Contacts of the helix formed by residues 54 - 60 (chain M) in PDB entry 1UW9
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 54 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52M VAL* 5.9 0.3 - - - +
53M SER* 1.3 81.9 - - - +
55M GLU* 1.3 65.4 + - - +
56M SER 3.3 2.5 - - - -
57M ALA* 3.0 21.4 + - + +
67M TYR* 5.7 1.6 - - - -
68M TYR* 4.0 7.7 - - - +
69M ASP* 3.5 3.1 - - - -
55P GLU 5.3 2.4 + - - -
56P SER* 5.4 4.6 + - - +
58P ILE* 3.7 25.2 - - + +
59P ARG* 2.8 49.6 + - + +
226R TYR* 5.8 2.6 - - - -
229R GLN* 4.9 4.6 + - - +
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Residues in contact with GLU 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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49M LYS* 4.5 5.5 + - - -
53M SER* 2.4 33.1 + - - -
54M ASN* 1.3 71.0 - - - +
56M SER* 1.3 63.4 + - - +
57M ALA 3.3 1.0 + - - -
58M ILE* 3.3 24.1 + - - +
69M ASP* 3.2 14.0 + - - +
70M ASN* 4.6 3.5 + - - +
1141M EDO 3.0 31.9 + - - +
58P ILE* 3.9 9.1 - - - +
54T ASN* 5.6 1.0 + - - -
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Residues in contact with SER 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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55M GLU* 1.3 72.3 - - - +
57M ALA* 1.3 55.9 + - - +
58M ILE* 3.0 7.2 - - - -
59M ARG* 2.9 32.0 + - - +
60M PHE* 3.8 7.7 - - - -
67M TYR* 3.4 18.0 + - - -
69M ASP* 2.7 32.2 + - - -
1141M EDO 4.2 6.8 + - - -
226O TYR* 3.6 29.6 - - - +
54T ASN* 5.6 3.6 - - - +
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Residues in contact with ALA 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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54M ASN* 3.0 19.8 + - + +
56M SER* 1.3 74.4 - - - +
58M ILE* 1.3 63.5 + - - +
59M ARG 3.1 0.4 - - - -
60M PHE* 3.0 44.7 + - + +
64M SER* 4.3 13.0 - - - -
67M TYR* 4.8 3.9 - - + -
58P ILE* 3.7 29.2 - - + +
59P ARG* 4.7 4.0 - - + +
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Residues in contact with ILE 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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55M GLU 3.3 19.7 + - - +
56M SER 3.0 0.8 - - - +
57M ALA* 1.3 77.7 - - - +
59M ARG* 1.3 74.0 + - + +
60M PHE 3.3 3.8 + - - +
58P ILE* 3.8 21.1 - - + +
54T ASN* 4.0 29.2 - - + +
55T GLU* 4.1 7.9 - - - +
57T ALA* 3.8 16.1 - - + +
58T ILE* 3.7 45.3 - - + +
64T SER* 5.4 0.2 - - - -
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Residues in contact with ARG 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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56M SER* 2.9 14.2 + - - +
58M ILE* 1.3 89.4 - - + +
60M PHE* 1.3 58.9 + - - +
226O TYR* 3.0 44.8 + - - +
258O LYS 5.1 0.5 - - - +
259O GLU 3.9 1.2 - - - +
260O LEU 4.3 2.2 - - - +
261O GLY* 3.0 27.5 + - - -
54T ASN* 2.9 40.3 + - + +
57T ALA* 4.8 5.2 - - + +
62T SER* 5.7 3.1 - - - -
64T SER* 2.8 62.8 + - - +
66T LEU 4.0 1.6 - - - +
67T TYR* 2.9 23.2 + - - -
68T TYR* 3.7 20.4 + - - -
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Residues in contact with PHE 60 (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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56M SER 3.8 12.1 - - - -
57M ALA* 3.0 32.4 + - + +
58M ILE 3.3 3.0 - - - +
59M ARG* 1.3 85.7 - - - +
61M GLY* 1.3 70.7 + - - +
63M VAL* 4.0 6.5 - - + -
64M SER* 4.0 17.9 - - - +
67M TYR* 3.6 57.7 - + + -
222O THR* 4.2 1.8 - - + -
226O TYR* 4.1 9.9 - + - -
259O GLU 3.1 5.6 - - - +
260O LEU* 3.4 42.2 - - + -
61T GLY 5.1 5.5 - - - +
62T SER* 5.3 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