Contacts of the strand formed by residues 399 - 405 (chain A) in PDB entry 5TOL
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 ARG 399 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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238A TYR* 3.5 45.9 + - + -
239A THR 3.3 14.8 - - - +
240A PRO* 4.3 1.8 - - + -
241A ILE* 3.6 4.1 - - - +
338A GLU* 2.8 43.5 + - + -
394A ASP* 2.8 57.2 + - + +
397A ARG* 3.3 50.7 - - - +
398A LYS* 1.3 79.1 - - - +
400A ILE* 1.3 66.5 + - - +
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Residues in contact with ILE 400 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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237A TRP 3.7 0.7 - - - +
238A TYR* 3.3 3.7 - - - -
239A THR* 2.7 43.0 + - + +
241A ILE* 3.7 23.8 - - + -
247A TYR* 3.8 26.0 - - + +
249A VAL* 3.8 20.2 - - + -
275A VAL* 4.2 7.6 - - + -
391A VAL* 3.8 18.2 - - + -
392A VAL 3.1 10.5 - - - +
393A PHE* 4.3 13.7 - - + -
399A ARG* 1.3 79.8 - - - +
401A GLY* 1.3 61.0 + - - +
402A PHE* 3.5 26.1 - - + -
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Residues in contact with GLY 401 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236A LEU* 4.1 7.6 - - - -
237A TRP 3.0 9.4 - - - -
238A TYR* 3.5 21.8 - - - -
390A TYR 3.4 0.3 - - - +
391A VAL* 3.2 9.4 - - - +
392A VAL* 2.7 42.8 + - - -
400A ILE* 1.3 73.6 - - - +
402A PHE* 1.3 63.2 + - - -
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Residues in contact with PHE 402 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236A LEU* 3.4 3.9 - - - +
237A TRP 2.7 32.5 + - - +
239A THR* 4.1 7.6 - - + -
249A VAL* 5.7 0.4 - - + -
275A VAL* 4.3 12.3 - - + -
335A LEU* 3.8 22.4 - - + -
344A PHE* 4.2 8.3 - + + -
346A ILE* 4.1 25.1 - - + -
381A MET* 3.6 32.3 - - + -
385A ILE* 4.4 6.5 - - + -
389A PHE* 4.1 23.3 - + + -
390A TYR 3.5 2.5 - - - -
391A VAL* 4.1 18.2 - - + -
400A ILE* 3.5 31.4 - - + -
401A GLY* 1.3 75.9 - - - -
403A ALA* 1.3 60.6 + - - +
418A VAL* 3.6 12.1 - - + +
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Residues in contact with ALA 403 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232A TYR* 3.5 32.8 - - + -
233A THR 4.1 0.7 - - - +
235A SER 3.5 14.1 - - - +
236A LEU* 3.4 19.7 - - + -
389A PHE* 3.3 5.0 - - - -
390A TYR 2.8 33.1 + - - +
402A PHE* 1.3 74.5 - - - +
404A VAL* 1.3 60.5 + - - +
405A SER 3.2 0.3 + - - -
418A VAL* 3.8 7.9 - - - -
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Residues in contact with VAL 404 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232A TYR* 3.2 5.5 - - - -
233A THR* 2.9 54.1 + - - +
235A SER 4.9 0.2 + - - -
388A GLY 4.2 4.7 - - - +
389A PHE* 4.4 2.5 - - + -
403A ALA* 1.3 69.9 - - - +
405A SER* 1.3 65.3 + - - +
408A HIS* 3.7 26.9 - - + -
415A THR* 4.5 4.3 - - + -
416A ALA 3.5 22.2 - - - +
417A ALA* 3.6 3.1 - - - -
418A VAL* 3.5 29.2 - - + +
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Residues in contact with SER 405 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201A GLN* 3.1 24.5 + - - +
202A LEU 5.1 0.7 + - - -
231A LEU 3.7 5.6 - - - -
233A THR* 5.7 0.2 - - - +
387A GLU 4.4 2.2 + - - -
388A GLY 3.2 23.1 + - - -
389A PHE* 3.6 20.0 - - - -
390A TYR 3.9 3.8 - - - +
403A ALA 3.2 2.0 + - - -
404A VAL* 1.3 74.3 - - - +
406A ALA* 1.3 56.8 + - - +
407A CYS* 3.1 19.6 + - - -
408A HIS* 2.9 31.6 + - - -
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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