Contacts of the strand formed by residues 343 - 350 (chain B) in PDB entry 3L5J
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 ASP 343 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341B ILE* 3.7 1.6 - - - +
342B LEU* 1.3 80.0 - - - +
344B TYR* 1.3 77.7 + - - +
359B THR* 4.2 18.6 - - + +
360B VAL 4.0 6.1 - - - +
361B ASN* 3.5 18.2 - - - +
380B VAL* 3.8 2.1 - - - +
381B ARG* 2.8 72.4 + - - +
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Residues in contact with TYR 344 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308B PRO* 4.7 6.1 - - + -
329B TRP* 3.6 28.7 - + + +
330B LYS 5.2 1.6 - - - -
331B THR* 4.2 19.5 + - - +
332B LEU* 6.0 0.4 - - + -
341B ILE* 3.5 35.3 - - + +
343B ASP* 1.3 79.3 - - - +
345B GLU* 1.3 63.2 + - - +
346B VAL 4.4 0.2 - - - -
359B THR* 3.5 10.0 - - - +
360B VAL* 3.1 35.6 + - + +
361B ASN 5.5 0.4 - - - -
362B ALA 3.1 31.2 - - - -
363B THR* 4.3 3.4 - - + +
378B LEU* 3.8 16.6 - - + -
379B THR 3.2 9.4 - - - +
380B VAL* 3.4 34.3 - - + -
381B ARG* 5.5 0.4 - - - -
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Residues in contact with GLU 345 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344B TYR* 1.3 75.5 - - - +
346B VAL* 1.3 69.9 + - - +
347B THR* 4.2 8.6 + - + +
357B ASN* 4.1 24.3 + - - +
358B TYR 3.3 18.6 - - - +
359B THR* 4.4 10.4 + - - +
377B THR* 3.9 1.9 + - - +
378B LEU* 3.4 4.9 + - - -
379B THR* 3.0 45.5 + - - +
386B LYS* 4.6 13.0 - - + +
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Residues in contact with VAL 346 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310B PHE* 4.8 2.2 - - + -
327B LEU* 3.8 24.5 - - + -
329B TRP* 4.0 17.7 - - + -
345B GLU* 1.3 74.6 - - - +
347B THR* 1.3 74.0 + - - +
348B LEU* 4.1 15.3 - - + -
357B ASN 3.7 0.2 - - - -
358B TYR* 2.8 38.1 + - + +
360B VAL* 4.6 3.3 - - + +
365B LEU* 3.9 26.5 - - + -
377B THR 3.3 15.7 - - - +
378B LEU* 3.8 16.6 - - + -
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Residues in contact with THR 347 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345B GLU* 4.7 13.7 - - + +
346B VAL* 1.3 81.2 - - - +
348B LEU* 1.3 63.6 + - - +
349B THR* 4.3 2.8 + - - -
355B LEU* 4.0 20.2 - - + +
356B GLN 3.2 9.0 - - - -
357B ASN* 3.4 19.7 - - - +
375B LEU 3.1 13.2 - - - +
377B THR* 2.6 43.4 + - - +
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Residues in contact with LEU 348 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327B LEU* 3.9 15.5 - - + -
346B VAL* 4.1 9.4 - - + -
347B THR* 1.3 68.8 - - - +
349B THR* 1.3 65.3 + - - +
350B ARG 4.3 0.7 - - - -
354B HIS 4.5 0.3 - - - +
355B LEU* 3.5 0.3 - - - -
356B GLN* 2.9 37.3 + - + +
358B TYR* 4.1 26.6 - - + +
365B LEU* 5.7 0.2 - - + -
367B VAL* 3.6 35.9 - - + -
369B LEU* 4.0 22.0 - - + -
374B TYR* 4.6 10.8 - - + -
375B LEU 3.4 2.0 - - - +
376B ALA* 3.4 29.8 - - + -
394B ILE* 4.9 4.3 - - + -
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Residues in contact with THR 349 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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347B THR* 4.3 3.8 + - - -
348B LEU* 1.3 73.1 + - - +
350B ARG* 1.3 65.9 + - - +
351B TRP 3.7 0.2 + - - -
353B SER 3.3 25.6 - - - +
354B HIS 4.1 8.7 - - - +
355B LEU* 3.1 24.6 - - + +
373B ARG 3.9 0.2 - - - +
374B TYR* 3.3 7.7 - - - -
375B LEU* 2.9 50.9 + - + +
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Residues in contact with ARG 350 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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348B LEU 4.3 0.2 - - - -
349B THR* 1.3 78.9 - - - +
351B TRP* 1.3 80.0 + - - +
352B LYS 3.2 0.9 + - - -
353B SER* 3.0 32.7 + - - +
354B HIS 4.4 4.8 + - - +
370B THR* 3.4 26.8 + - - +
372B ASP* 3.4 16.8 + - + -
374B TYR* 3.5 40.9 - - + +
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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