Contacts of the strand formed by residues 350 - 360 (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 ILE 350 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69B ARG* 3.9 36.6 - - - +
255F ARG* 2.9 21.4 + - - +
343F LEU* 3.6 39.9 - - + -
344F ALA 3.5 5.8 - - - +
345F GLY* 4.3 4.0 - - - -
349F GLY* 1.3 78.7 - - - +
351F SER* 1.3 66.5 + - - +
352F PHE* 4.2 10.2 - - + -
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Residues in contact with SER 351 (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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255F ARG* 4.0 16.6 + - - +
256F PRO* 3.1 30.4 + - - -
257F ILE* 4.8 0.9 - - - -
258F LEU* 4.4 15.1 + - - +
343F LEU* 3.5 1.2 - - - +
344F ALA* 2.7 36.5 + - - +
350F ILE* 1.3 77.5 - - - +
352F PHE* 1.3 69.4 + - - +
353F HIS* 5.2 4.2 + - - -
172G ALA 5.2 4.0 + - - -
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Residues in contact with PHE 352 (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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258F LEU* 3.8 2.7 - - - +
341F THR* 3.7 18.6 - - + -
342F CYS 3.1 16.8 - - - +
343F LEU* 3.7 23.8 - - + -
350F ILE* 4.2 9.2 - - + -
351F SER* 1.3 86.7 + - - +
353F HIS* 1.3 73.7 + - - +
354F SER* 4.7 8.5 - - - -
174G THR* 4.3 5.9 + - - -
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Residues in contact with HIS 353 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258F LEU* 3.4 44.8 + - + +
259F GLN 3.3 10.4 + - - -
262F LEU 3.1 29.2 + - - +
263F PRO* 3.4 11.5 - - + +
341F THR* 4.3 0.7 - - - -
342F CYS 2.9 31.1 + - - -
351F SER* 5.2 3.5 + - - -
352F PHE* 1.3 95.6 - - - +
354F SER* 1.3 61.5 + - - +
172G ALA 5.8 0.4 + - - -
174G THR* 4.0 12.0 + - - -
219G GLU* 3.3 41.0 + - + +
220G SER* 3.5 13.1 + - - -
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Residues in contact with SER 354 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263F PRO* 4.4 0.4 - - - -
293F HIS* 4.4 1.6 + - - -
339F GLU* 3.3 27.5 + - - -
340F TYR 3.2 6.1 - - - -
341F THR* 2.7 24.1 + - - +
352F PHE* 4.7 8.0 - - - -
353F HIS* 1.3 75.5 - - - +
355F ALA* 1.3 56.2 + - - +
208G LYS* 2.6 35.0 + - - +
219G GLU* 4.1 2.9 + - - +
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Residues in contact with ALA 355 (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* 3.3 36.3 - - + +
264F ALA 3.3 21.3 - - - +
265F ASN* 3.5 5.2 - - - -
276F PHE* 3.8 10.8 - - + -
339F GLU* 3.4 7.7 - - - +
340F TYR* 2.7 32.0 + - - +
354F SER* 1.3 72.3 - - - +
356F TRP* 1.3 61.1 + - - +
357F LEU 4.3 0.2 - - - -
208G LYS* 4.4 0.9 - - - +
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Residues in contact with TRP 356 (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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265F ASN* 2.5 24.8 + - - +
266F ALA 2.8 27.6 + - - +
276F PHE* 4.4 2.0 - - - -
337F ALA* 5.6 0.6 - - - +
338F GLY* 3.6 18.9 - - - +
339F GLU* 3.7 35.9 - - + -
355F ALA* 1.3 74.8 - - - +
357F LEU* 1.3 76.7 + - - +
358F THR* 3.4 24.6 - - + +
210G ARG* 3.5 49.2 - - + +
212G GLN* 6.0 0.7 - - + -
213G HIS* 6.1 1.6 - - - -
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Residues in contact with LEU 357 (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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266F ALA* 3.2 35.0 - - + +
267F SER* 4.0 2.2 - - - +
268F THR* 4.4 5.4 - - + -
274F VAL* 3.4 33.9 - - + -
276F PHE* 3.7 10.8 - - + -
329F ILE* 5.1 0.7 - - + -
332F VAL* 4.7 9.6 - - + -
336F ASP* 4.3 8.3 - - + +
337F ALA* 3.4 4.9 - - - +
338F GLY 2.8 33.6 + - - +
340F TYR* 3.7 37.7 - - + +
356F TRP* 1.3 79.0 + - - +
358F THR* 1.3 67.5 + - - +
359F VAL* 4.5 10.5 - - + -
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Residues in contact with THR 358 (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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265F ASN* 6.3 0.4 - - + -
266F ALA 2.7 13.1 + - - +
267F SER* 3.2 22.9 + - - -
268F THR 2.8 23.6 + - - +
337F ALA* 4.8 0.9 - - - -
356F TRP* 3.4 28.3 - - + +
357F LEU* 1.3 73.3 - - - +
359F VAL* 1.3 62.4 + - - +
360F LEU* 4.0 10.9 + - - +
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Residues in contact with VAL 359 (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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268F THR* 2.9 7.0 - - + +
270F VAL* 3.4 40.8 - - + +
332F VAL* 3.9 19.5 - - + -
333F THR 3.6 23.3 - - - +
334F PHE* 3.6 25.7 - - + -
336F ASP 4.8 0.4 - - - -
337F ALA* 4.1 25.2 - - + +
357F LEU* 4.1 7.0 + - + -
358F THR* 1.3 75.6 - - - +
360F LEU* 1.3 66.1 + - - +
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Residues in contact with LEU 360 (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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267F SER* 3.7 22.2 - - - +
268F THR* 2.6 18.9 + - - +
269F VAL* 2.9 11.0 - - + +
270F VAL* 2.8 33.1 + - - +
334F PHE* 4.0 3.8 - - - -
358F THR* 4.4 12.6 - - - +
359F VAL* 1.3 79.9 - - - +
361F PRO* 1.3 60.8 - - - +
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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