Contacts of the helix formed by residues 67 - 77 (chain M) in PDB entry 4XLR
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 GLU 67 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63M LEU* 3.3 29.7 - - + +
64M ALA* 3.1 26.7 + - + +
66M GLU* 1.3 85.1 - - + +
68M VAL* 1.3 64.9 + - - +
69M PRO* 3.5 1.1 - - - -
70M VAL* 3.2 26.0 - - + +
71M ILE* 3.7 9.0 - - - +
103M TYR* 2.4 29.9 + - - +
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Residues in contact with VAL 68 (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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63M LEU* 5.8 2.9 - - + -
64M ALA 4.2 1.8 - - - +
65M PRO 3.3 22.0 - - - +
67M GLU* 1.3 76.9 - - - +
69M PRO* 1.4 72.2 - - + +
71M ILE* 3.0 17.0 + - - +
72M LEU* 3.0 43.8 + - + +
140M VAL* 4.3 13.9 - - + -
143M SER* 4.0 10.3 - - - +
144M LEU* 3.5 39.9 - - + -
154M LEU* 5.0 1.3 - - + -
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Residues in contact with PRO 69 (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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65M PRO 4.8 1.3 - - - +
66M GLU* 3.2 20.2 - - - +
67M GLU 3.6 0.9 - - - -
68M VAL* 1.4 95.2 - - + +
70M VAL* 1.3 60.9 + - + +
72M LEU* 3.9 13.0 - - + +
73M ASP* 2.9 31.5 + - - +
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Residues in contact with VAL 70 (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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66M GLU 5.0 1.3 - - - +
67M GLU* 3.2 24.9 - - + +
69M PRO* 1.3 82.7 - - + +
71M ILE* 1.3 62.5 + - + +
73M ASP* 3.6 6.1 - - - +
74M LEU* 2.9 32.3 + - + +
103M TYR* 3.3 36.6 - - + +
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Residues in contact with ILE 71 (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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63M LEU* 3.7 21.3 - - + -
67M GLU 3.7 14.4 - - - +
68M VAL* 3.0 9.0 + - - +
70M VAL* 1.3 79.7 - - + +
72M LEU* 1.3 61.6 + - + +
73M ASP 3.1 1.1 - - - -
74M LEU* 2.9 19.7 + - + +
75M LEU* 2.9 14.1 + - + +
102M PRO* 3.7 9.6 - - + +
103M TYR* 3.6 45.8 - - + +
106M ALA* 3.6 16.1 - - + +
136M LEU* 3.8 20.2 - - + -
140M VAL* 5.0 7.6 - - + -
155M PHE* 5.0 9.4 - - + -
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Residues in contact with LEU 72 (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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68M VAL* 3.0 40.8 + - + +
69M PRO* 3.9 11.2 - - + +
71M ILE* 1.3 77.6 - - + +
73M ASP* 1.3 55.8 + - - +
75M LEU* 3.2 8.2 + - - +
76M LYS* 2.9 29.3 + - - +
140M VAL* 5.2 0.2 - - + -
154M LEU* 4.3 24.5 - - + +
155M PHE* 3.5 37.0 - - + -
157M GLU* 3.9 22.7 - - - +
158M ALA* 4.1 7.8 - - + +
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Residues in contact with ASP 73 (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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69M PRO 2.9 19.3 + - - +
70M VAL* 3.6 7.2 - - - +
72M LEU* 1.3 73.3 - - - +
74M LEU* 1.3 64.2 + - - +
75M LEU 3.0 5.6 + - - -
76M LYS* 4.5 4.3 - - - +
77M ASN* 3.4 23.7 + - - +
78M GLY* 3.4 14.7 + - - -
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Residues in contact with LEU 74 (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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70M VAL* 2.9 20.7 + - + +
71M ILE* 2.9 15.0 + - + +
73M ASP* 1.3 80.7 - - - +
75M LEU* 1.3 57.4 - - - +
78M GLY* 3.2 24.7 - - - -
103M TYR* 3.5 53.2 - - + +
106M ALA* 3.2 23.5 - - + +
107M GLN* 3.8 22.3 - - + +
110M GLY* 3.9 0.5 - - - -
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Residues in contact with LEU 75 (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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71M ILE* 2.9 12.2 + - + +
72M LEU* 3.3 11.0 - - - +
73M ASP 3.0 0.2 - - - -
74M LEU* 1.3 79.1 - - - +
76M LYS* 1.3 68.6 + - - +
77M ASN 3.5 0.3 + - - -
78M GLY 3.6 5.4 + - - +
106M ALA* 3.6 17.7 - - + +
109M ALA* 3.8 20.0 - - + -
110M GLY* 3.8 17.6 - - - +
113M ARG* 5.6 0.3 - - - +
133M ILE* 4.3 2.9 - - + -
136M LEU* 3.7 21.8 - - + -
155M PHE* 3.4 43.1 - - + -
158M ALA* 4.7 3.8 - - + -
159M TRP* 3.6 35.4 + - + +
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Residues in contact with LYS 76 (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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72M LEU 2.9 18.8 + - - +
73M ASP* 3.8 2.7 + - - +
75M LEU* 1.3 76.4 - - - +
77M ASN* 1.3 82.9 + - - +
78M GLY 5.2 0.2 - - - +
79M ARG* 5.3 4.5 + - - -
157M GLU* 5.4 3.1 - - - +
158M ALA* 3.2 34.5 - - + +
159M TRP* 3.7 18.0 + - + +
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Residues in contact with ASN 77 (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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73M ASP* 3.4 24.5 + - - +
76M LYS* 1.3 107.0 + - - +
78M GLY* 1.3 63.3 + - - +
79M ARG* 3.6 22.7 + - - +
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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