Contacts of the helix formed by residues 402 - 413 (chain M) in PDB entry 1L0V
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 PHE 402 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81M VAL* 4.0 17.9 - - + -
84M TYR* 5.0 1.6 - - + -
85M PHE* 3.3 55.6 - + + -
365M GLN 5.5 4.5 - - - -
367M CYS* 4.5 5.3 - - - -
377M VAL* 2.5 41.6 - - + +
383M VAL* 3.3 48.0 - - + -
385M LEU* 4.4 5.6 - - + -
398M GLU* 2.9 25.6 + - + +
399M LEU 4.4 0.4 - - - -
401M VAL* 1.3 86.9 - - + +
403M GLY* 1.3 55.6 + - - +
405M LEU* 3.9 26.0 - - + +
406M ALA 3.9 6.6 + - - -
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Residues in contact with GLY 403 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15M ALA 4.5 6.1 - - - -
18M ARG* 3.9 16.4 - - - -
19M ALA* 4.2 7.1 - - - -
377M VAL* 4.5 7.0 - - - -
399M LEU 3.7 16.3 + - - -
400M VAL 3.5 3.0 + - - -
401M VAL 3.5 0.4 - - - -
402M PHE* 1.3 78.9 - - - +
404M ARG* 1.3 68.2 + - - +
405M LEU 2.9 1.3 - - - -
406M ALA* 3.3 3.1 + - - +
407M GLY* 2.8 20.4 + - - -
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Residues in contact with ARG 404 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18M ARG* 3.2 30.8 - - - +
22M ALA* 3.4 24.8 + - + +
25M GLN* 5.9 2.2 + - - +
84M TYR* 5.8 2.0 - - - +
88M HIS* 6.1 5.6 - - - -
91M THR* 5.5 4.0 - - - +
92M GLU* 3.3 25.4 + - + +
400M VAL 3.7 9.5 + - - +
401M VAL 5.0 2.5 - - - +
403M GLY* 1.3 74.2 - - - +
405M LEU* 1.3 56.2 + - - +
407M GLY 2.9 0.3 + - - -
408M GLU* 2.6 67.0 + - + +
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Residues in contact with LEU 405 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84M TYR* 3.1 58.3 - - + +
365M GLN 4.8 7.9 - - - +
366M ASN* 4.4 14.6 - - + +
367M CYS* 5.3 7.2 - - - +
401M VAL 3.5 19.6 + - - +
402M PHE* 3.9 30.3 - - + +
403M GLY 2.9 1.0 - - - +
404M ARG* 1.3 78.5 - - - +
406M ALA* 1.3 55.8 + - - +
407M GLY 2.6 14.7 + - - -
408M GLU* 3.1 6.5 + - - +
409M GLN* 3.0 40.8 + - + +
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Residues in contact with ALA 406 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7M LEU* 5.1 0.2 - - - +
19M ALA* 5.7 2.2 - - + -
189M VAL* 3.9 29.3 - - + +
367M CYS* 4.1 17.2 - - + -
375M PHE* 4.4 11.7 - - + -
377M VAL* 4.0 24.5 - - + -
402M PHE 3.9 0.2 + - - -
403M GLY 3.3 6.4 + - - +
405M LEU* 1.3 77.7 - - - +
407M GLY* 1.3 55.9 + - - +
409M GLN* 4.6 2.7 - - - -
410M ALA* 3.1 29.2 - - - +
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Residues in contact with GLY 407 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7M LEU* 4.1 0.5 - - - +
9M ILE* 6.3 0.2 - - - -
19M ALA 4.1 17.7 - - - -
23M ALA* 4.2 18.2 - - - -
403M GLY 2.8 12.4 + - - -
404M ARG* 3.1 4.7 - - - -
405M LEU 2.6 6.9 + - - -
406M ALA* 1.3 73.0 - - - +
408M GLU* 1.3 66.6 - - - +
409M GLN 2.8 2.3 + - - -
410M ALA* 3.1 14.1 + - - +
411M THR* 3.5 11.3 + - - +
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Residues in contact with GLU 408 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22M ALA 4.4 11.9 + - - +
26M ALA* 5.6 7.2 - - + -
84M TYR* 3.5 21.0 + - - -
404M ARG* 2.6 58.5 + - + +
405M LEU* 3.8 5.8 - - - +
407M GLY* 1.3 69.2 - - - -
409M GLN* 1.3 63.9 + - - +
411M THR* 2.4 25.6 + - - -
412M GLU* 2.9 17.4 - - - +
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Residues in contact with GLN 409 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366M ASN* 2.8 38.9 + - + +
375M PHE* 3.6 20.2 - - + -
405M LEU* 3.0 31.9 + - + +
406M ALA* 4.8 0.9 - - - -
407M GLY 2.8 4.0 + - - -
408M GLU* 1.3 77.2 - - - +
410M ALA* 1.3 55.7 + - - +
411M THR 3.1 2.7 - - - -
412M GLU* 2.7 48.9 + - - +
413M ARG* 3.0 22.9 + - - +
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Residues in contact with ALA 410 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7M LEU* 3.5 19.3 - - + -
187M ALA* 3.4 19.2 - - - +
189M VAL* 3.8 17.5 - - + -
375M PHE* 3.3 19.2 - - + -
406M ALA 3.1 20.1 + - - +
407M GLY 3.1 1.6 + - - -
409M GLN* 1.3 77.3 - - - +
411M THR* 1.3 57.7 + - - +
413M ARG* 2.8 21.0 + - - +
414M ALA* 3.3 5.5 + - - +
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Residues in contact with THR 411 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7M LEU* 3.3 36.3 - - + +
23M ALA* 4.5 11.0 - - + -
26M ALA* 5.1 8.5 - - + +
27M ASN* 4.1 22.9 - - + +
407M GLY 3.5 5.1 + - - +
408M GLU* 2.4 29.0 + - - -
410M ALA* 1.3 69.0 - - - +
412M GLU* 1.3 65.6 + - - +
413M ARG 2.9 6.0 + - - -
414M ALA* 3.3 3.7 + - - +
415M ALA* 3.2 25.7 + - - +
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Residues in contact with GLU 412 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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408M GLU* 2.9 24.1 - - - +
409M GLN* 2.7 30.6 + - - +
411M THR* 1.3 79.5 + - - +
413M ARG* 1.3 67.8 + - - +
414M ALA 3.5 0.7 - - - -
415M ALA* 4.2 7.0 - - - -
416M THR* 3.4 25.5 + - - +
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Residues in contact with ARG 413 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166M HIS* 5.4 1.2 + - - -
186M ASN 3.2 9.3 - - - +
187M ALA* 5.2 0.9 - - + -
366M ASN* 5.4 5.7 + - - +
368M GLU* 2.9 35.9 + - - +
372M LYS* 3.8 22.2 - - + +
373M GLY* 4.3 9.5 - - - +
375M PHE* 3.3 36.0 - - + -
409M GLN* 3.0 27.5 + - - +
410M ALA 2.8 13.2 + - - +
412M GLU* 1.3 90.1 + - - +
414M ALA* 1.3 55.1 - - - +
416M THR* 4.5 9.5 + - - -
417M ALA* 4.0 10.6 - - - +
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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