Contacts of the strand formed by residues 334 - 339 (chain H) in PDB entry 5U07
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 334 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287H ALA* 3.4 2.1 - - - -
288H VAL* 2.9 46.3 + - + +
290H PHE* 3.6 33.7 - - + -
332H ASP 4.1 4.7 - - - +
333H ALA* 1.3 69.4 - - - +
335H ARG* 1.3 69.8 + - - +
353H TYR* 5.8 2.5 - - - +
363H MET* 3.9 13.9 - - + +
366H ALA* 4.6 28.5 - - + +
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Residues in contact with ARG 335 (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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285H HIS* 3.9 20.4 + - + +
286H ILE 3.7 4.5 - - - -
287H ALA* 4.3 7.2 - - + +
289H ARG* 5.2 5.4 - - - +
296H PHE* 5.9 3.6 - - - -
322H ALA* 5.3 6.8 + - - +
325H LEU 5.4 0.2 - - - -
326H ARG* 3.6 44.2 - - - +
331H ASP* 3.0 42.1 + - - -
333H ALA* 3.2 22.0 + - + +
334H ILE* 1.3 77.7 - - - +
336H GLY* 1.3 60.7 + - - +
348H ALA 3.7 20.8 + - - -
349H LEU* 3.9 11.9 - - - +
350H GLY* 4.1 6.0 - - - +
351H GLU* 4.0 11.8 + - - +
353H TYR* 4.9 0.3 + - - -
363H MET* 3.0 14.2 - - - +
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Residues in contact with GLY 336 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285H HIS* 3.4 4.8 + - - -
286H ILE 2.9 31.2 + - - +
335H ARG* 1.3 79.9 - - - +
337H TYR* 1.3 61.9 + - - -
349H LEU 3.2 10.5 + - - -
351H GLU 3.3 11.4 - - - -
359H LEU* 3.9 7.0 - - - +
363H MET* 3.2 13.5 - - - -
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Residues in contact with TYR 337 (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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283H LEU* 5.3 0.4 - - + -
284H VAL 3.1 13.5 - - - +
285H HIS* 4.3 2.2 - - - -
336H GLY* 1.3 75.0 - - - +
338H ALA* 1.3 61.0 + - - +
339H THR* 3.2 27.1 - - - +
344H THR 5.8 0.2 - - - -
345H ASP* 2.3 34.9 + - - -
346H LEU* 3.6 24.9 - - + -
349H LEU* 3.2 35.7 - - + -
350H GLY 3.3 20.6 - - - -
351H GLU 3.4 2.4 + - - -
352H ARG* 3.3 46.4 + - + +
353H TYR* 3.0 26.0 + - - +
359H LEU* 4.0 6.8 - - - +
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Residues in contact with ALA 338 (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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328G VAL* 5.3 1.3 - - + -
283H LEU* 3.7 0.3 - - - -
284H VAL 2.9 31.1 + - - -
337H TYR* 1.3 75.6 - - - +
339H THR* 1.3 62.5 + - - +
352H ARG* 5.0 0.4 - - - -
353H TYR 3.5 19.5 - - - +
354H ASP 5.0 1.6 - - - +
355H SER* 4.3 10.1 - - - +
356H TYR* 3.5 33.2 - - + -
359H LEU* 3.9 11.6 - - + +
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Residues in contact with THR 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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324G ARG* 2.9 26.4 + - - +
328G VAL* 3.8 6.2 - - - +
282H ASP 3.5 11.9 - - - +
283H LEU* 3.3 19.7 - - + +
337H TYR* 3.2 25.5 - - - -
338H ALA* 1.3 76.7 - - - +
340H VAL* 1.3 65.5 - - - +
341H GLU* 3.1 47.6 - - + +
346H LEU* 4.0 3.8 - - + +
352H ARG* 3.7 8.1 + - - +
353H TYR 5.0 0.4 + - - -
356H TYR* 5.1 0.7 - - - -
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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