.3 78.8 - - - +
326X ASN* 1.3 62.7 + - - +
328X GLY* 3.5 1.9 + - - -
329X CYS* 3.1 31.6 + - - -
348X HIS* 2.8 42.4 + - + +
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Residues in contact with ASN 326 (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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322X GLU* 3.1 23.0 + - - +
323X ASP* 3.9 4.0 - - - +
325X GLU* 1.3 79.3 - - - +
327X LEU* 1.3 58.6 + - - +
329X CYS* 3.5 9.6 + - - +
330X ARG* 3.0 55.9 + - - +
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Residues in contact with LEU 327 (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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298X GLN* 4.0 13.2 - - - +
308X MET* 3.6 34.5 - - + +
311X TYR* 3.5 29.2 - - + -
312X GLY* 4.1 6.3 - - - +
315X LEU* 3.9 14.4 - - + -
323X ASP 2.8 21.2 + - - +
324X VAL 3.6 4.0 - - - +
326X ASN* 1.3 69.5 - - - +
328X GLY* 1.3 61.0 + - - +
330X ARG* 3.5 19.3 + - + +
331X LEU* 2.9 38.1 + - + +
344X VAL* 3.7 24.2 - - + -
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Residues in contact with GLY 328 (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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324X VAL 2.8 19.7 + - - -
325X GLU* 3.8 2.9 - - - -
326X ASN 3.3 0.2 - - - -
327X LEU* 1.3 69.3 - - - +
329X CYS* 1.3 64.1 + - - +
331X LEU* 3.3 3.3 + - - +
332X PHE* 3.1 33.9 + - - -
344X VAL* 3.7 20.3 - - - +
345X SER* 4.7 9.2 - - - -
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Residues in contact with CYS 329 (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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53E PHE* 6.3 2.2 - - - -
54E LEU* 5.3 13.0 - - - -
325X GLU 3.1 18.3 + - - +
326X ASN* 3.6 12.6 - - - +
328X GLY* 1.3 75.6 - - - +
330X ARG* 1.3 61.5 + - + +
332X PHE* 3.5 4.0 + - - +
333X ASN* 3.1 36.6 + - - +
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Residues in contact with ARG 330 (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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298X GLN* 3.9 30.2 + - - +
308X MET* 6.4 0.9 - - + -
311X TYR* 5.8 1.8 - - - -
323X ASP* 4.4 4.9 + - - +
326X ASN* 3.0 41.7 + - - +
327X LEU* 3.5 29.7 - - + +
329X CYS* 1.3 74.5 - - - +
331X LEU* 1.3 57.6 + - + +
333X ASN* 3.4 5.6 + - - +
334X ILE* 3.0 40.3 + - + +
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Residues in contact with LEU 331 (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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305X ILE* 4.3 19.3 - - + +
308X MET* 3.7 43.5 - - + -
327X LEU* 2.9 22.8 + - + +
328X GLY 3.3 4.4 + - - +
330X ARG* 1.3 74.1 - - + +
332X PHE* 1.3 61.9 + - - +
334X ILE* 3.3 14.7 - - + +
335X SER* 2.9 25.1 + - - +
340X GLU 3.9 10.1 - - - +
341X PRO* 3.8 33.5 - - + +
344X VAL* 3.6 27.1 - - + -
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Residues in contact with PHE 332 (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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53E PHE* 6.0 7.6 - - + +
54E LEU* 5.9 5.2 - - + -
57E SER* 3.1 35.0 - - - -
328X GLY 3.1 29.5 + - - +
329X CYS* 4.0 4.7 - - - +
331X LEU* 1.3 72.3 - - - +
333X ASN* 1.3 68.2 - - - +
335X SER 2.8 21.1 - - - +
336X ASP* 4.1 17.2 - - - +
341X PRO* 3.6 30.5 - - + -
342X TRP* 3.9 31.4 - + - -
345X SER* 3.3 25.8 - - - -
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Residues in contact with ASN 333 (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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53E PHE* 4.2 29.7 - - - +
329X CYS* 3.1 24.9 + - - +
330X ARG* 3.6 5.8 - - - +
332X PHE* 1.3 80.7 - - - +
334X ILE* 1.3 64.9 + - + +
335X SER* 3.3 0.7 + - - -
94Y ARG* 4.4 7.2 - - - -
149Y LEU* 6.1 0.2 - - - +
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Residues in contact with ILE 334 (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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302X PRO 4.9 5.2 - - - +
303X TYR* 3.5 55.6 - - + -
304X LEU 4.7 1.3 - - - +
305X ILE* 4.0 21.5 - - + -
308X MET* 6.4 0.4 - - + -
330X ARG* 3.0 25.2 + - + +
331X LEU* 3.3 21.8 - - + +
333X ASN* 1.3 78.0 - - + +
335X SER* 1.3 77.3 + - - +
92Y GLU* 5.5 0.6 - - + -
93Y TYR* 4.9 2.4 + - - +
94Y ARG* 3.7 31.7 + - + +
95Y ASN* 4.7 3.1 - - - +
149Y LEU* 5.3 2.6 - - - +
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Residues in contact with SER 335 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305X ILE* 3.3 28.1 - - - +
331X LEU 2.9 14.5 + - - +
332X PHE* 2.8 22.6 - - - +
333X ASN 3.3 1.9 - - - -
334X ILE* 1.3 85.1 - - - +
336X ASP* 1.3 62.1 + - - +
338X HIS* 3.3 20.8 - - - +
341X PRO* 4.2 6.6 - - - +
91Y LYS 4.7 8.3 - - - -
92Y GLU* 4.9 4.9 - - - -
93Y TYR* 5.3 3.6 - - - -
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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