Contacts of the helix formed by residues 340 - 357 (chain A) in PDB entry 1LBI
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 340 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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326A ARG 3.0 27.9 + - - -
327A LYS* 3.6 19.3 - - - +
329A THR 3.4 15.1 + - - -
330A LEU* 3.0 42.0 - - - +
338A SER* 4.3 8.3 - - - -
339A PRO* 1.3 76.1 - - + +
341A ALA* 1.3 65.1 + - - +
342A LEU 3.2 0.9 + - - -
343A ALA* 3.2 13.6 + - - +
344A ASP* 3.4 36.9 + - - +
354C SER* 5.0 5.2 - - - +
357C GLU* 4.0 11.5 + - - +
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Residues in contact with ALA 341 (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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266A ALA* 6.1 2.7 - - + -
330A LEU* 3.8 26.9 - - + -
337A ALA* 3.4 29.4 - - + +
338A SER* 3.4 2.8 + - - -
340A ARG* 1.3 80.3 - - - +
342A LEU* 1.3 58.1 + - - +
344A ASP* 3.7 9.9 + - - +
345A SER* 3.3 24.6 + - - -
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Residues in contact with LEU 342 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336A THR* 5.1 0.2 - - + -
337A ALA* 3.6 19.7 - - + -
338A SER 2.8 27.6 + - - +
341A ALA* 1.3 69.6 - - - +
343A ALA* 1.3 63.0 - - - +
345A SER* 2.5 22.9 + - - -
346A LEU* 3.2 17.0 - - - +
349B LEU* 3.9 21.8 - - + +
352B GLN* 3.7 42.6 - - + +
353B VAL* 4.4 9.0 - - + +
356B LEU* 3.7 35.0 - - + -
353C VAL* 4.2 14.1 - - + -
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Residues in contact with ALA 343 (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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339A PRO 3.2 20.2 + - - +
340A ARG 3.2 4.9 + - - +
342A LEU* 1.3 77.3 - - - +
344A ASP* 1.3 64.4 + - - +
346A LEU 3.4 0.9 + - - -
347A MET* 3.1 31.3 + - + +
350C ALA* 3.2 41.0 - - + +
353C VAL* 4.8 1.1 - - - -
354C SER* 3.5 15.0 - - - +
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Residues in contact with ASP 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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327A LYS* 3.9 30.6 + - - +
340A ARG* 3.4 34.4 + - - +
341A ALA* 3.9 8.1 - - - +
342A LEU 3.3 0.4 - - - -
343A ALA* 1.3 78.0 - - - +
345A SER* 1.3 65.0 + - - +
347A MET* 3.5 19.1 + - - +
348A GLN* 3.4 22.9 + - - +
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Residues in contact with SER 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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341A ALA 3.3 10.6 + - - -
342A LEU* 2.5 34.3 + - - -
344A ASP* 1.3 77.3 - - - +
346A LEU* 1.3 61.4 + - - +
348A GLN* 3.7 5.5 + - - +
349A LEU* 3.4 19.6 + - - +
349B LEU* 3.2 31.3 - - - +
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Residues in contact with LEU 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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342A LEU 3.2 15.9 - - - +
343A ALA 3.4 1.5 + - - +
345A SER* 1.3 76.2 + - - +
347A MET* 1.3 52.5 + - - +
348A GLN 3.1 1.8 - - - -
349A LEU* 2.6 29.5 + - - +
350A ALA* 2.7 18.5 + - - +
346B LEU* 4.3 13.5 - - + -
349B LEU* 3.3 34.8 - - + -
353B VAL* 5.2 1.3 - - + -
346C LEU* 4.0 9.0 - - + +
350C ALA* 3.4 40.6 - - + +
353C VAL* 3.9 16.2 - - + -
346D LEU* 3.9 28.3 - - + -
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Residues in contact with MET 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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343A ALA* 3.1 24.7 + - + +
344A ASP* 3.5 20.8 + - - +
346A LEU* 1.3 78.4 - - - +
348A GLN* 1.3 55.2 + - - +
349A LEU 3.3 0.2 - - - -
350A ALA* 3.8 1.2 - - - +
351A ARG* 2.8 41.8 + - + +
347C MET* 3.6 27.7 - - + +
350C ALA* 3.6 16.6 - - + -
351C ARG* 3.3 50.9 - - + +
354C SER* 6.1 0.7 - - - -
260D SER* 4.0 9.6 - - - +
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Residues in contact with GLN 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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344A ASP 3.4 13.9 + - - +
345A SER* 4.0 5.8 - - - +
346A LEU 2.8 2.2 + - - -
347A MET* 1.3 74.9 - - - +
349A LEU* 1.3 60.4 + - - +
351A ARG* 3.8 6.6 - - - +
352A GLN* 2.8 52.3 + - - +
258B THR* 2.5 36.0 + - - +
259B GLU* 3.8 14.1 - - - +
261B GLY* 3.0 22.9 - - - +
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Residues in contact with LEU 349 (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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345A SER 3.4 12.8 + - - +
346A LEU* 2.6 15.0 + - - +
348A GLN* 1.3 77.1 - - - +
350A ALA* 1.3 57.2 + - - +
352A GLN* 3.0 22.5 + - - +
353A VAL* 2.8 35.7 + - + +
342B LEU* 3.3 50.4 - - + +
345B SER* 4.0 22.0 - - - +
346B LEU* 3.7 25.6 - - + +
349B LEU* 4.8 4.7 - - + -
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Residues in contact with ALA 350 (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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346A LEU 2.7 13.6 + - - +
347A MET 4.0 0.2 - - - +
349A LEU* 1.3 71.8 - - - +
351A ARG* 1.3 54.8 + - - +
353A VAL* 2.7 32.1 + - - +
354A SER 2.9 10.0 + - - -
343C ALA* 3.5 19.2 - - - +
346C LEU* 3.6 21.4 - - + +
347C MET* 3.3 34.5 - - + -
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Residues in contact with ARG 351 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347A MET* 2.8 36.0 + - - +
348A GLN* 3.9 6.3 - - - +
350A ALA* 1.3 76.9 - - - +
352A GLN* 1.3 59.3 + - - +
354A SER* 3.4 18.8 - - - -
355A ARG* 3.3 17.6 + - - +
230B MET* 4.5 19.0 - - - +
234B ASN* 4.7 7.5 + - - +
259B GLU 4.0 19.6 + - - -
260B SER* 3.6 18.6 - - - +
347C MET* 3.5 27.6 - - + +
351C ARG* 5.9 2.2 - - - +
230D MET* 4.7 18.4 - - - +
234D ASN* 5.0 13.3 + - - +
259D GLU 4.1 15.7 + - - -
260D SER* 4.8 8.1 + - - +
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Residues in contact with GLN 352 (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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348A GLN* 2.8 48.2 + - - +
349A LEU* 3.0 16.6 + - - +
351A ARG* 1.3 76.7 - - - +
353A VAL* 1.3 52.5 - - - +
355A ARG* 3.2 14.6 + - - +
356A LEU* 2.7 37.3 + - - +
261B GLY* 3.6 26.0 - - - +
337B ALA 5.1 3.2 - - - +
338B SER* 4.4 8.5 + - - -
342B LEU* 3.3 28.6 - - + +
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Residues in contact with VAL 353 (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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349A LEU* 2.8 25.0 + - + +
350A ALA* 2.7 20.2 + - - +
352A GLN* 1.3 68.0 - - - +
354A SER* 1.3 63.3 + - - +
356A LEU* 3.5 16.7 - - + +
357A GLU* 4.0 7.1 - - - +
342B LEU* 3.9 13.5 - - + -
339C PRO* 3.3 27.2 - - - +
342C LEU* 4.0 12.3 - - + -
343C ALA* 3.8 15.0 - - - +
346C LEU* 4.8 3.6 - - + -
353D VAL* 3.8 32.8 - - + -
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Residues in contact with SER 354 (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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350A ALA 2.9 7.5 + - - -
351A ARG* 3.4 13.7 - - - -
353A VAL* 1.3 80.5 - - - +
355A ARG* 1.3 63.4 + - - +
357A GLU 5.2 1.2 - - - -
339C PRO* 3.9 21.4 - - - +
340C ARG* 4.7 12.5 + - - +
343C ALA* 3.5 15.5 - - - +
347C MET* 4.7 7.3 - - - +
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Residues in contact with ARG 355 (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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351A ARG* 3.3 14.8 + - - +
352A GLN* 3.2 15.7 + - - +
354A SER* 1.3 80.9 - - - +
356A LEU* 1.3 69.8 + - - +
357A GLU 3.6 5.2 - - - -
238B VAL* 5.2 17.3 - - + -
260B SER* 2.7 34.7 + - - -
261B GLY* 3.2 25.3 + - - -
262B LEU* 3.4 33.3 - - - +
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Residues in contact with LEU 356 (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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352A GLN 2.7 20.4 + - - +
353A VAL* 3.5 13.5 - - - +
354A SER 3.4 0.2 - - - -
355A ARG* 1.3 76.6 - - - +
357A GLU* 1.3 75.5 + - + +
337B ALA* 3.0 43.6 - - + +
338B SER 3.2 9.0 - - - +
342B LEU* 3.1 17.5 - - + -
353D VAL* 3.7 18.4 - - + -
357D GLU* 3.2 35.4 - - - +
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Residues in contact with GLU 357 (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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353A VAL* 4.0 7.2 + - - +
354A SER 5.2 0.7 - - - -
355A ARG 3.5 6.7 + - - -
356A LEU* 1.3 103.5 - - + +
336C THR 4.3 0.9 - - - +
339C PRO* 3.4 35.9 - - + +
342C LEU* 3.4 33.3 - - - +
352D GLN 4.5 0.5 - - - +
353D VAL* 3.8 10.1 - - - +
356D LEU* 2.9 61.8 - - + +
357D GLU* 4.8 0.7 - - + +
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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