Contacts of the helix formed by residues 314 - 324 (chain A) in PDB entry 4IO8
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 LEU 314 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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198A PHE* 5.8 1.1 - - + -
310A PHE 4.9 0.2 - - - +
311A ARG* 3.2 44.4 + - - +
312A SER 3.1 1.0 - - - -
313A THR* 1.3 85.4 - - - +
315A GLU* 1.4 58.7 + - + +
317A VAL* 3.2 13.0 + - + +
318A GLU* 3.0 37.3 + - - +
349A LEU* 3.5 45.1 - - + +
350A LEU* 4.5 7.0 - - + +
353A PHE* 3.7 31.4 - - + -
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Residues in contact with GLU 315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311A ARG 4.8 2.4 - - - +
312A SER* 3.2 27.4 + - - +
314A LEU* 1.4 75.8 - - + +
316A PRO* 1.4 64.0 - - + +
318A GLU* 3.0 19.5 + - - +
319A LYS* 2.8 53.1 + - - +
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Residues in contact with PRO 316 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205A PHE* 3.7 20.0 - - + -
207A VAL* 4.0 6.3 - - + +
223A ALA* 3.3 11.6 - - + +
224A GLY* 3.5 39.0 - - - +
225A ASP* 5.8 0.9 - - + -
312A SER 3.1 26.0 - - - +
313A THR* 3.6 9.6 - - - +
315A GLU* 1.4 80.0 - - + +
317A VAL* 1.3 55.1 + - - +
319A LYS* 3.9 12.3 - - + +
320A ALA* 3.0 29.6 + - - +
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Residues in contact with VAL 317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A LEU* 4.2 7.1 - - + +
198A PHE* 3.8 23.3 - - + -
207A VAL* 3.9 19.7 - - + -
313A THR 3.3 19.1 - - - +
314A LEU* 3.2 12.7 + - + +
315A GLU 3.2 1.0 - - - -
316A PRO* 1.3 73.9 - - - +
318A GLU* 1.4 57.9 + - - +
320A ALA* 3.6 2.9 + - - +
321A LEU* 3.1 29.4 + - + +
350A LEU* 4.3 5.4 - - + -
353A PHE* 3.6 29.4 - - + -
354A PHE* 3.8 23.1 - - + -
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Residues in contact with GLU 318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314A LEU* 3.0 22.4 + - - +
315A GLU* 3.0 19.6 + - - +
317A VAL* 1.4 74.1 - - - +
319A LYS* 1.4 63.2 - - + +
321A LEU* 3.5 6.1 + - - +
322A ARG* 3.1 25.6 + - - +
353A PHE* 3.5 32.9 - - + -
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Residues in contact with LYS 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223A ALA* 4.3 9.0 - - + -
315A GLU* 2.8 49.7 + - - +
316A PRO* 4.0 14.2 - - + +
318A GLU* 1.4 70.8 - - + +
320A ALA* 1.4 58.3 + - - +
322A ARG* 3.4 6.2 + - - +
323A ASP* 2.9 40.4 + - - +
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Residues in contact with ALA 320 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207A VAL* 3.9 21.1 - - + +
209A ILE* 3.5 16.4 - - + -
221A ALA* 3.1 22.4 - - + +
222A THR 5.3 0.4 - - - +
223A ALA* 4.2 11.1 - - + +
316A PRO 3.0 19.7 + - - +
317A VAL 3.8 4.0 - - - +
318A GLU 3.4 0.2 - - - -
319A LYS* 1.4 75.3 - - - +
321A LEU* 1.4 55.5 + - - +
323A ASP* 4.5 1.3 - - - -
324A ALA* 3.0 27.7 + - - +
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Residues in contact with LEU 321 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196A LEU* 4.8 4.5 - - + -
209A ILE* 3.8 10.3 - - + -
317A VAL 3.1 18.6 + - - +
318A GLU* 3.8 5.6 - - - +
320A ALA* 1.4 75.9 - - - +
322A ARG* 1.3 55.6 + - - +
324A ALA* 3.5 0.9 + - - -
325A LYS 3.0 8.0 + - - -
326A LEU* 2.9 42.6 + - + +
327A ASP 4.1 12.1 - - - +
328A LYS* 4.1 19.5 - - + +
331A ILE* 3.7 37.2 - - + -
353A PHE* 3.7 33.0 - - + -
354A PHE* 4.5 4.0 - - + -
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Residues in contact with ARG 322 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318A GLU 3.1 18.2 + - - +
319A LYS* 3.8 6.1 - - - +
321A LEU* 1.3 73.0 - - - +
323A ASP* 1.3 66.3 + - - +
325A LYS* 3.6 28.0 + - - +
326A LEU 5.0 0.9 - - - -
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Residues in contact with ASP 323 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220A LYS 4.6 4.4 - - - +
221A ALA* 4.0 11.7 - - + +
222A THR 4.7 10.9 + - - +
223A ALA* 5.6 1.0 - - - +
319A LYS* 2.9 26.8 + - - +
320A ALA* 3.8 5.4 - - - +
322A ARG* 1.3 73.3 - - - +
324A ALA* 1.4 58.4 + - - +
325A LYS* 3.1 18.1 + - - +
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Residues in contact with ALA 324 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209A ILE* 3.9 13.9 - - + -
220A LYS* 3.9 28.0 + - + +
221A ALA* 3.8 12.1 - - + +
320A ALA 3.0 18.2 + - - +
321A LEU 3.5 2.7 + - - +
323A ASP* 1.4 73.4 - - - +
325A LYS* 1.4 66.2 + - - +
326A LEU* 3.4 29.3 - - + +
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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