Contacts of the helix formed by residues 45 - 59 (chain M) in PDB entry 6K4Y
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 GLY 45 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38M ARG* 5.2 0.2 - - - -
43M ASP 4.1 1.2 + - - -
44M LEU* 1.3 77.6 - - - +
46M ASN* 1.3 61.7 + - - -
47M ALA 3.5 2.2 - - - -
48M VAL* 3.4 21.5 - - - +
49M VAL* 3.0 27.9 + - - +
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Residues in contact with ASN 46 (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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38M ARG* 3.3 31.2 + - - +
44M LEU 5.3 0.5 - - - +
45M GLY* 1.3 72.5 - - - +
47M ALA* 1.3 56.2 + - - +
49M VAL* 3.5 3.1 + - - +
50M ASN* 2.7 41.8 + - - +
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Residues in contact with ALA 47 (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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46M ASN* 1.3 75.5 - - - +
48M VAL* 1.3 56.1 + - + +
50M ASN* 3.8 11.8 - - + +
51M SER* 2.3 39.3 + - - +
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Residues in contact with VAL 48 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18M LYS* 3.9 18.2 - - + -
44M LEU* 3.9 29.2 - - + -
45M GLY* 3.3 24.9 + - - +
46M ASN 3.2 0.8 - - - -
47M ALA* 1.3 77.4 - - + +
49M VAL* 1.3 61.3 + - - +
51M SER* 3.2 5.8 + - - -
52M ASN* 2.8 35.2 + - - +
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Residues in contact with VAL 49 (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 ILE* 4.1 13.0 - - + -
34M ALA 4.8 0.7 - - - +
37M VAL* 3.7 24.7 - - + -
38M ARG* 3.7 33.4 - - + +
41M HIS* 4.3 12.1 - - + -
44M LEU* 3.7 20.4 - - + +
45M GLY 3.0 20.3 + - - +
46M ASN 3.8 0.7 - - - +
48M VAL* 1.3 73.7 - - - +
50M ASN* 1.3 58.6 + - - +
52M ASN* 3.1 8.8 + - - +
53M ILE* 2.9 45.6 + - + +
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Residues in contact with ASN 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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34M ALA* 4.9 1.6 - - - +
38M ARG* 3.4 25.7 + - - +
46M ASN* 2.7 33.0 + - - +
47M ALA* 3.8 10.5 - - + +
49M VAL* 1.3 76.2 - - - +
51M SER* 1.3 56.9 + - - +
53M ILE* 3.8 13.5 - - - +
54M GLY* 2.9 22.2 + - - -
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Residues in contact with SER 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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47M ALA* 2.3 30.2 + - - +
48M VAL* 3.2 9.6 + - - -
50M ASN* 1.3 75.5 - - - +
52M ASN* 1.3 61.6 + - - +
54M GLY* 3.0 4.5 + - - -
55M VAL* 2.9 31.4 + - - +
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Residues in contact with ASN 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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16M ASN* 3.9 7.6 + - - +
18M LYS* 3.4 30.3 - - - +
19M THR* 3.6 32.5 + - - +
22M ILE* 3.4 22.8 - - + +
44M LEU* 4.0 0.4 - - - +
48M VAL* 2.8 32.4 + - - +
49M VAL 3.1 5.1 + - - +
51M SER* 1.3 73.1 - - - +
53M ILE* 1.3 62.3 + - - +
55M VAL* 3.0 14.0 + - - +
56M LEU* 3.0 30.5 + - - +
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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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22M ILE* 4.4 14.1 - - + -
26M ILE* 4.7 9.0 - - + -
34M ALA* 4.2 22.4 - - + -
37M VAL* 4.9 6.5 - - + -
49M VAL* 2.9 38.1 + - + +
50M ASN* 3.8 11.9 - - - +
52M ASN* 1.3 75.7 - - - +
54M GLY* 1.3 58.0 + - - +
56M LEU* 4.3 5.6 - - - +
57M ILE* 2.8 54.5 + - + +
62M VAL* 5.2 5.6 - - + -
64M LYS* 6.1 0.2 - - + -
69M LEU* 4.5 21.3 - - + -
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Residues in contact with GLY 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 ASN 2.9 17.6 + - - -
51M SER* 3.0 7.7 + - - -
53M ILE* 1.3 77.9 - - - +
55M VAL* 1.3 50.0 + - - +
57M ILE* 4.3 5.7 - - - +
58M LYS* 2.7 36.2 + - - +
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Residues in contact with VAL 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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14M VAL 5.0 1.3 - - - +
15M LEU* 4.3 12.6 - - + -
19M THR* 5.0 6.7 - - + +
51M SER* 2.9 19.1 + - - +
52M ASN* 3.0 16.3 + - - +
54M GLY* 1.3 76.5 - - - +
56M LEU* 1.3 55.0 + - - +
58M LYS* 3.3 21.7 - - - +
59M LYS* 2.6 61.0 + - + +
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Residues in contact with LEU 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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15M LEU* 4.4 17.5 - - + -
19M THR* 3.3 31.0 - - - +
22M ILE* 4.8 3.8 - - + -
23M LEU* 3.8 26.0 - - + +
26M ILE* 4.0 15.0 - - + -
52M ASN 3.0 12.5 + - - +
53M ILE* 3.4 5.1 + - - +
55M VAL* 1.3 72.3 - - + +
57M ILE* 1.3 55.9 + - - +
59M LYS* 3.4 3.0 - - + -
60M GLY 2.7 10.7 + - - -
61M LEU* 2.7 52.5 + - + -
62M VAL* 3.5 34.2 + - + +
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Residues in contact with ILE 57 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53M ILE* 2.8 40.2 + - + +
54M GLY* 4.3 4.9 - - - +
56M LEU* 1.3 73.0 - - - +
58M LYS* 1.3 62.4 + - - +
60M GLY* 2.8 18.0 + - - +
62M VAL* 3.3 20.6 - - + +
63M GLU* 4.7 5.2 - - + -
64M LYS* 5.0 19.3 - - + -
69M LEU* 5.6 0.4 - - + -
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Residues in contact with LYS 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 GLY 2.7 23.3 + - - +
55M VAL* 3.3 25.5 - - - +
57M ILE* 1.3 78.6 - - - +
59M LYS* 1.3 91.5 + - + +
60M GLY 3.5 0.2 + - - -
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Residues in contact with LYS 59 (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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14M VAL* 3.3 48.5 + - + +
15M LEU* 3.7 16.2 - - + -
55M VAL* 2.6 30.0 + - - +
56M LEU* 3.9 4.5 - - + +
58M LYS* 1.3 99.8 - - + +
60M GLY* 1.3 61.5 + - - +
61M LEU* 3.3 26.4 + - + +
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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