Contacts of the strand formed by residues 338 - 345 (chain H) 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 GLY 338 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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293H HIS 5.4 3.8 - - - -
337H ALA* 1.3 76.4 - - - +
339H GLU* 1.3 59.1 + - - -
340H TYR* 3.5 10.0 - - - -
356H TRP* 3.5 14.3 - - - -
357H LEU 2.8 36.4 + - - -
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Residues in contact with GLU 339 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292H LYS* 3.6 1.6 - - - +
293H HIS* 2.9 80.8 + - + +
338H GLY* 1.3 71.0 - - - -
340H TYR* 1.3 63.5 + - - +
354H SER* 3.2 25.7 + - - -
355H ALA 3.4 12.1 - - - +
356H TRP* 3.6 43.9 - - + +
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Residues in contact with TYR 340 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263H PRO* 4.5 2.0 - - + +
276H PHE* 3.6 30.7 - + + -
290H TRP* 5.2 6.3 - + + -
291H ILE 3.5 4.7 - - - +
292H LYS* 4.5 10.5 - - + +
312H LEU* 3.7 30.1 - - + -
327H LEU* 4.0 9.9 - - + -
329H ILE* 3.2 31.4 - - + +
336H ASP* 2.6 41.8 + - - +
337H ALA 4.6 0.2 - - - -
338H GLY 3.5 14.4 - - - -
339H GLU* 1.3 72.4 - - - +
341H THR* 1.3 62.4 + - - +
353H HIS 4.1 0.2 - - - +
354H SER* 3.2 2.6 - - - -
355H ALA* 2.7 39.8 + - + +
357H LEU* 3.7 17.6 - - + +
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Residues in contact with THR 341 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263H PRO* 5.2 0.4 - - - -
289H GLN 3.8 0.5 - - - +
290H TRP* 3.4 9.6 - - - -
291H ILE* 2.7 51.8 + - + +
293H HIS* 3.0 23.5 + - - +
340H TYR* 1.3 75.0 - - - +
342H CYS* 1.3 64.6 + - - +
343H LEU* 3.8 4.6 + - + +
352H PHE* 3.7 31.0 - - + -
353H HIS 3.5 11.2 - - - +
354H SER* 2.8 23.4 + - - +
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Residues in contact with CYS 342 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258H LEU* 3.6 7.0 - - + +
263H PRO* 4.1 6.0 - - + +
278H CYS* 2.5 50.0 - - + -
280H VAL* 4.7 0.9 - - - -
288H ILE* 3.6 22.4 - - - -
289H GLN 3.8 3.6 - - - -
290H TRP* 3.9 19.4 - - + -
341H THR* 1.3 72.9 - - - +
343H LEU* 1.3 61.3 + - - +
352H PHE* 3.1 4.3 - - - -
353H HIS 2.9 33.8 + - - +
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Residues in contact with LEU 343 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287H HIS 3.4 2.3 - - - +
288H ILE* 3.3 5.6 - - - +
289H GLN* 3.0 64.1 + - + +
291H ILE* 3.8 21.5 - - + -
341H THR* 3.8 3.3 + - + -
342H CYS* 1.3 73.9 - - - +
344H ALA* 1.3 62.3 + - - +
345H GLY* 5.9 0.2 - - - -
350H ILE* 3.2 39.3 - - + -
351H SER 3.5 7.2 - - - +
352H PHE* 3.6 19.1 - - + -
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Residues in contact with ALA 344 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256H PRO* 3.7 19.4 - - + +
258H LEU* 3.6 28.9 - - + -
280H VAL* 4.0 14.6 - - + -
286H PRO* 5.0 0.9 - - + -
287H HIS 3.3 5.8 - - - +
288H ILE* 4.4 7.0 - - + -
342H CYS 4.1 0.8 + - - -
343H LEU* 1.3 77.0 - - - +
345H GLY* 1.3 58.5 + - - +
350H ILE* 3.5 1.4 - - - +
351H SER* 2.8 38.6 + - - +
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Residues in contact with GLY 345 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69D ARG* 3.7 21.3 - - - +
256H PRO* 3.7 4.9 - - - +
285H GLN 4.2 0.3 - - - +
286H PRO* 3.5 1.6 - - - +
287H HIS* 2.8 42.5 + - - +
343H LEU* 5.3 0.4 - - - +
344H ALA* 1.3 75.8 - - - +
346H ASN* 1.3 60.7 + - - -
349H GLY 3.3 9.2 - - - -
350H ILE* 4.1 4.7 - - - -
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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