Contacts of the strand formed by residues 334 - 339 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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287F ALA* 3.3 2.8 - - - -
288F VAL* 2.9 45.8 + - + +
290F PHE* 3.5 34.5 - - + -
332F ASP 4.0 5.2 - - - +
333F ALA* 1.3 69.7 - - - +
335F ARG* 1.3 67.7 + - - +
353F TYR* 5.8 2.7 - - - +
363F MET* 3.8 15.3 - - + +
366F ALA* 4.4 30.1 - - + +
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Residues in contact with ARG 335 (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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285F HIS* 3.8 22.7 + - - +
286F ILE 3.6 4.0 - - - -
287F ALA* 4.0 11.7 - - + +
289F ARG* 3.5 26.2 - - - +
296F PHE* 5.7 5.5 - - - -
322F ALA* 5.4 6.1 + - - +
325F LEU* 5.4 0.6 - - - +
326F ARG* 2.7 64.2 - - - +
329F TRP 5.1 1.8 + - - -
331F ASP* 4.6 5.1 + - - +
333F ALA* 3.2 18.0 + - - +
334F ILE* 1.3 78.5 - - - +
336F GLY* 1.3 59.5 + - - +
348F ALA 3.9 19.5 - - - -
349F LEU* 3.9 8.5 - - - +
350F GLY* 4.1 6.4 - - - +
351F GLU* 4.0 12.1 + - - +
353F TYR* 4.9 0.7 + - - -
363F MET* 3.0 16.1 - - - +
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Residues in contact with GLY 336 (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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285F HIS* 3.3 5.3 + - - -
286F ILE 2.9 31.4 + - - +
335F ARG* 1.3 78.9 - - - +
337F TYR* 1.3 59.8 + - - -
349F LEU 3.2 10.7 + - - -
351F GLU 3.3 12.8 - - - -
353F TYR* 4.4 0.7 - - - -
359F LEU* 4.0 7.1 - - - +
363F MET* 3.2 11.9 - - - -
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Residues in contact with TYR 337 (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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283F LEU* 5.2 0.7 - - + -
284F VAL 3.0 14.1 - - - +
285F HIS* 4.2 3.6 - - - -
336F GLY* 1.3 73.8 - - - +
338F ALA* 1.3 60.1 + - - +
339F THR* 3.2 27.8 - - - +
344F THR 5.6 0.7 - - - -
345F ASP* 3.1 37.2 + - + +
346F LEU* 4.3 10.9 - - + -
347F ALA* 5.6 0.6 - - - -
349F LEU* 3.3 44.4 - - + -
350F GLY 3.4 19.7 - - - -
351F GLU 3.4 2.6 + - - -
352F ARG* 3.2 43.0 - - + +
353F TYR* 2.9 26.5 + - - +
359F LEU* 4.1 7.2 - - - +
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Residues in contact with ALA 338 (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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328E VAL* 5.2 1.3 - - + -
283F LEU* 3.7 0.3 - - - -
284F VAL 2.9 30.1 + - - -
337F TYR* 1.3 74.3 - - - +
339F THR* 1.3 61.9 + - - +
352F ARG* 4.8 0.9 - - - -
353F TYR 3.3 21.5 - - - +
354F ASP 4.8 1.8 - - - +
355F SER* 4.3 10.3 - - - +
356F TYR* 3.5 33.8 - - + -
359F LEU* 4.1 9.6 - - + +
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Residues in contact with THR 339 (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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324E ARG* 3.2 26.6 + - - +
328E VAL* 4.0 6.2 - - - +
282F ASP 3.4 12.6 - - - +
283F LEU* 3.3 18.8 - - + +
337F TYR* 3.2 24.7 - - - -
338F ALA* 1.3 76.9 - - - +
340F VAL* 1.3 65.5 + - - +
341F GLU* 3.1 46.9 - - + +
344F THR 5.8 1.6 - - - +
352F ARG* 3.3 11.5 + - - +
356F TYR* 4.9 1.1 - - - -
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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