Contacts of the helix formed by residues 44 - 51 (chain 3) in PDB entry 1LMB
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 GLN 44 (chain 3).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31 T 3.9 19.1 - - + +
41 A 3.1 44.0 + - - -
333 GLN* 2.9 42.1 + - + -
343 GLU* 3.8 32.9 - - + +
373 ALA* 3.5 12.8 - - - +
433 GLY* 1.3 69.7 - - - -
453 SER* 1.3 57.3 + - - +
473 VAL* 3.1 3.3 + - - +
483 GLY* 2.8 33.0 + - - -
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Residues in contact with SER 45 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51 C 3.0 13.3 + - - +
61 C 5.2 0.2 - - - -
352 T 3.5 15.2 - - - +
362 G 2.6 38.6 + - - -
372 G 3.0 17.3 + - - -
433 GLY* 4.8 2.2 - - - -
443 GLN* 1.3 85.0 + - - +
463 GLY* 1.3 58.7 + - - +
483 GLY* 3.4 1.6 + - - -
493 ALA* 3.0 28.2 + - - +
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Residues in contact with GLY 46 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342 G 4.4 3.1 + - - -
352 T 3.4 21.2 + - - +
423 MET* 3.3 24.0 - - - +
433 GLY 3.0 6.7 + - - -
453 SER* 1.3 76.5 - - - +
473 VAL* 1.3 63.9 + - - +
493 ALA* 3.4 5.8 + - - +
503 LEU* 3.4 25.3 + - - +
553 ASN* 4.9 1.0 + - - -
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Residues in contact with VAL 47 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333 GLN* 3.8 20.4 - - + +
363 VAL* 4.4 6.5 - - + -
373 ALA* 3.4 36.1 - - + +
403 MET* 4.2 14.1 - - - -
423 MET* 4.0 13.0 - - + -
433 GLY 3.2 2.8 + - - +
443 GLN 3.1 7.1 + - - +
463 GLY* 1.3 75.6 - - - +
483 GLY* 1.3 67.6 + - - +
503 LEU* 3.1 11.1 + - + +
513 PHE* 3.0 51.1 + - + -
653 LEU* 5.5 0.9 - - + -
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Residues in contact with GLY 48 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41 A 5.0 2.7 - - - -
333 GLN* 3.6 22.2 - - - -
443 GLN* 2.8 17.1 + - - -
453 SER 3.4 2.0 + - - -
473 VAL* 1.3 79.0 - - - +
493 ALA* 1.3 56.2 + - - +
513 PHE* 3.3 2.1 + - - -
523 ASN* 2.9 44.5 + - - +
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Residues in contact with ALA 49 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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342 G 5.5 0.2 - - - +
352 T 5.3 2.9 - - + +
453 SER 3.0 16.8 + - - +
463 GLY* 3.6 4.7 - - - +
473 VAL 3.2 0.4 - - - -
483 GLY* 1.3 74.7 - - - +
503 LEU* 1.3 61.8 + - - +
523 ASN 3.6 0.2 + - - -
533 GLY 3.4 1.7 + - - -
543 ILE* 2.8 48.4 + - + -
553 ASN* 3.2 35.5 + - - +
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Residues in contact with LEU 50 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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342 G 3.8 21.3 - - - +
153 ALA* 3.6 12.8 - - - +
183 LEU* 4.6 6.8 - - + +
403 MET* 4.4 12.6 - - + -
423 MET* 4.4 9.0 - - + -
463 GLY 3.4 15.0 - - - +
473 VAL* 3.1 10.0 + - + +
493 ALA* 1.3 75.6 - - - +
513 PHE* 1.3 66.8 + - + +
523 ASN 3.2 0.7 + - - -
533 GLY* 3.3 9.7 + - - -
553 ASN* 3.8 19.8 - - + +
563 ALA 3.8 24.2 - - - +
573 LEU* 4.3 20.7 - - + +
613 ASN* 4.5 8.5 - - + +
653 LEU* 4.3 20.2 - - + -
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Residues in contact with PHE 51 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153 ALA* 3.4 18.6 - - - +
163 ARG* 5.3 0.2 - - - -
183 LEU* 3.7 36.3 - - + -
193 LYS* 3.6 30.3 - - + +
223 TYR* 3.6 47.8 - + + -
333 GLN* 3.9 27.8 - - + +
363 VAL* 4.6 5.4 - - + -
473 VAL* 3.0 33.1 + - + +
483 GLY* 3.8 6.7 - - - +
503 LEU* 1.3 79.1 - - + +
523 ASN* 1.3 63.2 + - - +
533 GLY 3.6 0.5 + - - -
653 LEU* 4.1 21.8 - - + -
693 LEU* 5.2 2.9 - - + -
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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