Contacts of the helix formed by residues 315 - 328 (chain H) in PDB entry 3EXG
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 GLN 315 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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351E ALA* 5.2 0.8 - - - +
218H HIS* 5.2 3.1 - - - -
310H ASP* 3.0 34.6 + - + +
311H ASN* 3.9 19.1 + - - +
313H ILE* 3.2 16.0 + - + +
314H PRO* 1.3 75.6 - - - +
316H VAL* 1.3 68.7 + - + +
317H LYS* 3.6 31.4 + - + +
318H ASP* 2.8 44.4 + - - +
319H ILE* 3.1 17.8 + - - +
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Residues in contact with VAL 316 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218H HIS* 3.3 23.9 - - + +
221H GLU* 3.6 29.2 - - + +
222H ALA* 3.2 42.4 - - + +
225H VAL* 5.6 1.8 - - + -
315H GLN* 1.3 67.8 - - + +
317H LYS* 1.3 58.1 + - - +
318H ASP 2.4 17.3 + - - -
319H ILE* 2.9 17.2 + - - +
320H ILE* 2.9 20.2 + - + +
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Residues in contact with LYS 317 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311H ASN* 5.3 3.4 + - - -
315H GLN* 3.6 28.9 + - + +
316H VAL* 1.3 80.1 - - - +
318H ASP* 1.3 73.6 + - - +
320H ILE* 3.7 10.7 + - - +
321H PHE* 3.3 21.8 + - - +
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Residues in contact with ASP 318 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351E ALA* 3.7 22.9 - - + +
352E ASN* 3.4 22.9 + - - +
355E ILE* 3.9 14.5 - - - +
295H VAL* 4.5 7.6 - - + +
315H GLN* 2.8 47.4 + - - +
316H VAL 2.4 12.7 + - - -
317H LYS* 1.3 87.9 - - - +
319H ILE* 1.3 63.4 + - - +
320H ILE 3.2 0.7 - - - -
321H PHE* 3.2 3.8 + - - +
322H ALA* 3.1 18.2 + - - +
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Residues in contact with ILE 319 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209H VAL* 4.8 2.2 - - + -
215H PRO* 5.9 0.2 - - + -
218H HIS* 4.1 24.5 - - + +
219H CYS* 4.0 20.6 - - - +
222H ALA* 4.3 10.1 - - + -
260H VAL* 5.2 1.6 - - + -
262H VAL* 3.8 43.7 - - + -
295H VAL* 4.4 14.4 - - + -
314H PRO* 4.7 2.7 - - + -
315H GLN 3.2 15.3 - - - +
316H VAL* 3.7 4.5 - - - +
318H ASP* 1.3 73.3 - - - +
320H ILE* 1.3 63.7 + - - +
322H ALA* 3.1 2.8 + - - +
323H ILE* 2.9 41.4 + - + +
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Residues in contact with ILE 320 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222H ALA* 3.8 26.5 - - + +
225H VAL* 3.7 34.8 - - + -
226H LEU* 4.1 11.6 - - + +
316H VAL* 2.9 20.7 + - + +
317H LYS* 3.7 12.6 - - - +
319H ILE* 1.3 77.3 - - - +
321H PHE* 1.3 57.7 + - - +
323H ILE* 4.0 7.1 - - - +
324H LYS* 3.0 52.5 + - + +
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Residues in contact with PHE 321 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352E ASN* 4.0 17.0 - - - +
354E TRP* 3.7 27.4 - + + -
355E ILE* 6.4 0.2 - - + -
317H LYS 3.3 11.8 + - - +
318H ASP* 3.2 10.8 + - - +
319H ILE 3.1 1.0 - - - -
320H ILE* 1.3 80.0 - - - +
322H ALA* 1.3 57.4 + - - +
324H LYS* 4.2 3.9 - - + +
325H LYS* 3.0 64.5 + - + +
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Residues in contact with ALA 322 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352E ASN* 4.7 2.9 - - + +
354E TRP* 4.0 22.9 - - + -
260H VAL* 4.2 11.2 - - + -
293H VAL* 4.1 5.4 - - + +
295H VAL* 3.7 30.3 - - + -
318H ASP 3.1 6.6 + - - +
319H ILE 3.1 5.2 + - - +
321H PHE* 1.3 77.0 - - - +
323H ILE* 1.3 65.6 + - - +
325H LYS* 3.4 1.7 + - - +
326H THR* 3.0 28.2 + - - -
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Residues in contact with ILE 323 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207H ILE* 4.1 21.8 - - + -
209H VAL* 4.0 27.6 - - + -
222H ALA* 4.9 5.4 - - + -
226H LEU* 3.5 35.4 - - + -
231H VAL* 4.7 1.1 - - + -
233H CYS* 4.1 4.7 - - - -
260H VAL* 4.3 16.2 - - + -
319H ILE* 2.9 39.5 + - + +
320H ILE* 4.0 3.8 - - - +
322H ALA* 1.3 75.9 - - - +
324H LYS* 1.3 64.3 + - + +
326H THR* 3.0 4.3 + - - -
327H LEU* 2.9 32.5 + - + +
329H ILE* 6.0 0.4 - - + -
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Residues in contact with LYS 324 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226H LEU* 3.8 21.1 - - + -
229H GLU* 3.6 30.0 + - - -
320H ILE* 3.0 29.2 + - + +
321H PHE* 4.2 5.8 - - + +
323H ILE* 1.3 75.9 - - + +
325H LYS* 1.3 64.1 + - - +
328H ASN* 3.0 20.1 + - - -
329H ILE* 3.4 44.9 + - + +
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Residues in contact with LYS 325 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354E TRP* 3.3 49.6 - - + +
321H PHE* 3.0 55.9 + - + +
322H ALA 3.6 5.4 - - - +
324H LYS* 1.3 79.0 - - - +
326H THR* 1.3 60.7 + - - +
328H ASN* 3.5 13.6 + - - +
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Residues in contact with THR 326 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354E TRP* 5.1 0.7 - - - -
207H ILE* 4.1 10.3 - - + -
258H HIS* 3.8 25.3 + - + -
259H LEU 4.7 4.5 - - - +
260H VAL* 3.9 2.3 - - + +
290H ALA* 3.6 34.8 - - + +
291H PRO 4.3 9.1 + - - +
293H VAL* 3.2 23.7 - - - +
322H ALA 3.0 14.6 + - - -
323H ILE 3.0 7.4 + - - -
325H LYS* 1.3 73.6 - - - +
327H LEU* 1.3 57.9 + - - +
328H ASN* 3.0 11.3 + - - +
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Residues in contact with LEU 327 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206H HIS* 3.6 21.3 - - + +
207H ILE* 4.1 19.7 - - + -
231H VAL* 3.6 31.2 - - + -
258H HIS* 3.4 39.4 + - + +
323H ILE* 2.9 20.8 + - + +
326H THR* 1.3 74.3 - - - +
328H ASN* 1.3 66.5 + - - +
329H ILE* 2.9 34.2 + - + +
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Residues in contact with ASN 328 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324H LYS 3.0 9.7 + - - -
325H LYS* 3.9 9.2 - - - +
326H THR 3.0 6.1 - - - +
327H LEU* 1.3 78.7 - - - +
329H ILE* 1.3 62.1 + - - +
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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
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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