Contacts of the strand formed by residues 342 - 348 (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 GLN 342 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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237A TRP* 3.9 24.7 - - - -
238A TYR 5.5 0.2 + - - -
337A GLY* 2.7 40.1 + - - -
338A GLU* 3.1 24.7 + - - +
339A VAL* 3.0 29.4 + - + +
340A THR 3.1 4.0 + - - +
341A ASN* 1.3 80.7 - - - +
343A SER* 1.3 77.8 + - - +
344A PHE* 4.3 1.6 - - - +
421A PRO* 3.7 22.4 - - + -
422A PHE 3.3 4.9 - - - +
423A VAL* 6.1 0.9 - - + -
427A MET* 3.4 9.1 - - - +
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Residues in contact with SER 343 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252A VAL* 3.9 14.8 - - - -
334A TYR* 3.8 8.5 - - - -
335A LEU 3.2 17.5 - - - -
337A GLY 3.8 1.3 - - - +
341A ASN 4.3 0.4 + - - -
342A GLN* 1.3 86.8 + - - +
344A PHE* 1.3 64.7 + - - +
421A PRO* 3.6 1.4 - - - +
422A PHE* 2.9 40.1 + - - +
424A THR* 2.9 25.0 + - - -
427A MET* 3.9 4.5 - - - -
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Residues in contact with PHE 344 (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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237A TRP* 3.5 52.5 - + + -
238A TYR 3.2 31.4 - - - -
239A THR* 3.8 4.5 - - - -
333A LEU 3.9 0.2 - - - +
334A TYR* 3.1 7.4 - - - +
335A LEU* 2.8 63.5 + - + -
336A MET 3.8 10.8 - - - -
337A GLY* 4.3 5.6 - - - -
342A GLN* 4.3 3.8 - - - -
343A SER* 1.3 77.3 - - - +
345A ARG* 1.3 64.8 + - - +
346A ILE* 4.0 11.9 - - + -
402A PHE* 4.2 6.1 - + + -
418A VAL* 3.9 12.1 - - + -
419A GLU 3.4 13.5 - - - +
420A GLY* 4.3 0.7 - - - -
422A PHE* 4.2 4.9 - - - -
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Residues in contact with ARG 345 (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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255A GLU* 4.1 5.1 + - - -
332A SER* 3.7 21.0 + - - -
333A LEU 3.2 10.3 - - - +
334A TYR* 2.7 54.0 + - + -
344A PHE* 1.3 75.1 - - - +
346A ILE* 1.3 63.3 + - - +
347A THR* 3.9 6.2 + - - +
417A ALA 3.7 0.9 - - - +
418A VAL* 3.3 5.9 - - - +
419A GLU* 2.7 77.0 + - + +
422A PHE* 3.3 28.8 - - + -
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Residues in contact with ILE 346 (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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331A ILE 3.7 0.5 - - - +
332A SER* 3.0 4.0 - - - -
333A LEU* 2.8 56.1 + - + +
335A LEU* 4.3 8.1 - - + -
344A PHE* 4.0 21.8 - - + -
345A ARG* 1.3 78.3 - - - +
347A THR* 1.3 60.3 - - - +
348A ILE* 5.6 0.7 - - + -
381A MET* 3.7 30.3 - - + -
385A ILE* 4.1 7.9 - - + -
389A PHE* 3.6 26.9 - - + -
402A PHE* 4.1 23.6 - - + -
417A ALA 3.4 2.9 - - - -
418A VAL* 4.1 11.0 - - + -
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Residues in contact with THR 347 (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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330A VAL* 3.6 34.3 - - + -
331A ILE 3.3 3.8 - - - +
332A SER* 2.6 23.8 + - - +
345A ARG* 3.9 14.4 + - - +
346A ILE* 1.3 76.2 - - - +
348A ILE* 1.3 64.9 - - - +
389A PHE* 3.6 3.4 - - - -
415A THR 5.0 5.6 - - - +
416A ALA* 3.3 10.6 - - - +
417A ALA* 2.9 38.6 + - + -
419A GLU* 4.5 3.6 + - - -
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Residues in contact with ILE 348 (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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282A LEU* 4.8 7.0 - - + -
330A VAL* 3.5 6.2 - - - +
331A ILE* 2.8 53.0 + - + +
346A ILE* 5.6 1.1 - - + -
347A THR* 1.3 74.1 - - - +
349A LEU* 1.3 65.1 + - - +
352A GLN* 3.8 15.5 - - + +
353A TYR* 4.1 17.8 - - + -
384A VAL* 3.8 31.4 - - + +
385A ILE* 3.9 31.4 - - + +
388A GLY* 5.1 1.1 - - - -
389A PHE* 3.5 30.7 - - + -
416A ALA* 4.9 0.2 - - - -
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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