Contacts of the strand formed by residues 374 - 381 (chain A) 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 TYR 374 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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323A ARG* 4.4 3.6 - - - -
348A LEU* 4.2 14.1 - - + -
349A THR 3.4 6.1 - - - -
350A ARG* 3.3 40.4 - - + -
356A GLN* 4.2 12.2 + - - -
369A LEU* 3.5 39.8 - - + +
370A THR* 2.9 58.4 + - - +
372A ASP 3.5 8.1 - - - -
373A ARG* 1.3 96.6 - - - +
375A LEU* 1.3 62.7 + - - +
376A ALA 4.0 0.3 + - - -
393A THR* 3.6 3.1 - - - +
394A ILE* 2.8 55.9 + - + +
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Residues in contact with LEU 375 (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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347A THR* 3.5 2.8 + - - +
348A LEU* 3.5 4.5 - - - -
349A THR* 3.1 41.2 + - - +
373A ARG* 4.0 22.7 - - - +
374A TYR* 1.3 73.0 - - - +
376A ALA* 1.3 64.8 + - - +
377A THR* 4.4 11.6 - - + +
391A VAL* 3.4 28.7 - - + -
392A LEU 3.2 18.2 - - - +
393A THR* 4.8 4.3 - - - +
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Residues in contact with ALA 376 (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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310A PHE* 3.8 22.0 - - + -
327A LEU* 4.5 2.9 - - + -
347A THR 3.3 4.3 - - - -
348A LEU* 3.4 22.7 - - + -
374A TYR 4.0 0.8 + - - -
375A LEU* 1.3 72.8 - - - +
377A THR* 1.3 67.3 + - - +
391A VAL* 3.3 6.1 - - - -
392A LEU* 2.9 43.0 + - + +
394A ILE* 4.6 9.9 - - + -
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Residues in contact with THR 377 (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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310A PHE* 4.2 2.2 - - - -
345A GLU 4.1 1.0 + - - -
346A VAL* 3.2 10.2 - - - +
347A THR* 2.7 57.0 + - - +
375A LEU* 4.4 15.0 - - + +
376A ALA* 1.3 81.2 - - - +
378A LEU* 1.3 63.2 + - - +
379A THR* 5.7 1.4 - - - +
389A ALA* 4.2 15.7 - - + -
390A ALA 3.4 5.4 - - - -
391A VAL* 4.1 15.0 - - + -
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Residues in contact with LEU 378 (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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308A PRO* 3.9 24.9 - - + +
310A PHE* 3.5 34.3 - - + -
329A TRP* 3.4 39.3 - - + -
344A TYR* 3.7 33.2 - - + -
345A GLU 3.3 7.6 - - - +
346A VAL* 4.1 12.6 - - + -
377A THR* 1.3 77.7 - - - +
379A THR* 1.3 70.8 + - - +
388A ASP 3.8 2.1 - - - +
389A ALA* 3.3 2.8 - - - -
390A ALA* 2.9 34.2 + - + +
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Residues in contact with THR 379 (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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344A TYR* 3.3 2.7 - - - -
345A GLU* 2.9 48.3 + - - +
377A THR* 5.6 1.6 - - - +
378A LEU* 1.3 81.3 - - - +
380A VAL* 1.3 62.8 + - - +
381A ARG* 3.8 2.3 + - - +
386A LYS* 4.2 19.2 - - + +
387A SER* 3.4 22.9 - - - +
389A ALA* 3.4 29.6 - - + +
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Residues in contact with VAL 380 (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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304A PRO* 3.6 8.6 - - + +
308A PRO* 3.7 14.7 - - + +
332A LEU* 3.7 25.1 - - + -
337A ALA* 5.9 0.2 - - + -
341A ILE* 3.5 34.3 - - + -
343A ASP 3.7 3.4 - - - -
344A TYR* 3.4 32.8 - - + -
379A THR* 1.3 72.0 - - - +
381A ARG* 1.3 63.9 + - - +
386A LYS* 3.7 0.5 - - - -
387A SER* 2.9 47.3 + - - +
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Residues in contact with ARG 381 (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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341A ILE* 3.9 2.4 - - - -
342A LEU* 3.0 60.9 + - - +
343A ASP* 2.9 50.9 + - - +
345A GLU* 6.5 0.7 - - + -
379A THR 3.8 2.7 + - - +
380A VAL* 1.3 78.0 - - - +
382A ASN* 1.3 70.5 + - - +
383A LEU* 5.0 3.8 + - - +
385A GLY* 3.5 11.0 - - - +
386A LYS* 3.4 39.4 - - + +
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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