Contacts of the helix formed by residues 312 - 317 (chain E) in PDB entry 5IXM
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 TYR 312 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286E ARG* 5.1 9.2 - - - +
311E ASP* 1.3 78.0 - - - +
313E SER* 1.3 70.1 + - - +
315E LEU* 3.2 37.6 - - + +
316E PHE* 4.0 20.2 - + - -
336E GLY* 3.6 20.0 - - - -
337E LEU 3.7 3.1 + - - -
338E THR* 3.3 17.5 + - - -
353E SER* 3.7 19.3 - - - -
354E VAL 3.6 7.2 - - - -
355E GLY* 3.6 30.3 - - - -
383E ALA* 3.8 9.1 - - - +
384E GLY* 4.5 11.9 + - - +
385E ASP* 3.2 30.0 - - + +
401E GLN* 5.7 0.2 - - - +
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Residues in contact with SER 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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286E ARG* 6.1 1.6 - - - +
311E ASP* 3.1 19.9 + - - -
312E TYR* 1.3 82.8 - - - +
314E GLY* 1.3 56.7 + - - +
315E LEU 2.9 11.0 + - - -
316E PHE* 2.9 22.9 + - - +
317E ARG* 3.8 2.4 + - - +
104F ARG* 3.5 22.6 + - - -
126F GLU* 4.9 6.3 - - - -
130F GLN* 4.4 4.2 + - - -
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Residues in contact with GLY 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 SER* 3.4 16.6 + - - -
311E ASP* 2.8 23.1 + - - -
313E SER* 1.3 72.0 - - - +
315E LEU* 1.3 61.4 + - - +
316E PHE 3.1 0.4 - - - -
317E ARG* 3.2 47.6 + - - +
357E ILE* 5.2 1.6 - - - +
126F GLU* 5.3 0.2 - - - -
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Residues in contact with LEU 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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288E GLN* 4.8 0.9 + - - -
310E SER* 4.1 4.0 - - - +
311E ASP 3.3 9.2 + - - +
312E TYR* 3.2 37.2 - - + +
313E SER 2.9 1.0 + - - -
314E GLY* 1.3 78.2 - - - +
316E PHE* 1.3 67.0 + - + +
317E ARG 3.3 4.3 + - - +
332E GLN* 5.4 1.2 + - - -
334E SER* 2.9 25.7 + - - -
335E THR 4.8 1.3 - - - +
355E GLY* 3.5 29.6 - - - -
356E GLN* 3.9 6.1 - - - +
357E ILE* 3.6 35.5 - - + +
381E VAL* 3.9 18.4 - - + -
383E ALA* 3.8 16.8 - - + -
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Residues in contact with PHE 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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262E LYS* 4.9 5.2 + - - -
286E ARG* 3.5 68.6 - - + +
288E GLN* 3.3 44.8 + - + +
312E TYR* 4.0 33.9 - + - -
313E SER* 2.9 12.5 + - - +
315E LEU* 1.3 83.7 - - + +
317E ARG* 1.3 62.4 + - - +
318E ASP 3.6 1.6 + - - -
334E SER* 3.4 28.5 - - - -
335E THR 4.0 4.0 - - - -
336E GLY* 3.9 21.8 - - - -
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Residues in contact with ARG 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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288E GLN* 5.0 1.2 + - - -
290E LEU* 4.8 4.2 - - - +
308E MET* 3.6 35.3 - - - +
309E GLN 2.6 37.0 + - - -
310E SER* 3.5 12.1 - - - +
311E ASP* 4.7 2.6 + - - +
313E SER 3.8 2.0 + - - +
314E GLY* 3.2 31.4 + - - +
315E LEU 4.4 2.9 - - - +
316E PHE* 1.3 78.1 - - - +
318E ASP* 1.3 66.1 + - - +
319E ARG* 3.2 30.8 + - + +
332E GLN* 5.2 5.0 + - - -
122F VAL* 4.5 5.6 - - - -
123F LEU* 4.4 4.0 - - - +
126F GLU* 2.6 51.6 + - - +
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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