Contacts of the helix formed by residues 306 - 314 (chain E) in PDB entry 4IG9
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 PRO 306 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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302E PHE* 3.2 47.8 - - + +
303E ARG 4.7 3.1 - - - +
304E LYS 4.2 3.4 - - - +
305E ASP* 1.3 87.8 - - - +
307E ARG* 1.3 67.1 + - + +
308E PRO* 3.5 1.1 - - - -
309E PHE* 3.5 5.1 + - - +
310E PHE* 3.2 30.9 + - + -
392E VAL* 4.4 23.3 - - + -
406E ILE* 5.2 4.5 - - + -
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Residues in contact with ARG 307 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287E PHE* 3.7 32.6 - - + -
305E ASP* 2.9 30.6 + - - +
306E PRO* 1.3 80.7 - - + +
308E PRO* 1.4 67.2 - - + +
310E PHE* 3.2 6.9 + - - +
311E LYS* 3.2 21.5 + - - +
392E VAL* 4.8 15.3 - - + -
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Residues in contact with PRO 308 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283E LEU* 3.7 13.8 - - + +
287E PHE* 3.9 28.5 - - + -
290E LEU* 4.2 20.9 - - + -
296E MET* 5.0 8.5 - - + -
301E TYR* 4.0 18.6 - - + +
305E ASP* 3.3 29.4 - - - +
306E PRO 3.6 0.4 - - - -
307E ARG* 1.4 94.9 - - + +
309E PHE* 1.3 62.7 + - + +
311E LYS* 3.5 1.7 + - + +
312E PHE* 3.2 21.7 + - - +
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Residues in contact with PHE 309 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296E MET* 3.2 34.5 - - + +
297E PHE* 4.7 4.9 - + - -
302E PHE* 3.7 24.9 - + + -
306E PRO* 3.5 7.4 + - + +
307E ARG 3.2 0.6 - - - -
308E PRO* 1.3 81.2 - - + +
310E PHE* 1.3 60.1 + + - +
312E PHE* 3.2 29.5 + + - +
313E ALA* 2.7 35.9 + - + +
366E PHE* 4.0 18.8 - + - -
408E LYS* 5.7 0.2 - - + -
409E PRO* 3.9 29.2 - - + -
411E ILE* 4.0 13.2 - - + -
413E PHE* 3.5 27.8 - + - -
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Residues in contact with PHE 310 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302E PHE* 3.4 25.8 - + - -
306E PRO* 3.2 27.3 + - + +
307E ARG* 3.2 6.3 + - - +
309E PHE* 1.3 78.4 - + - +
311E LYS* 1.3 64.3 + - - +
313E ALA* 3.6 5.8 - - + -
314E LYS* 3.4 17.3 + - - +
387E ILE* 3.6 44.7 - - + +
390E GLN* 5.4 7.0 - - - +
391E VAL 6.1 1.3 - - - +
392E VAL* 4.6 11.2 - - + -
393E PRO* 3.6 27.6 - - + -
406E ILE* 3.6 15.7 - - + -
407E MET 3.5 19.5 - - - -
409E PRO* 3.7 25.4 - - + -
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Residues in contact with LYS 311 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279E ILE* 5.4 0.2 - - - -
282E ARG* 4.6 8.7 + - - +
283E LEU* 3.7 25.6 - - + +
286E ASP* 3.5 24.2 + - - +
287E PHE* 4.2 13.2 - - + -
307E ARG 3.2 14.6 + - - +
308E PRO* 3.9 5.4 - - + +
310E PHE* 1.3 76.9 - - - +
312E PHE* 1.3 62.9 + - - +
314E LYS* 3.6 19.2 - - - +
315E GLU* 3.8 21.5 + - - +
390E GLN* 3.5 39.0 - - + +
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Residues in contact with PHE 312 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273E PHE* 3.5 23.6 - + + -
279E ILE* 3.5 32.3 - - + -
283E LEU* 4.5 2.4 - - + +
296E MET* 4.0 15.3 - - - -
297E PHE* 3.8 24.9 - + - -
308E PRO 3.2 14.1 + - - +
309E PHE* 3.3 43.3 - + - +
311E LYS* 1.3 78.7 - - - +
313E ALA* 1.3 62.6 + - - +
315E GLU* 3.3 17.0 + - - +
316E ILE* 3.4 39.0 + - + +
347E ILE* 4.5 5.2 - - + -
366E PHE* 4.1 13.9 - + - -
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Residues in contact with ALA 313 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309E PHE* 2.7 25.7 + - + +
310E PHE* 3.8 15.5 - - + +
311E LYS 3.3 0.4 - - - -
312E PHE* 1.3 80.4 - - + +
314E LYS* 1.3 61.0 + - - +
315E GLU 3.1 1.1 + - - -
316E ILE* 3.6 2.5 + - - -
317E TYR* 3.3 27.3 + - - -
366E PHE* 3.6 30.1 - - + -
387E ILE* 4.2 11.9 - - + -
409E PRO* 5.2 0.2 - - + -
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Residues in contact with LYS 314 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310E PHE 3.4 5.1 + - - +
311E LYS* 3.6 13.7 - - - +
312E PHE 3.3 0.8 - - - -
313E ALA* 1.3 78.0 - - - +
315E GLU* 1.3 65.7 + - + +
317E TYR* 3.9 10.5 - - - +
320E GLN* 2.8 20.6 + - - +
387E ILE* 3.6 30.5 - - + +
388E PHE* 3.8 41.2 + - + +
390E GLN* 3.7 29.7 - - + +
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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