Contacts of the helix formed by residues 309 - 320 (chain E) in PDB entry 4MNE
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 ALA 309 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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630C LYS* 6.0 2.2 - - - -
307E PRO 3.8 2.2 + - - -
308E MET* 1.3 76.7 - - - +
310E ILE* 1.3 68.1 + - - +
311E PHE 4.3 4.7 - - - +
312E GLU* 3.1 23.6 + - + +
313E LEU* 3.2 10.1 + - - +
612F GLN* 6.3 3.4 - - - -
613F LEU* 5.7 3.8 - - + -
625F ILE 5.4 0.9 - - - +
626F ARG 4.6 4.9 - - - +
627F MET* 3.9 34.8 - - + +
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Residues in contact with ILE 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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224E VAL* 3.8 20.0 - - + -
225E GLY* 3.5 36.3 - - - +
226E THR* 3.6 19.8 + - - +
227E ARG 3.9 20.6 - - - +
228E SER* 4.4 4.3 - - - -
308E MET 3.8 1.2 + - - -
309E ALA* 1.3 73.3 - - - +
311E PHE* 1.3 61.2 + - + +
313E LEU* 3.1 8.6 + - + +
314E LEU* 2.9 39.3 + - + +
613F LEU* 4.9 9.8 - - + +
663F ASP* 4.0 20.4 - - - +
666F ILE* 4.3 12.8 - - + -
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Residues in contact with PHE 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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309E ALA* 3.3 2.8 - - - +
310E ILE* 1.3 81.9 - - - +
312E GLU* 1.3 61.3 + - + +
314E LEU* 3.5 5.3 + - + +
315E ASP* 2.9 39.5 + - + +
625F ILE* 3.5 30.5 + - + +
626F ARG* 3.5 44.0 - - + +
628F GLN* 4.1 12.6 - - - -
666F ILE* 4.0 17.7 - - - -
667F PHE* 3.7 34.3 - + - -
670F GLY 3.8 15.5 - - - -
671F ARG* 4.1 18.6 - - + -
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Residues in contact with GLU 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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630C LYS* 5.8 4.0 - - - -
308E MET* 3.2 42.0 - - + +
309E ALA* 3.1 23.8 + - + +
311E PHE* 1.3 84.3 - - + +
313E LEU* 1.3 51.8 + - - +
315E ASP* 3.2 6.9 + - + +
316E TYR* 2.8 34.8 + - - +
626F ARG 5.0 2.0 + - - +
627F MET 5.7 1.4 - - - +
628F GLN* 6.6 0.7 - - + -
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Residues in contact with LEU 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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226E THR 3.3 26.7 - - - +
227E ARG* 3.6 22.4 - - + -
228E SER 4.3 1.6 - - - +
261E TYR* 4.0 13.0 - - + +
263E ILE* 3.4 37.6 - - + +
308E MET* 3.7 27.1 - - + +
309E ALA 3.2 10.1 + - - +
310E ILE* 3.1 9.2 + - + +
312E GLU* 1.3 77.9 - - - +
314E LEU* 1.3 67.1 + - + +
316E TYR* 3.2 7.3 + - - +
317E ILE* 3.0 29.1 + - + +
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Residues in contact with LEU 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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228E SER* 3.4 36.3 - - - +
235E LEU* 3.9 19.4 - - + +
310E ILE* 2.9 28.6 + - + +
311E PHE* 3.9 4.5 - - - +
313E LEU* 1.3 72.8 - - + +
315E ASP* 1.3 64.2 + - - +
317E ILE* 3.3 5.3 + - + +
318E VAL* 3.1 27.4 + - - +
663F ASP* 3.2 35.9 - - + +
666F ILE* 3.8 24.2 - - + -
667F PHE* 3.8 21.3 - - + +
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Residues in contact with ASP 315 (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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311E PHE* 2.9 33.7 + - + +
312E GLU* 3.4 8.7 - - + +
314E LEU* 1.3 75.1 - - - +
316E TYR* 1.3 58.8 + - - +
318E VAL 3.2 1.2 + - - -
319E ASN* 2.6 63.6 + - - +
628F GLN* 5.8 0.9 + - - -
667F PHE* 3.7 12.2 - - - -
671F ARG* 2.9 29.3 + - - -
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Residues in contact with TYR 316 (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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263E ILE* 4.0 23.8 - - + -
264E PRO* 4.0 15.9 - - + -
265E PRO* 3.2 36.1 - - + +
308E MET* 4.6 11.9 - - + -
312E GLU 2.8 16.1 + - - +
313E LEU* 3.4 9.2 - - - +
315E ASP* 1.3 74.2 - - - +
317E ILE* 1.3 59.6 + - - +
320E GLU* 2.7 73.0 + - + +
321E PRO* 4.1 16.4 + - - +
323E PRO* 6.2 2.0 - - + -
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Residues in contact with ILE 317 (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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228E SER* 4.1 23.8 - - - +
230E MET 4.0 14.1 - - - +
232E PRO* 4.0 8.9 - - + +
235E LEU* 3.9 16.2 - - + -
247E TRP* 3.8 25.7 - - + -
251E LEU* 4.9 3.1 - - + -
261E TYR* 4.1 2.5 - - - +
263E ILE* 3.6 35.7 - - + -
313E LEU* 3.0 21.7 + - + +
314E LEU* 3.6 11.4 - - + +
316E TYR* 1.3 76.0 - - - +
318E VAL* 1.3 63.6 + - - +
320E GLU 3.8 1.4 - - - +
344E LYS* 3.4 22.9 + - - +
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Residues in contact with VAL 318 (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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232E PRO* 4.3 11.7 - - + +
235E LEU* 3.7 29.8 - - + -
236E GLN* 3.4 32.5 - - + +
314E LEU 3.1 17.4 + - - +
315E ASP 3.8 2.9 - - - +
317E ILE* 1.3 76.8 - - - +
319E ASN* 1.3 71.1 + - - +
344E LYS* 3.2 18.4 + - - -
667F PHE* 3.7 28.0 - - + -
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Residues in contact with ASN 319 (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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315E ASP* 2.6 41.8 + - - +
318E VAL* 1.3 94.6 - - - +
320E GLU* 1.3 76.4 + - + +
321E PRO* 4.5 1.6 - - - +
344E LYS* 3.9 2.8 + - - -
667F PHE* 4.7 1.8 - - - -
671F ARG* 3.3 22.5 + - - +
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Residues in contact with GLU 320 (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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316E TYR* 2.7 71.5 + - + +
317E ILE* 3.8 2.3 - - - +
319E ASN* 1.3 85.5 - - + +
321E PRO* 1.3 77.1 - - + +
344E LYS* 2.4 30.3 + - - +
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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