Contacts of the strand formed by residues 287 - 293 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66B ALA* 3.6 16.2 - - + -
67B GLU 3.2 12.2 + - - -
68B GLU* 3.2 35.5 - - + -
69B ARG* 3.7 17.6 + - + +
286F PRO* 1.3 73.8 - - - +
288F ILE* 1.3 73.2 + - - +
289F GLN* 4.1 22.8 + - + -
314F ALA* 4.3 13.6 - - + +
315F ALA* 3.1 22.6 + - + -
343F LEU* 3.4 4.9 - - - +
344F ALA* 3.3 2.9 - - - -
345F GLY* 2.8 36.1 + - - +
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Residues in contact with ILE 288 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B PHE* 3.8 33.4 - - + -
278F CYS* 5.4 0.4 - - - -
280F VAL* 4.0 20.4 - - + -
286F PRO* 4.0 5.6 + - + -
287F HIS* 1.3 80.4 - - - +
289F GLN* 1.3 67.1 + - - +
290F TRP* 4.8 2.2 - - - +
315F ALA* 2.8 35.0 + - + +
321F ASP* 4.9 2.2 - - - +
324F ILE* 3.7 39.0 - - + +
325F GLU* 4.7 7.0 - - + -
342F CYS* 3.9 24.9 - - - -
343F LEU 3.3 2.9 - - - +
344F ALA* 4.0 17.3 - - + -
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Residues in contact with GLN 289 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287F HIS* 4.1 19.5 + - + +
288F ILE* 1.3 78.8 - - - +
290F TRP* 1.3 65.5 + - - +
291F ILE* 3.8 16.8 - - + +
311F VAL* 3.7 25.9 - - + +
313F LYS 3.0 14.6 - - - +
314F ALA* 3.9 12.2 - - + +
324F ILE* 5.0 0.2 - - - -
341F THR 3.8 0.2 - - - +
342F CYS* 3.8 1.7 - - - -
343F LEU* 3.0 59.5 + - + +
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Residues in contact with TRP 290 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263F PRO* 3.7 30.1 - - + -
276F PHE* 3.4 42.8 - + + -
278F CYS* 3.5 28.7 - - + -
288F ILE* 4.8 3.3 - - + +
289F GLN* 1.3 77.2 - - - +
291F ILE* 1.3 61.8 + - - +
311F VAL* 3.6 2.6 - - - +
312F LEU* 2.9 28.6 + - + -
313F LYS* 2.7 34.4 + - + +
324F ILE* 2.9 29.6 + - + -
325F GLU* 3.6 5.7 - - - +
326F VAL 4.4 0.2 - - - -
327F LEU* 3.7 40.1 - - + +
340F TYR* 4.9 2.2 - - + -
341F THR 3.4 24.7 - - - -
342F CYS* 3.7 12.1 - - + -
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Residues in contact with ILE 291 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289F GLN* 3.8 31.6 - - + +
290F TRP* 1.3 81.4 - - - +
292F LYS* 1.3 66.1 + - - +
293F HIS* 4.4 4.4 + - + +
309F LEU* 3.6 36.8 - - + -
310F LYS 3.4 11.4 - - - +
311F VAL* 4.7 6.1 - - + +
312F LEU* 3.5 3.1 - - - -
339F GLU 3.9 0.5 - - - +
340F TYR* 3.5 3.8 - - - +
341F THR* 2.7 52.9 + - + +
343F LEU* 4.2 24.5 - - + -
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Residues in contact with LYS 292 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291F ILE* 1.3 74.0 - - - +
293F HIS* 1.3 63.8 + - - +
294F VAL* 3.6 12.6 + - + +
309F LEU* 3.6 2.1 - - - -
310F LYS* 2.9 30.2 + - + +
312F LEU* 3.0 31.8 - - + +
339F GLU 3.6 6.5 - - - +
340F TYR* 4.5 14.1 - - + +
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Residues in contact with HIS 293 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291F ILE* 4.4 5.6 + - + -
292F LYS* 1.3 75.7 - - - +
294F VAL* 1.3 63.0 + - - +
307F PRO* 5.6 6.5 - - + -
308F TYR 3.5 7.0 - - - +
309F LEU* 4.7 16.0 - - + +
338F GLY* 5.4 3.5 - - - -
339F GLU* 2.8 69.4 + - + +
341F THR* 3.0 33.0 - - + -
354F SER* 4.4 1.7 + - - -
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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