Contacts of the helix formed by residues 61 - 69 (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 ASN 61 (chain 3).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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342 G 3.2 32.4 + - - -
403 MET* 3.7 24.6 - - + +
423 MET* 4.8 3.7 - - - +
503 LEU* 4.5 14.5 - - + +
563 ALA 5.2 0.8 + - - -
573 LEU* 4.9 2.5 - - + -
583 ASN* 3.0 39.0 + - - +
603 TYR* 1.3 82.0 - - - +
623 ALA* 1.3 65.2 - - - +
643 LEU* 3.4 5.8 + - - +
653 LEU* 3.0 31.1 + - + +
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Residues in contact with ALA 62 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
573 LEU* 4.6 7.4 - - + +
583 ASN 3.1 19.9 + - - +
593 ALA 3.8 4.0 - - - +
613 ASN* 1.3 78.4 - - - +
633 ALA* 1.4 56.8 + - - +
653 LEU* 3.3 2.7 + - - -
663 ALA* 2.9 30.3 + - - +
733 VAL* 4.2 8.3 - - + -
763 PHE* 3.5 28.5 - - + -
803 ILE* 4.0 25.4 - - + -
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Residues in contact with ALA 63 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
593 ALA 3.0 18.9 + - - +
603 TYR* 3.1 4.7 + - + +
623 ALA* 1.4 74.9 - - - +
643 LEU* 1.3 66.1 + - + +
663 ALA* 3.5 1.9 + - - +
673 LYS* 3.2 29.3 + - - +
733 VAL* 4.1 3.7 - - - +
843 ILE* 4.4 2.9 - - + -
864 GLU 5.0 0.7 - - - +
874 MET* 3.8 35.9 - - + +
904 ALA* 3.7 16.4 - - + +
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Residues in contact with LEU 64 (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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393 LYS 5.1 2.0 - - - +
403 MET* 3.9 49.4 - - + +
603 TYR* 2.9 55.8 + - + +
613 ASN* 3.6 9.0 - - - +
623 ALA 3.3 0.2 - - - -
633 ALA* 1.3 77.6 - - + +
653 LEU* 1.3 52.3 + - - +
673 LYS* 3.1 14.5 + - + +
683 ILE* 2.8 39.9 + - + +
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Residues in contact with LEU 65 (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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183 LEU* 3.8 35.7 - - + -
363 VAL* 3.7 19.1 - - + -
403 MET* 3.6 25.1 - - + -
473 VAL* 5.5 1.1 - - + -
503 LEU* 4.3 16.2 - - + -
513 PHE* 4.1 18.4 - - + -
573 LEU* 3.8 16.8 - - + -
613 ASN 3.0 16.6 + - - +
623 ALA* 3.7 4.3 - - - +
643 LEU* 1.3 75.5 - - - +
663 ALA* 1.4 60.4 + - - +
683 ILE* 3.2 4.5 + - + -
693 LEU* 2.9 42.7 + - + +
763 PHE* 4.5 2.5 - - + -
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Residues in contact with ALA 66 (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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623 ALA 2.9 17.0 + - - +
633 ALA 3.6 5.6 - - - +
653 LEU* 1.4 74.2 - - - +
673 LYS* 1.3 58.7 + - - +
693 LEU 3.7 0.2 - - - -
703 LYS* 2.9 25.1 + - - -
713 VAL* 3.0 36.6 + - - +
723 SER 4.2 1.1 - - - -
733 VAL* 3.7 28.5 - - + +
763 PHE* 4.2 3.7 - - + -
904 ALA* 3.9 7.2 - - + -
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Residues in contact with LYS 67 (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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633 ALA* 3.2 14.2 + - - +
643 LEU* 3.1 16.1 + - + +
663 ALA* 1.3 78.2 - - - +
683 ILE* 1.3 62.5 + - + +
703 LYS* 3.4 21.3 + - - +
713 VAL 5.0 0.4 - - - -
864 GLU* 2.8 38.9 + - - +
894 GLU* 3.0 27.2 + - - -
904 ALA* 4.2 14.6 - - + +
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Residues in contact with ILE 68 (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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293 LEU* 3.6 13.2 - - - +
313 LEU* 4.1 19.7 - - + +
363 VAL* 4.1 20.4 - - + +
393 LYS* 3.7 43.3 - - + +
403 MET* 3.4 33.9 - - + -
643 LEU* 2.8 26.3 + - + +
653 LEU* 3.2 5.4 + - - +
673 LYS* 1.3 74.3 - - + +
693 LEU* 1.4 60.8 + - + +
703 LYS* 3.4 6.1 + - - +
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Residues in contact with LEU 69 (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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183 LEU* 3.6 34.5 - - + +
213 ILE* 4.2 19.3 - - + +
223 TYR* 3.9 31.0 - - + +
253 LYS* 2.7 40.0 + - + +
293 LEU* 3.6 7.9 - - + +
313 LEU* 4.0 22.2 - - + -
363 VAL* 5.4 1.8 - - + -
513 PHE* 5.2 1.6 - - + -
653 LEU* 2.9 31.9 + - + +
663 ALA 4.2 1.6 - - - +
683 ILE* 1.4 74.1 - - + +
703 LYS* 1.3 57.3 + - - +
713 VAL* 3.4 13.5 - - + +
763 PHE* 5.2 0.4 - - + -
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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