Contacts of the strand formed by residues 287 - 293 (chain E) in PDB entry 1II4
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 HIS 287 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66A ALA* 3.5 20.2 - - + -
67A GLU 3.2 11.5 + - - -
68A GLU* 3.3 44.0 - - + +
69A ARG* 3.7 7.1 + - + +
70A GLY 5.3 0.4 - - - +
286E PRO* 1.3 74.4 - - - +
288E ILE* 1.3 70.9 + - - +
289E GLN* 4.0 23.7 + - + -
314E ALA* 4.3 13.8 - - + +
315E ALA* 3.1 24.6 + - + -
343E LEU* 3.4 4.2 - - - +
344E ALA* 3.3 2.9 - - - -
345E GLY 2.7 34.3 + - - +
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Residues in contact with ILE 288 (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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26A PHE* 3.7 29.2 - - + -
278E CYS* 5.1 0.9 - - - -
280E VAL* 3.7 23.3 - - + -
286E PRO* 4.1 3.8 + - + +
287E HIS* 1.3 82.5 - - - +
289E GLN* 1.3 67.8 + - - +
290E TRP* 4.9 2.5 - - - +
315E ALA* 2.8 34.4 + - + +
321E ASP* 5.1 1.5 + - - +
324E ILE* 3.6 37.4 - - + +
325E GLU* 4.6 7.2 - - + -
342E CYS* 3.7 27.6 - - - -
343E LEU 3.3 3.1 - - - +
344E ALA* 4.0 14.8 - - + -
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Residues in contact with GLN 289 (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 HIS* 4.0 18.8 + - + -
288E ILE* 1.3 78.3 - - - +
290E TRP* 1.3 65.4 + - - +
291E ILE* 3.5 25.9 + - + +
311E VAL* 3.9 17.8 - - + +
313E LYS 3.0 15.0 - - - +
314E ALA* 3.9 12.6 - - + -
324E ILE* 4.9 0.4 - - - -
341E THR 3.8 0.2 - - - +
342E CYS* 3.8 2.6 - - - -
343E LEU* 3.0 56.4 + - + +
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Residues in contact with TRP 290 (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 PRO* 3.8 17.9 - - + -
276E PHE* 3.4 48.0 - + + -
278E CYS* 3.4 31.9 - - + -
288E ILE* 4.9 3.5 - - + +
289E GLN* 1.3 75.3 - - - +
291E ILE* 1.3 64.4 + - - +
311E VAL* 3.6 2.1 - - - +
312E LEU* 2.9 28.3 + - + -
313E LYS* 2.7 34.9 + - + +
324E ILE* 2.8 31.1 + - + -
325E GLU* 3.5 6.4 - - - +
327E LEU* 3.7 41.0 - - + +
340E TYR* 4.9 1.8 - - + -
341E THR* 3.3 24.2 - - - -
342E CYS* 3.7 15.3 - - + -
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Residues in contact with ILE 291 (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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289E GLN* 3.5 34.1 - - + +
290E TRP* 1.3 80.7 - - - +
292E LYS* 1.3 67.6 + - - +
293E HIS* 4.6 3.7 - - + -
309E LEU* 3.6 38.6 - - + -
310E LYS 3.4 12.6 - - - +
311E VAL* 4.6 7.2 - - + -
312E LEU* 4.6 3.4 - - - +
339E GLU 3.9 0.5 - - - +
340E TYR* 3.5 2.8 - - - +
341E THR* 2.6 53.0 + - + +
343E LEU* 4.2 22.9 - - + -
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Residues in contact with LYS 292 (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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291E ILE* 1.3 75.5 - - - +
293E HIS* 1.3 65.3 + - - +
294E VAL* 3.6 12.2 + - + +
309E LEU* 3.6 1.9 - - - -
310E LYS* 2.9 33.3 + - + +
312E LEU* 3.7 29.1 - - + +
339E GLU 3.6 6.3 - - - +
340E TYR* 4.5 12.8 - - + +
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Residues in contact with HIS 293 (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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291E ILE* 4.6 5.3 + - + -
292E LYS* 1.3 73.5 - - - +
294E VAL* 1.3 63.2 + - - +
307E PRO* 5.7 2.4 - - + +
308E TYR 3.5 5.1 + - - +
309E LEU* 4.2 21.7 - - + +
338E GLY* 5.4 3.3 - - - -
339E GLU* 2.7 72.6 + - + +
341E THR* 2.9 26.8 + - + -
354E SER* 4.2 1.9 + - - -
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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