Contacts of the helix formed by residues 343 - 355 (chain A) in PDB entry 1LMU
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 GLY 343 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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339A GLU 4.6 0.6 + - - -
340A HIS* 2.9 13.9 + - - -
342A ALA* 1.3 76.0 - - - +
344A ARG* 1.3 62.9 + - - +
345A GLN* 3.2 2.7 - - - -
346A ALA* 2.9 22.3 + - - +
347A VAL* 3.0 18.8 + - - +
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Residues in contact with ARG 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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340A HIS 3.7 2.4 + - - -
341A PHE* 2.9 55.9 + - + +
342A ALA* 3.2 8.8 + - - +
343A GLY* 1.3 75.9 - - - +
345A GLN* 1.3 72.4 + - + +
347A VAL* 3.2 2.8 + - - +
348A MET* 2.8 41.6 + - + +
366A PRO* 3.1 32.6 + - - +
367A ASP* 5.1 6.4 + - - +
410A TYR* 3.6 15.0 + - - +
414A PHE* 3.6 31.9 - - + -
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Residues in contact with GLN 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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342A ALA 4.4 12.7 + - - +
343A GLY* 5.6 0.2 - - - -
344A ARG* 1.3 94.0 + - + +
346A ALA* 1.3 63.8 + - + +
348A MET* 3.1 10.6 + - - +
349A ASN* 2.9 29.7 + - - +
366A PRO* 6.5 0.9 - - + -
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Residues in contact with ALA 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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343A GLY* 2.9 13.0 + - - +
345A GLN* 1.3 83.1 - - + +
347A VAL* 1.3 62.7 + - + +
349A ASN* 3.2 9.4 + - - +
350A ALA* 3.1 21.0 + - - +
388A ALA* 4.1 24.6 - - + +
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Residues in contact with VAL 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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340A HIS 5.8 0.9 - - - +
343A GLY* 3.0 17.4 + - - +
344A ARG 3.5 5.6 - - - +
346A ALA* 1.3 77.7 - - + +
348A MET* 1.3 62.3 + - - +
350A ALA* 3.1 5.5 + - - +
351A ILE* 3.0 28.8 + - + +
385A ILE* 5.4 4.0 - - + -
386A PRO* 3.9 33.4 - - + +
387A THR 4.2 11.7 - - - -
388A ALA* 4.5 2.9 - - + +
410A TYR* 3.6 38.1 - - + +
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Residues in contact with MET 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 ARG* 2.8 33.7 + - + +
345A GLN* 3.1 9.2 + - - +
347A VAL* 1.3 76.0 - - - +
349A ASN* 1.3 63.6 + - - +
351A ILE* 3.0 14.4 + - + +
352A SER* 3.0 24.5 + - - -
359A LEU* 3.8 14.5 - - + +
364A VAL* 4.5 15.3 - - + -
366A PRO* 4.0 16.4 - - + -
410A TYR* 4.9 3.1 - - + -
411A LEU* 4.4 13.2 - - + -
414A PHE* 3.6 47.6 - - + -
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Residues in contact with ASN 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 GLN 2.9 13.7 + - - +
346A ALA* 3.4 12.1 - - - +
348A MET* 1.3 77.4 - - - +
350A ALA* 1.3 61.4 + - - +
352A SER* 3.2 23.0 + - - -
353A VAL* 3.4 15.6 + - - +
390A SER* 4.5 10.4 - - - -
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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 ALA 3.1 2.9 + - - +
347A VAL 3.1 5.9 + - - +
349A ASN* 1.3 76.8 - - - +
351A ILE* 1.3 65.5 + - - +
353A VAL* 3.0 12.8 + - - +
354A HIS* 3.0 22.7 + - - +
387A THR 3.1 27.8 - - - +
388A ALA 3.5 12.1 + - - +
389A ARG 3.3 22.2 - - - +
390A SER* 4.5 7.0 - - - +
403A TYR* 4.3 2.0 - - - +
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Residues in contact with ILE 351 (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 VAL* 3.0 21.4 + - + +
348A MET* 3.0 13.7 + - - +
350A ALA* 1.3 76.2 - - - +
352A SER* 1.3 56.6 + - - +
355A ALA* 2.7 35.2 + - + +
358A LEU* 4.2 10.3 - - + -
359A LEU* 4.0 21.1 - - + -
386A PRO* 4.3 3.4 - - + -
403A TYR* 3.8 17.3 - - - +
407A ALA* 3.8 28.3 - - + +
410A TYR* 3.9 19.7 - - + -
411A LEU* 3.7 27.4 - - + -
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Residues in contact with SER 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 MET 3.0 13.4 + - - -
349A ASN* 3.3 14.6 + - - -
351A ILE* 1.3 79.3 - - - +
353A VAL* 1.3 63.7 + - - +
355A ALA 4.2 3.8 - - - -
356A PRO* 3.4 23.4 - - - +
359A LEU* 3.6 26.1 - - - +
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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 ASN* 3.7 21.5 - - - +
350A ALA* 3.0 6.6 + - - +
352A SER* 1.3 81.2 - - - +
354A HIS* 1.3 67.5 + - + +
356A PRO* 3.4 13.5 - - - +
390A SER* 3.5 32.3 - - - +
391A SER 4.8 0.7 - - - +
392A SER* 4.1 23.1 - - - -
393A VAL 5.3 0.2 - - - +
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Residues in contact with HIS 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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325A LEU* 3.4 23.8 - - + +
350A ALA* 3.0 20.5 + - - +
353A VAL* 1.3 83.5 - - + +
355A ALA* 1.3 57.5 + - - +
356A PRO* 3.2 6.2 - - - +
389A ARG* 2.9 30.9 + - + +
390A SER 4.6 4.0 - - - -
391A SER 3.6 15.4 + - - -
393A VAL* 3.1 42.0 - - + +
395A LEU* 4.2 11.7 - - + +
400A ALA* 5.8 4.9 - - - +
403A TYR* 3.2 40.2 + + + +
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Residues in contact with ALA 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 ILE* 2.7 26.4 + - + +
352A SER 3.7 1.0 - - - +
354A HIS* 1.3 75.1 - - - +
356A PRO* 1.3 65.8 - - - +
357A ASP* 3.2 6.4 + - - +
358A LEU* 3.3 40.0 + - + +
359A LEU 4.1 2.6 + - - -
403A TYR* 4.2 14.1 - - + -
404A THR* 4.2 13.5 - - - +
407A ALA* 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