Contacts of the helix formed by residues 61 - 69 (chain 4) 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 4).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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131 G 5.3 2.0 - - - +
141 G 3.5 24.0 + - - -
404 MET* 3.6 20.9 - - + +
424 MET* 4.4 3.9 - - - +
504 LEU* 4.1 21.8 - - + +
564 ALA 5.0 2.4 + - - -
574 LEU* 4.4 9.0 - - + -
584 ASN* 2.8 35.1 + - - +
604 TYR* 1.3 79.3 - - - +
624 ALA* 1.3 66.3 + - - +
644 LEU* 3.3 6.8 + - - +
654 LEU* 3.0 30.6 + - - +
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Residues in contact with ALA 62 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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574 LEU* 4.2 12.3 - - + +
584 ASN 3.1 17.4 + - - +
594 ALA 3.8 0.9 - - - +
614 ASN* 1.3 80.4 - - - +
634 ALA* 1.3 61.8 + - - +
654 LEU* 3.5 0.4 + - - -
664 ALA* 3.0 21.0 + - - +
734 VAL* 4.0 7.2 - - + -
764 PHE* 3.3 28.3 - - + -
804 ILE* 3.8 29.8 - - + -
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Residues in contact with ALA 63 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
863 GLU 5.0 0.9 - - - +
873 MET* 3.9 27.8 - - + +
903 ALA* 3.7 22.2 - - + +
594 ALA 3.1 18.3 + - - +
604 TYR* 3.2 5.4 + - + +
624 ALA* 1.3 76.8 - - - +
644 LEU* 1.3 63.5 + - + +
664 ALA* 3.3 3.6 + - - +
674 LYS* 3.1 30.1 + - - +
734 VAL* 4.0 5.8 - - + +
844 ILE* 4.7 0.9 - - + -
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Residues in contact with LEU 64 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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394 LYS 5.4 2.2 - - - +
404 MET* 4.5 38.4 - - + +
604 TYR* 3.0 50.5 + - + +
614 ASN* 3.4 11.0 - - - +
634 ALA* 1.3 79.4 - - + +
654 LEU* 1.3 57.8 + - - +
674 LYS* 3.3 15.4 + - + +
684 ILE* 3.0 36.5 + - + +
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Residues in contact with LEU 65 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184 LEU* 3.9 26.0 - - + -
364 VAL* 3.7 19.7 - - + -
404 MET* 3.7 25.6 - - + -
474 VAL* 5.5 0.4 - - + -
504 LEU* 4.1 17.7 - - + -
514 PHE* 4.0 19.5 - - + -
574 LEU* 3.9 24.7 - - + -
614 ASN 3.0 18.1 + - - +
624 ALA 4.0 3.1 - - - +
644 LEU* 1.3 77.1 - - - +
664 ALA* 1.3 66.7 + - - +
684 ILE* 3.7 5.3 - - + -
694 LEU* 2.8 36.9 + - + +
764 PHE* 4.6 1.1 - - + -
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Residues in contact with ALA 66 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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903 ALA* 4.1 6.5 - - + -
624 ALA 3.0 18.1 + - - +
634 ALA 3.5 5.6 - - - +
654 LEU* 1.3 76.5 - - - +
674 LYS* 1.3 58.5 + - - +
694 LEU 3.6 0.3 - - - -
704 LYS* 2.8 24.3 + - - -
714 VAL* 3.0 30.1 + - - +
734 VAL* 3.7 26.0 - - + +
764 PHE* 4.0 13.0 - - + -
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Residues in contact with LYS 67 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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863 GLU* 2.5 37.3 + - - +
873 MET* 4.7 1.2 - - - +
893 GLU* 3.6 26.6 + - - -
903 ALA* 4.0 17.4 - - + +
634 ALA* 3.1 16.9 + - - +
644 LEU* 3.6 18.0 - - + +
654 LEU 3.1 0.2 - - - -
664 ALA* 1.3 80.2 - - - +
684 ILE* 1.3 64.1 + - + +
704 LYS* 3.2 21.9 + - - +
714 VAL 5.2 0.2 - - - -
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Residues in contact with ILE 68 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294 LEU* 3.9 12.6 - - - +
314 LEU* 4.3 17.5 - - + +
364 VAL* 4.1 31.4 - - + -
394 LYS* 3.6 47.0 + - + +
404 MET* 3.7 23.8 - - + -
644 LEU* 3.0 25.1 + - + +
654 LEU* 3.2 6.9 + - - +
674 LYS* 1.3 78.1 - - + +
694 LEU* 1.3 63.6 + - + +
704 LYS* 3.2 5.8 + - - +
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Residues in contact with LEU 69 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184 LEU* 3.7 32.3 - - + +
214 ILE* 4.2 23.8 - - + +
224 TYR* 4.2 28.0 - - + -
254 LYS* 3.1 28.4 + - + +
294 LEU* 3.9 7.4 - - + -
314 LEU* 3.7 26.5 - - + -
364 VAL* 5.5 1.8 - - + -
514 PHE* 5.3 1.8 - - + -
654 LEU* 2.8 27.9 + - + +
664 ALA* 4.1 2.0 - - - +
684 ILE* 1.3 79.7 - - + +
704 LYS* 1.3 67.0 + - - +
714 VAL* 3.8 8.3 - - + +
764 PHE* 5.4 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