Contacts of the helix formed by residues 47 - 55 (chain M) in PDB entry 5IYB
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 ASP 47 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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67A ARG* 5.4 1.6 + - - +
267A GLN* 4.1 18.9 + - - +
841B ARG* 5.8 2.7 + - - -
45M VAL* 3.4 11.7 + - - +
46M ILE* 1.3 74.6 - - - +
48M VAL* 1.3 50.4 - - - +
49M GLY* 1.6 39.2 + - - -
50M SER* 2.7 17.4 + - - +
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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
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65A ILE* 4.8 10.3 - - + -
78A MET* 4.9 2.2 - - + -
265A VAL* 4.1 25.3 - - + +
266A MET* 5.0 2.1 - - - -
1069B ILE* 3.4 33.9 - - + -
1070B LEU* 5.4 0.9 - - - +
44M ARG 4.8 0.2 - - - +
45M VAL* 3.7 31.2 - - + -
46M ILE 2.9 8.5 - - - +
47M ASP* 1.3 72.6 - - - +
49M GLY* 1.3 60.7 + - - +
50M SER 3.1 4.0 - - - -
51M GLU* 3.2 46.4 + - - +
52M TRP 4.6 1.0 + - - -
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Residues in contact with GLY 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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265A VAL* 4.7 2.2 - - - +
266A MET* 3.9 6.7 - - - -
267A GLN* 3.1 55.4 + - - +
47M ASP* 1.6 21.7 + - - -
48M VAL* 1.3 70.8 - - - +
50M SER* 1.3 57.0 + - - -
51M GLU 3.4 0.4 + - - -
52M TRP* 4.2 6.1 + - - +
53M ARG* 4.2 6.4 - - - +
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Residues in contact with SER 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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267A GLN* 4.1 6.6 + - - -
1075B MET* 3.9 11.2 - - - +
1080B ARG* 3.5 31.0 + - - +
27M TYR* 6.2 0.5 - - - -
46M ILE* 3.6 22.0 + - - -
47M ASP* 2.7 18.2 + - - +
48M VAL 3.1 0.2 - - - -
49M GLY* 1.3 72.3 - - - +
51M GLU* 1.3 62.9 + - - +
52M TRP 3.6 0.2 - - - -
53M ARG* 3.3 9.2 + - - +
54M THR 3.3 16.1 + - - -
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Residues in contact with GLU 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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1067B ILE 3.1 11.2 - - - +
1068B GLN* 3.2 24.1 - - + +
1069B ILE* 2.6 37.7 + - - +
1070B LEU* 3.0 32.4 + - + +
1075B MET* 4.2 13.7 - - - -
46M ILE* 4.5 4.2 - - + +
48M VAL* 3.2 38.3 + - - +
50M SER* 1.3 74.3 - - - +
52M TRP* 1.3 66.2 + - - +
54M THR* 3.1 23.4 - - - +
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Residues in contact with TRP 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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266A MET* 4.2 28.9 - - + +
267A GLN* 6.4 0.2 - - + -
1070B LEU* 4.2 12.4 - - + +
48M VAL 4.6 1.2 + - - -
49M GLY 4.2 3.7 + - - +
50M SER 3.6 0.4 - - - -
51M GLU* 1.3 77.5 - - - +
53M ARG* 1.3 83.3 + - + +
54M THR 3.1 3.6 + - - -
55M PHE* 3.0 51.0 - + - -
63M ASP* 3.1 28.9 - - - -
65M SER 3.2 20.7 + - - -
66M ARG* 3.5 24.7 - - + -
67M VAL* 3.3 33.7 - - + +
68M GLY 5.7 0.4 - - - -
58Y C 5.7 8.3 - - - -
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Residues in contact with ARG 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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266A MET 6.1 0.2 - - - -
267A GLN* 3.4 40.3 - - + +
268A GLY* 5.2 1.6 - - - +
1080B ARG* 3.6 28.0 + - - +
49M GLY 4.2 7.8 + - - +
50M SER* 3.3 14.5 + - - +
52M TRP* 1.3 96.9 - - + +
54M THR* 1.3 61.0 + - - +
55M PHE* 3.4 8.1 + - - +
56M SER* 4.6 3.6 + - - -
57Y A 5.2 7.0 + - - +
58Y C 5.9 8.6 - - - -
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Residues in contact with THR 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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1068B GLN* 3.4 14.7 + - - +
1075B MET* 3.3 28.5 - - - +
1076B GLU* 3.0 50.6 + - + +
1079B SER* 4.9 6.6 + - - -
1080B ARG* 4.4 6.6 + - - +
50M SER 3.3 4.2 + - - -
51M GLU 3.1 22.2 - - - +
52M TRP 3.1 5.0 - - - +
53M ARG* 1.3 79.7 - - - +
55M PHE* 1.3 70.7 + - + +
56M SER* 3.9 4.7 + - - -
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Residues in contact with PHE 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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1076B GLU* 4.5 10.1 - - + +
52M TRP* 3.0 59.9 - + - -
53M ARG* 4.0 6.1 - - - +
54M THR* 1.3 87.0 - - + +
56M SER* 1.3 74.1 + - - +
57M ASN* 5.2 2.2 - - - +
58M ASP* 5.4 11.2 - - + -
59M LYS 5.4 3.8 - - - -
60M ALA* 4.9 12.6 - - + -
63M ASP* 3.1 29.6 - - - -
64M PRO* 6.3 0.2 - - + -
65M SER* 3.7 26.5 - - - -
56Y G 4.2 3.5 - - - +
57Y A 4.3 4.0 + - - -
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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