Contacts of the helix formed by residues 49 - 58 (chain M) in PDB entry 4LLL
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 THR 49 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48M LEU* 1.3 78.0 - - - +
50M GLN* 1.3 77.0 + - + +
51M ASN* 3.0 28.7 - - + +
52M ASP* 3.6 26.0 + - - +
53M ILE* 3.2 23.6 + - - +
88M ARG* 4.2 33.7 + - + +
89M LYS 6.0 0.2 - - - +
90M ASN* 3.7 19.4 + - - +
91M ILE* 4.8 2.5 - - - -
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Residues in contact with GLN 50 (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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49M THR* 1.3 80.8 - - + +
51M ASN* 1.3 66.8 + - - +
53M ILE* 3.4 3.8 + - - +
54M ALA* 3.1 21.5 + - - +
61M GLY 5.4 1.8 + - - -
64M VAL* 4.1 6.7 - - + +
65M SER* 4.0 21.4 + - - +
68M LEU* 4.2 26.6 - - + +
79M ARG* 2.8 30.0 + - - -
89M LYS* 3.6 30.0 + - - +
91M ILE* 4.6 3.1 - - + -
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Residues in contact with ASN 51 (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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49M THR* 3.0 15.4 - - + +
50M GLN* 1.3 80.0 - - - +
52M ASP* 1.3 65.8 + - - +
54M ALA* 2.9 20.6 + - - +
55M LYS* 3.1 12.7 + - - +
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Residues in contact with ASP 52 (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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39M TYR* 4.1 9.0 + - - +
46M ASP* 5.6 0.3 - - - +
47M GLY 4.9 1.2 - - - +
48M LEU* 4.2 22.0 - - + +
49M THR* 3.6 34.4 + - - +
50M GLN 3.5 0.2 - - - -
51M ASN* 1.3 78.3 - - - +
53M ILE* 1.3 61.7 + - - +
55M LYS* 3.5 7.1 + - - +
56M ALA* 3.2 20.3 + - - +
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Residues in contact with ILE 53 (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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36M THR* 4.0 19.7 - - + -
39M TYR* 4.2 5.2 - - + -
40M LEU* 4.7 1.8 - - + -
48M LEU* 3.9 26.7 - - + -
49M THR 3.2 17.5 + - - +
50M GLN 3.4 7.4 + - - +
51M ASN 3.1 0.6 - - - -
52M ASP* 1.3 73.2 - - - +
54M ALA* 1.3 67.5 + - - +
56M ALA* 3.1 8.1 + - - +
57M LEU* 2.9 44.6 + - + +
64M VAL* 4.0 12.1 - - + -
68M LEU* 4.1 13.5 - - + -
91M ILE* 4.0 28.3 - - + -
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Residues in contact with ALA 54 (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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50M GLN 3.1 12.9 + - - +
51M ASN* 2.9 14.4 + - - +
53M ILE* 1.3 77.6 - - - +
55M LYS* 1.3 63.1 + - - +
57M LEU* 3.1 1.2 + - - +
58M GLN 3.0 18.9 + - - -
59M ARG 3.4 23.7 + - - +
61M GLY* 4.8 9.2 - - - +
64M VAL* 3.6 21.5 - - + +
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Residues in contact with LYS 55 (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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51M ASN 3.1 7.7 + - - +
52M ASP* 3.9 9.6 - - - +
54M ALA* 1.3 77.9 - - - +
56M ALA* 1.3 63.2 + - - +
58M GLN* 3.4 24.1 + - - +
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Residues in contact with ALA 56 (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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39M TYR* 3.3 45.8 - - + +
52M ASP 3.2 6.7 + - - +
53M ILE 3.1 10.6 + - - +
55M LYS* 1.3 78.9 - - - +
57M LEU* 1.3 64.0 + - + +
58M GLN* 3.6 4.5 + - - +
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Residues in contact with LEU 57 (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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32M GLU* 4.1 28.8 - - + +
35M HIS* 4.5 13.0 - - + -
36M THR* 3.3 30.7 - - - +
39M TYR* 6.2 2.0 - - + -
53M ILE* 2.9 30.0 + - + +
54M ALA 3.9 1.8 - - - +
56M ALA* 1.3 79.9 - - + +
58M GLN* 1.3 71.8 + - - +
59M ARG* 3.2 21.4 - - + +
64M VAL* 4.2 9.9 - - + -
67M LEU* 3.8 17.5 - - + -
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Residues in contact with GLN 58 (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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54M ALA 3.0 6.5 + - - -
55M LYS* 3.4 16.1 + - - +
56M ALA 3.3 5.0 - - - +
57M LEU* 1.3 78.5 - - - +
59M ARG* 1.3 69.5 + - - +
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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