Contacts of the helix formed by residues 340 - 357 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354A SER* 4.7 12.8 + - - +
283C ILE 3.8 5.9 + - - -
284C PRO* 4.2 6.1 - - - +
285C PRO* 3.4 15.2 - - - +
327C LYS* 3.2 54.6 + - - +
330C LEU* 6.0 6.1 - - + -
338C SER* 3.4 4.5 + - - +
339C PRO* 1.3 80.0 - - + +
341C ALA* 1.3 60.9 + - - +
343C ALA* 3.9 5.4 - - - -
344C ASP* 2.5 56.7 + - - +
259D GLU* 2.8 40.7 + - - +
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Residues in contact with ALA 341 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263C ARG* 3.5 37.0 - - - +
266C ALA* 5.3 0.7 - - + -
337C ALA 4.5 2.7 - - - +
338C SER* 3.3 17.9 + - - +
340C ARG* 1.3 81.0 - - - +
342C LEU* 1.3 63.4 + - - +
344C ASP* 3.3 10.1 + - - +
345C SER* 3.3 16.1 + - - -
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Residues in contact with LEU 342 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353A VAL* 4.0 9.6 - - + -
357A GLU* 3.4 35.4 - - - +
337C ALA* 3.8 14.6 - - + +
338C SER 2.9 26.1 + - - +
339C PRO 4.1 0.2 - - - +
341C ALA* 1.3 76.5 - - - +
343C ALA* 1.3 56.6 + - - +
345C SER* 2.9 20.7 + - - -
346C LEU* 3.1 19.2 + - - +
349D LEU* 3.5 22.0 - - + +
352D GLN* 3.1 47.6 - - + +
353D VAL* 3.8 9.2 - - + +
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Residues in contact with ALA 343 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350A ALA* 3.5 30.9 - - - +
353A VAL* 3.8 6.7 - - + +
354A SER* 3.5 25.1 - - - +
339C PRO 3.2 18.8 + - - +
340C ARG 4.0 3.6 - - - +
341C ALA 3.3 0.2 - - - -
342C LEU* 1.3 74.5 - - - +
344C ASP* 1.3 65.7 + - - +
345C SER 3.0 2.2 + - - -
346C LEU* 4.6 1.1 - - - -
347C MET* 3.5 24.5 + - + +
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Residues in contact with ASP 344 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354A SER* 5.6 0.2 + - - -
340C ARG* 2.5 51.8 + - - +
341C ALA* 3.3 6.0 + - - +
343C ALA* 1.3 77.1 - - - +
345C SER* 1.3 59.5 + - - +
347C MET* 3.8 6.4 + - - +
348C GLN* 3.1 33.1 + - + +
258D THR* 4.2 19.1 - - - +
259D GLU* 4.4 14.4 - - - +
261D GLY* 4.7 2.6 - - - -
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Residues in contact with SER 345 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341C ALA 3.3 11.4 + - - -
342C LEU* 2.9 14.0 + - - -
344C ASP* 1.3 77.6 - - - +
346C LEU* 1.3 58.2 + - - +
347C MET 3.3 0.7 - - - -
348C GLN* 3.4 12.7 + - - +
349C LEU* 3.1 30.8 + - - +
349D LEU* 3.7 21.8 - - - -
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Residues in contact with LEU 346 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346A LEU* 4.0 8.5 - - + +
350A ALA* 3.6 21.5 - - + +
353A VAL* 4.8 6.1 - - + -
346B LEU* 3.5 42.2 - - + -
342C LEU 3.1 32.2 + - - +
343C ALA* 3.5 3.3 + - - +
345C SER* 1.3 74.6 - - - +
347C MET* 1.3 59.6 + - - +
348C GLN 3.2 0.2 - - - -
349C LEU* 3.6 12.2 - - + +
350C ALA* 2.8 29.1 + - - +
346D LEU* 4.5 8.1 - - + -
349D LEU* 3.4 37.5 - - + -
353D VAL* 4.4 8.5 - - + -
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Residues in contact with MET 347 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347A MET* 3.6 22.0 - - + +
350A ALA* 3.3 19.1 - - + +
351A ARG* 3.5 56.8 - - + +
354A SER* 4.7 9.2 - - - +
343C ALA 3.5 15.2 + - - +
344C ASP* 4.2 4.9 - - - +
345C SER 3.3 0.6 - - - -
346C LEU* 1.3 76.0 - - - +
348C GLN* 1.3 59.5 + - - +
350C ALA* 3.8 5.3 - - - +
351C ARG* 3.0 35.9 + - - +
259D GLU 3.9 21.3 - - - +
260D SER 4.3 2.5 - - - +
261D GLY* 3.9 14.6 - - - +
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Residues in contact with GLN 348 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344C ASP* 3.1 27.5 + - + +
345C SER* 3.6 11.3 + - - +
346C LEU 3.2 0.2 - - - -
347C MET* 1.3 75.1 - - - +
349C LEU* 1.3 66.1 + - + +
351C ARG* 3.6 4.5 + - - +
352C GLN* 3.4 26.9 + - - +
261D GLY* 3.6 23.5 + - - +
262D LEU 5.7 0.4 - - - -
263D ARG* 4.0 30.8 - - - +
267D ASP* 5.6 0.2 + - - -
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Residues in contact with LEU 349 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345C SER* 3.1 15.1 + - - +
346C LEU* 3.6 7.0 - - + +
347C MET 3.3 0.2 - - - -
348C GLN* 1.3 74.8 - - + +
350C ALA* 1.3 55.7 + - - +
352C GLN* 2.8 45.3 + - - +
353C VAL* 3.0 14.2 + - + +
342D LEU* 4.3 13.8 - - + +
345D SER* 3.9 27.4 - - - +
346D LEU* 3.3 34.5 - - + +
349D LEU* 3.6 29.6 - - + -
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Residues in contact with ALA 350 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343A ALA* 3.2 36.7 - - - +
346A LEU* 3.4 23.2 - - + +
347A MET* 3.6 17.7 - - + -
346C LEU 2.8 18.6 + - - +
347C MET 3.8 0.9 - - - +
349C LEU* 1.3 75.9 - - - +
351C ARG* 1.3 56.2 + - - +
353C VAL* 3.2 2.3 + - - +
354C SER 2.9 26.2 + - - -
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Residues in contact with ARG 351 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347A MET* 3.3 33.5 - - - +
351A ARG* 5.9 2.4 - - - +
347C MET 3.0 26.3 + - - +
348C GLN 3.6 5.8 - - - +
349C LEU 3.2 0.6 - - - -
350C ALA* 1.3 72.3 - - - +
352C GLN* 1.3 57.1 + - - +
354C SER* 3.5 17.8 + - - -
355C ARG* 3.7 15.6 - - - +
233D LEU* 4.8 15.9 + - - +
234D ASN* 6.0 2.2 - - - +
238D VAL* 3.8 27.1 - - - +
260D SER* 3.1 32.6 + - - +
261D GLY 4.1 4.5 - - - +
262D LEU* 3.5 39.0 - - + +
267D ASP* 5.7 2.6 - - - +
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Residues in contact with GLN 352 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348C GLN* 3.4 13.7 + - - +
349C LEU* 2.8 24.2 + - - +
351C ARG* 1.3 78.0 - - - +
353C VAL* 1.3 64.5 - - - +
354C SER 3.4 0.7 - - - -
355C ARG* 4.0 16.0 + - - +
356C LEU* 4.3 2.1 + - - +
263D ARG* 4.7 19.1 + - - -
335D GLN 5.8 1.2 - - - +
338D SER* 3.0 44.9 + - - +
342D LEU* 3.9 21.7 - - + +
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Residues in contact with VAL 353 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339A PRO* 3.2 16.3 - - + +
342A LEU* 4.2 13.5 - - + -
343A ALA* 4.8 2.5 - - - -
346A LEU* 3.9 17.5 - - + -
353B VAL* 4.2 15.0 - - + -
356B LEU* 3.8 26.2 - - + -
349C LEU* 3.2 21.3 - - + +
350C ALA* 3.6 4.3 - - - +
352C GLN* 1.3 77.3 - - - +
354C SER* 1.3 53.9 + - - +
356C LEU* 2.6 41.7 + - + +
342D LEU* 3.6 21.3 - - + -
346D LEU* 5.2 1.1 - - + -
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Residues in contact with SER 354 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339A PRO* 3.3 14.3 + - - +
340A ARG* 4.6 3.1 + - - +
343A ALA* 3.5 13.2 - - - -
347A MET* 6.1 0.7 - - - -
350C ALA 2.9 13.1 + - - -
351C ARG* 3.5 29.1 + - - +
353C VAL* 1.3 77.3 - - - +
355C ARG* 1.3 56.1 + - - +
356C LEU 3.1 2.6 + - - -
357C GLU* 2.6 33.3 - - - +
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Residues in contact with ARG 355 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351C ARG 3.7 24.2 - - - +
352C GLN* 4.0 16.4 - - - +
353C VAL 3.0 0.9 + - - -
354C SER* 1.3 76.4 + - - +
356C LEU* 1.3 58.2 - - - +
357C GLU* 3.2 17.1 + - - +
267D ASP* 5.8 1.3 - - - -
332D PRO 5.3 2.4 + - - -
334D THR* 3.5 42.7 + - - +
335D GLN 3.4 23.4 + - - -
336D THR* 3.5 42.1 - - + +
338D SER* 4.8 5.8 + - - +
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Residues in contact with LEU 356 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339A PRO* 3.7 19.2 - - + +
353B VAL* 5.4 0.9 - - + +
356B LEU* 4.3 16.2 - - + -
357B GLU* 4.1 21.8 - - + +
353C VAL* 2.6 24.2 + - - +
354C SER 3.1 2.6 - - - -
355C ARG* 1.3 74.1 - - - +
357C GLU* 1.3 57.0 + - - +
336D THR 4.8 5.8 - - - +
337D ALA 5.4 0.2 - - - +
338D SER* 3.6 34.5 - - - +
342D LEU* 3.4 31.6 - - + -
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Residues in contact with GLU 357 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339A PRO* 3.1 34.4 - - + +
340A ARG* 4.0 11.6 + - - +
354C SER 2.6 24.5 - - - +
355C ARG* 3.2 11.3 - - - +
356C LEU* 1.3 79.0 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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