Contacts of the helix formed by residues 322 - 340 (chain X) in PDB entry 3G90
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 322 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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321X ASP* 1.3 86.1 + - - +
323X GLU* 1.3 55.7 + - - +
324X HIS* 4.0 6.7 + - - +
325X ASN* 3.3 29.3 + - - +
326X LYS* 2.8 39.2 + - - +
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Residues in contact with GLU 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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322X SER* 1.3 71.3 - - - +
324X HIS* 1.3 65.5 + - - +
326X LYS* 3.3 27.7 + - - +
327X LEU* 3.1 24.4 + - - +
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Residues in contact with HIS 324 (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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163X HIS* 5.0 0.4 - - + -
164X GLU* 2.9 38.7 + - - -
322X SER* 3.4 6.1 + - - +
323X GLU* 1.3 77.8 - - - +
325X ASN* 1.3 71.5 + - - +
327X LEU* 3.5 8.0 + - + +
328X LYS* 3.1 61.3 + - + +
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Residues in contact with ASN 325 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162X ASP* 6.0 1.0 - - - +
163X HIS* 3.5 19.3 + - - +
164X GLU* 5.0 2.3 - - - +
319X PRO* 3.4 39.4 - - - +
320X ALA* 3.8 1.6 - - - -
321X ASP* 2.9 26.9 + - - +
322X SER* 3.3 20.3 + - - +
323X GLU 3.2 0.4 - - - -
324X HIS* 1.3 91.3 + - - +
326X LYS* 1.3 60.0 + - - +
329X ALA* 2.9 24.9 + - - +
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Residues in contact with LYS 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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320X ALA* 3.3 33.9 + - + +
321X ASP* 4.1 13.5 + - - +
322X SER 2.8 22.3 + - - +
323X GLU* 3.3 30.7 + - - +
325X ASN* 1.3 72.9 - - - +
327X LEU* 1.3 62.5 + - - +
329X ALA* 3.5 4.5 - - - +
330X SER* 3.4 19.8 + - - -
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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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323X GLU 3.1 16.1 + - - +
324X HIS* 3.9 8.7 - - + +
326X LYS* 1.3 74.1 - - - +
328X LYS* 1.3 69.6 + - - +
330X SER* 2.8 26.2 + - - +
331X GLN* 3.1 34.8 + - + +
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Residues in contact with LYS 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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163X HIS* 3.3 33.0 - - + +
164X GLU* 5.0 2.9 - - - +
167X SER* 6.3 0.2 - - - -
324X HIS* 3.1 51.3 + - + +
327X LEU* 1.3 80.8 - - - +
329X ALA* 1.3 55.5 + - - +
331X GLN* 3.0 29.9 + - - +
332X ALA* 2.8 35.2 + - - +
357X PRO 3.7 15.6 + - - -
358X TYR* 3.7 19.5 + - + +
361X VAL* 4.4 15.8 - - - +
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Residues in contact with ALA 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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163X HIS* 3.5 10.6 + - - +
315X ASP* 4.3 13.0 - - - +
318X PHE* 3.7 35.9 - - + -
319X PRO 4.3 2.2 - - - +
320X ALA* 4.6 3.6 - - + -
325X ASN 2.9 18.0 + - - +
326X LYS* 3.5 10.5 - - - +
327X LEU 3.4 0.2 - - - -
328X LYS* 1.3 74.5 - - - +
330X SER* 1.3 57.7 + - - +
332X ALA* 3.5 3.0 + - - +
333X ARG* 3.1 30.4 + - - +
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Residues in contact with SER 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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326X LYS 3.4 7.5 + - - -
327X LEU* 2.8 30.5 + - - +
329X ALA* 1.3 75.8 - - - +
331X GLN* 1.3 61.1 + - - +
333X ARG* 4.1 17.8 - - - +
334X ASP* 3.1 27.0 + - - +
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Residues in contact with GLN 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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327X LEU* 3.1 39.9 + - + +
328X LYS* 3.0 43.8 + - - +
330X SER* 1.3 77.2 - - - +
332X ALA* 1.3 64.0 + - - +
334X ASP* 3.5 4.7 + - - -
335X LEU* 3.1 20.3 + - - +
356X HIS* 3.2 14.5 + - - +
357X PRO* 3.8 29.3 - - + +
358X TYR* 4.0 14.2 - - + +
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Residues in contact with ALA 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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163X HIS* 4.6 0.7 - - + -
166X MET* 5.7 1.6 - - - -
253X MET* 3.1 33.1 - - + +
318X PHE* 4.0 20.0 - - + -
328X LYS 2.8 18.2 + - - +
329X ALA* 3.7 5.6 - - - +
331X GLN* 1.3 72.2 - - - +
333X ARG* 1.3 57.6 + - - +
335X LEU* 3.6 1.0 + - - -
336X LEU* 3.1 18.4 + - - +
358X TYR* 3.7 28.8 - - + +
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Residues in contact with ARG 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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309X PHE* 3.7 16.9 - - + +
310X PRO* 3.6 38.3 - - - +
313X PHE* 3.0 34.9 + - + +
314X PRO* 4.0 1.6 - - - +
315X ASP* 2.7 44.1 + - - +
318X PHE* 4.1 10.4 - - + -
329X ALA 3.1 17.6 + - - +
330X SER* 4.1 22.1 - - - +
332X ALA* 1.3 74.8 - - - +
334X ASP* 1.3 64.8 + - - +
336X LEU* 3.3 9.3 + - - +
337X SER* 3.0 23.4 + - - -
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Residues in contact with ASP 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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330X SER 3.1 19.2 + - - +
331X GLN* 3.6 6.5 - - - +
333X ARG* 1.3 76.0 - - - +
335X LEU* 1.3 61.5 + - - +
337X SER* 2.5 27.5 + - - -
338X LYS* 3.0 34.8 + - - +
356X HIS* 3.0 24.8 - - + +
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Residues in contact with LEU 335 (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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170X LEU* 5.3 2.2 - - + -
174X LEU* 5.8 0.2 - - + -
253X MET* 4.3 13.2 - - - -
331X GLN 3.1 8.8 + - - +
332X ALA 3.9 3.4 - - - +
333X ARG 3.3 0.2 - - - -
334X ASP* 1.3 76.7 - - - +
336X LEU* 1.3 62.1 + - - +
338X LYS* 3.1 7.7 + - + +
339X MET* 3.1 57.1 + - + +
348X ILE* 5.1 4.7 - - + -
353X ALA* 4.1 11.4 - - + +
356X HIS* 3.5 42.3 - - + +
358X TYR* 4.2 15.5 - - + -
359X ILE* 3.8 31.0 - - + -
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Residues in contact with LEU 336 (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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250X GLY* 3.6 25.6 - - - +
253X MET* 3.8 22.6 - - + -
254X GLY* 3.8 16.2 - - - +
257X VAL* 4.7 8.3 - - + -
309X PHE* 3.9 8.3 - - + -
313X PHE* 3.8 38.1 - - + -
318X PHE* 4.7 3.4 - - + -
332X ALA 3.1 18.2 + - - +
333X ARG* 3.4 13.9 - - - +
334X ASP 3.3 0.2 - - - -
335X LEU* 1.3 75.4 - - - +
337X SER* 1.3 54.0 + - - +
338X LYS 3.1 0.2 + - - -
339X MET* 3.2 2.9 + - - -
340X LEU* 2.8 55.4 + - + +
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Residues in contact with SER 337 (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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309X PHE* 3.6 41.7 - - - -
333X ARG 3.0 12.1 + - - -
334X ASP* 2.5 28.5 + - - -
336X LEU* 1.3 74.6 - - - +
338X LYS* 1.3 62.6 + - - +
339X MET 3.6 0.2 - - - -
340X LEU 4.2 2.0 - - - +
341X VAL* 3.3 16.9 - - - +
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Residues in contact with LYS 338 (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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334X ASP* 3.0 42.6 + - - +
335X LEU* 3.1 8.2 + - + +
336X LEU 3.1 0.8 - - - -
337X SER* 1.3 82.1 - - - +
339X MET* 1.3 59.9 + - - +
341X VAL* 3.4 15.0 - - - +
346X LYS 4.6 0.8 - - - +
347X ARG* 3.7 0.7 - - - +
348X ILE* 3.0 60.4 + - + +
356X HIS* 4.4 13.3 + - + +
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Residues in contact with MET 339 (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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170X LEU* 6.2 0.7 - - - -
174X LEU* 4.0 15.0 - - + -
246X ILE* 3.7 38.4 - - + +
247X TRP* 4.0 9.7 - - - -
249X VAL* 4.0 24.0 - - + +
250X GLY* 3.9 15.3 - - - -
253X MET* 4.8 7.2 - - - +
335X LEU* 3.1 35.5 + - + +
336X LEU* 3.9 2.9 - - - +
338X LYS* 1.3 76.7 - - - +
340X LEU* 1.3 58.5 + - - +
341X VAL 2.9 11.3 + - - -
347X ARG* 3.4 18.7 + - - +
348X ILE* 3.8 6.3 - - + -
353X ALA* 3.5 30.5 - - + -
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Residues in contact with LEU 340 (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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247X TRP* 4.0 18.6 - - + +
250X GLY* 3.8 24.9 - - - +
251X CYS* 3.9 18.6 - - - +
262X LEU* 3.7 22.4 - - + -
263X PHE* 4.1 16.8 - - + -
279X LEU* 3.9 17.2 - - + +
309X PHE* 3.6 30.7 - - + -
313X PHE* 4.1 11.0 - - + -
336X LEU* 2.8 34.9 + - + +
337X SER 4.2 0.3 - - - +
339X MET* 1.3 71.9 - - - +
341X VAL* 1.3 64.4 + - - +
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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
------------------------------------------------------------
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