Contacts of the helix formed by residues 310 - 323 (chain H) in PDB entry 3DV0
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 310 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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215H GLU* 3.2 22.2 - - - +
305H SER 4.8 6.5 - - - +
308H LEU* 4.3 8.2 + - + +
309H PRO* 1.3 75.4 - - - +
311H PHE* 1.3 71.6 + - + +
312H LYS* 3.7 25.2 - - - +
313H ASP* 2.8 35.1 + - - +
314H VAL* 3.3 13.5 + - - +
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Residues in contact with PHE 311 (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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215H GLU* 2.9 41.7 + - - +
218H LYS* 3.5 48.2 - - + -
219H ALA* 3.5 5.5 - - - +
222H GLU* 4.8 8.5 - - + -
310H ASN* 1.3 83.2 - - + +
312H LYS* 1.3 94.9 + - + +
313H ASP 3.2 0.2 - - - -
314H VAL* 3.3 3.2 + - - -
315H ILE* 3.0 46.9 + - + +
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Residues in contact with LYS 312 (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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310H ASN* 3.1 17.3 + - - +
311H PHE* 1.3 110.1 - - + +
313H ASP* 1.3 60.5 + - - +
315H ILE* 3.6 8.1 + - + +
316H GLU* 3.1 27.6 + - - +
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Residues in contact with ASP 313 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362E TYR* 5.8 1.7 + - - -
365E LYS* 3.8 21.1 + - - -
291H VAL* 4.0 19.2 - - + +
308H LEU 4.1 2.1 - - - +
309H PRO* 3.4 8.9 - - - +
310H ASN* 2.8 37.5 + - - +
312H LYS* 1.3 77.6 - - - +
314H VAL* 1.3 60.0 + - - +
316H GLU* 3.6 9.8 - - - +
317H THR* 3.0 35.3 + - - +
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Residues in contact with VAL 314 (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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206H ILE* 3.7 37.7 - - + -
212H MET* 5.9 0.4 - - - -
215H GLU* 4.2 9.2 - - + +
216H SER* 4.4 6.3 - - - +
219H ALA* 3.8 12.1 - - + -
257H ILE* 4.0 10.9 - - + +
259H VAL* 4.1 26.7 - - + -
291H VAL* 4.4 8.7 - - + -
309H PRO 6.0 0.2 - - - -
310H ASN 3.5 14.8 - - - +
311H PHE* 3.3 11.6 + - - +
313H ASP* 1.3 75.6 - - - +
315H ILE* 1.3 55.5 + - - +
317H THR* 3.3 0.9 + - - -
318H ALA* 2.6 38.1 + - - +
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Residues in contact with ILE 315 (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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219H ALA* 3.4 20.2 - - + +
222H GLU* 3.7 28.9 - - + -
223H LEU* 4.3 9.9 - - + +
226H GLU* 5.3 3.4 - - - +
311H PHE* 3.0 37.7 + - + +
312H LYS* 3.7 7.9 - - + +
314H VAL* 1.3 77.1 - - - +
316H GLU* 1.3 63.7 + - - +
318H ALA* 3.4 6.1 + - - +
319H LYS* 3.0 49.2 + - + +
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Residues in contact with GLU 316 (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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365E LYS* 4.0 23.8 + - - -
312H LYS 3.1 15.3 + - - +
313H ASP* 3.6 12.8 - - - +
314H VAL 3.2 0.2 - - - -
315H ILE* 1.3 80.8 - - - +
317H THR* 1.3 58.2 + - - +
319H LYS* 3.2 9.2 + - - +
320H LYS* 2.9 55.2 + - + +
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Residues in contact with THR 317 (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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257H ILE* 4.1 9.2 - - + -
289H LEU* 3.7 34.1 - - + -
290H ARG 4.4 5.8 + - - +
291H VAL* 3.2 31.1 - - + +
313H ASP* 3.0 14.7 + - - +
314H VAL 4.0 0.7 - - - -
316H GLU* 1.3 72.1 - - - +
318H ALA* 1.3 66.0 + - - +
320H LYS* 3.2 17.8 + - + +
321H VAL* 3.1 23.4 + - - +
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Residues in contact with ALA 318 (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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204H ILE* 3.7 23.6 - - + +
206H ILE* 4.7 2.2 - - + -
223H LEU* 3.9 29.6 - - + -
257H ILE* 4.0 8.9 - - + +
314H VAL 2.6 23.9 + - - +
315H ILE 3.6 4.7 - - - +
317H THR* 1.3 72.4 - - - +
319H LYS* 1.3 58.4 + - - +
321H VAL* 3.4 4.5 + - - +
322H MET* 3.1 31.1 + - + +
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Residues in contact with LYS 319 (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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223H LEU* 4.4 13.9 - - + -
226H GLU* 3.0 38.0 + - - -
228H ILE* 4.6 12.6 - - + -
315H ILE* 3.0 36.3 + - + +
316H GLU* 3.5 6.1 - - - +
318H ALA* 1.3 74.2 - - - +
320H LYS* 1.3 68.2 + - - +
321H VAL 2.9 3.0 + - - -
322H MET* 3.0 6.5 + - - +
323H ASN* 3.0 37.8 + - - +
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Residues in contact with LYS 320 (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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289H LEU* 4.0 21.3 - - + +
316H GLU* 2.9 54.4 + - + +
317H THR* 3.2 18.8 + - + +
319H LYS* 1.3 74.7 - - - +
321H VAL* 1.3 63.5 - - - +
323H ASN* 3.8 4.5 + - - +
324H PHE* 3.4 20.3 + - - +
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Residues in contact with VAL 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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204H ILE* 4.1 9.2 - - + -
255H ARG* 3.3 40.0 + - + -
256H ALA 4.5 4.0 - - - +
257H ILE* 3.3 30.7 - - + -
286H ALA* 4.3 10.8 - - + -
287H PRO* 4.1 8.7 - - + +
289H LEU* 3.9 21.1 - - + -
317H THR 3.1 7.9 + - - +
318H ALA 3.4 8.5 - - - +
319H LYS 2.9 1.2 - - - -
320H LYS* 1.3 75.0 - - - +
322H MET* 1.3 58.0 + - - +
324H PHE* 2.7 35.2 + - - +
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Residues in contact with MET 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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203H ASP* 3.9 22.2 - - + -
204H ILE* 3.9 22.4 - - + -
228H ILE* 4.0 34.5 - - + -
255H ARG* 3.4 52.5 + - - +
318H ALA 3.3 15.0 - - - +
319H LYS* 3.0 8.6 + - + +
321H VAL* 1.3 79.7 - - - +
323H ASN* 1.3 63.2 + - - +
324H PHE* 3.4 2.6 + - - +
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Residues in contact with ASN 323 (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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319H LYS* 3.0 30.8 + - - +
320H LYS* 3.9 5.8 - - - +
322H MET* 1.3 81.5 - - - +
324H PHE* 1.3 67.5 + - - +
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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