Contacts of the helix formed by residues 66 - 75 (chain A) in PDB entry 1JUL
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 PRO 66 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52A TYR* 3.5 30.1 - - + +
64A ARG 3.2 7.4 - - - +
65A ASP* 1.3 91.8 - - - +
67A ILE* 1.3 67.0 + - + +
69A TYR* 3.7 1.9 - - - +
70A SER* 2.9 34.2 + - - -
95A THR* 3.9 24.2 - - + +
98A LYS* 6.3 1.3 - - + -
99A ILE* 3.9 10.2 - - + +
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Residues in contact with ILE 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A ASP* 3.1 10.0 + - - +
66A PRO* 1.3 81.1 - - + +
68A GLU* 1.3 68.4 + - - +
70A SER* 3.2 3.7 + - - -
71A LYS* 2.8 59.4 + - + +
98A LYS* 3.9 30.1 - - + +
99A ILE* 4.0 11.4 - - + +
102A SER* 3.8 24.5 - - - +
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Residues in contact with GLU 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A ARG* 6.3 0.4 - - + -
65A ASP* 2.9 30.7 + - + +
67A ILE* 1.3 87.1 - - - +
69A TYR* 1.3 62.2 + - - +
71A LYS* 3.9 15.5 + - - +
72A PHE* 3.0 25.0 + - - +
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Residues in contact with TYR 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A ALA* 4.0 2.7 - - + +
51A GLU 2.9 28.7 + - - -
52A TYR* 3.7 37.9 - + + -
64A ARG* 3.4 26.8 - - + +
65A ASP 3.1 18.6 + - - +
66A PRO 3.7 3.1 - - - +
68A GLU* 1.3 76.9 - - - +
70A SER* 1.3 64.9 + - - +
72A PHE* 3.5 4.5 - - - +
73A MET* 3.0 59.6 + - + +
80A LEU* 4.4 8.5 - - + -
236A LEU* 3.6 41.6 - - - +
237A MET* 4.0 9.4 + - - -
240A PRO* 4.1 7.9 - - + -
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Residues in contact with SER 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A PRO 2.9 21.6 + - - -
67A ILE* 3.8 5.2 - - - -
69A TYR* 1.3 83.0 - - - +
71A LYS* 1.3 57.6 + - - +
73A MET* 3.4 3.4 + - - +
74A GLU* 2.9 28.1 + - - +
80A LEU* 3.6 26.3 - - - +
82A ILE* 4.6 1.0 - - - +
99A ILE* 3.4 33.6 - - - +
102A SER* 6.0 0.4 - - - -
103A VAL* 3.6 11.9 - - - +
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Residues in contact with LYS 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A ILE* 2.8 42.6 + - + +
68A GLU* 4.0 17.6 + - - +
70A SER* 1.3 70.7 - - - +
72A PHE* 1.3 65.4 + - - +
74A GLU* 3.6 19.5 + - - +
75A ARG* 3.8 17.4 + - - +
102A SER* 4.5 17.3 - - - +
103A VAL* 4.1 15.7 - - + -
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Residues in contact with PHE 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A GLU 3.0 18.4 + - - +
69A TYR* 3.5 5.8 - - - +
71A LYS* 1.3 76.7 - - - +
73A MET* 1.3 77.2 + - + +
75A ARG* 3.2 18.6 + - - +
76A TYR* 3.4 39.8 - + - -
240A PRO* 3.5 30.5 - - + -
241A GLU* 3.9 22.2 - - + -
243A ILE* 3.9 14.1 - - + -
244A LYS* 4.3 15.3 - - - -
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Residues in contact with MET 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A ALA* 3.7 20.2 - - + -
69A TYR* 3.0 56.4 + - + +
70A SER 3.9 1.3 - - - +
72A PHE* 1.3 82.5 - - + +
74A GLU* 1.3 62.1 + - - +
75A ARG 3.0 2.6 + - - -
76A TYR* 3.8 1.6 - - - +
77A ALA* 2.8 37.7 + - + +
80A LEU* 3.9 19.1 - - + -
105A ILE* 4.1 1.5 - - - +
236A LEU* 4.1 14.8 - - + -
240A PRO* 3.8 28.3 - - + +
243A ILE* 3.8 22.2 - - + -
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Residues in contact with GLU 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A ARG* 5.4 2.6 + - - -
70A SER 2.9 16.9 + - - +
71A LYS* 3.6 16.5 - - - +
72A PHE 3.2 0.6 - - - -
73A MET* 1.3 76.9 - - - +
75A ARG* 1.3 62.5 + - + +
76A TYR 3.7 0.3 + - - -
77A ALA 4.5 2.8 - - - +
102A SER 4.6 3.5 - - - +
103A VAL* 3.5 17.3 - - + +
104A SER* 2.8 35.0 + - - -
105A ILE* 3.7 34.0 - - + +
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Residues in contact with ARG 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A LYS* 3.8 17.0 + - - +
72A PHE* 3.2 12.7 + - - +
73A MET 3.0 0.8 - - - -
74A GLU* 1.3 83.8 + - + +
76A TYR* 1.3 81.5 + - + +
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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