Contacts of the helix formed by residues 103 - 113 (chain Z) in PDB entry 3J7Y
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 ILE 103 (chain Z).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2081A U 4.2 10.3 - - - +
101Z LYS* 3.5 17.1 + - + -
102Z ASN* 1.3 82.9 + - - +
104Z PRO* 1.3 62.3 - - + +
105Z SER* 4.4 0.7 - - - -
106Z VAL* 3.2 34.1 + - + +
107Z ASN* 2.7 40.5 + - - +
84j MET* 3.7 7.9 - - - -
53o TYR 4.9 1.3 - - - +
54o MET* 3.5 40.6 - - + -
59o GLU* 3.5 15.3 - - + +
62o HIS* 4.0 21.1 - - + +
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Residues in contact with PRO 104 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103Z ILE* 1.3 88.7 - - + +
105Z SER* 1.3 56.9 + - - +
107Z ASN* 3.7 8.2 - - + +
108Z ALA* 3.0 30.8 + - - +
111Z LYS* 5.7 0.3 - - - -
52o PRO* 4.6 12.3 - - + -
54o MET 4.9 0.2 - - - +
55o THR* 4.2 13.2 - - - +
56o ARG* 3.4 60.1 + - + +
59o GLU* 3.5 7.4 - - - +
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Residues in contact with SER 105 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2060A A 4.5 6.5 + - - -
2080A U 3.7 12.8 - - - -
2081A U 3.1 40.6 + - - -
103Z ILE* 4.4 1.6 - - - -
104Z PRO* 1.3 78.7 - - - +
106Z VAL* 1.3 64.0 + - - +
108Z ALA* 3.4 9.5 + - - +
109Z LYS* 3.7 18.6 + - - -
56o ARG* 4.2 9.5 + - - +
59o GLU* 2.8 30.6 + - - -
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Residues in contact with VAL 106 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2081A U 3.8 1.8 - - - +
2082A G 3.6 28.9 - - - -
89Z LEU* 4.6 4.3 - - + -
100Z HIS* 3.7 27.1 - - + +
101Z LYS* 3.4 28.3 - - + +
103Z ILE* 3.2 28.7 + - + +
105Z SER* 1.3 76.5 - - - +
107Z ASN* 1.3 61.5 + - - +
108Z ALA 3.4 0.2 + - - -
109Z LYS* 3.4 10.0 + - - +
110Z LEU* 3.2 33.4 + - + +
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Residues in contact with ASN 107 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67Z HIS* 3.5 16.2 + - - -
101Z LYS 4.4 0.3 - - - +
102Z ASN* 2.8 29.3 + - - +
103Z ILE 2.7 37.2 + - - +
104Z PRO* 3.9 6.5 - - + +
106Z VAL* 1.3 73.3 - - - +
108Z ALA* 1.3 58.9 + - - +
110Z LEU* 3.7 4.3 - - - +
111Z LYS* 2.9 43.4 + - - +
49o LEU* 3.8 27.8 + - + +
52o PRO* 3.9 14.8 - - - +
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Residues in contact with ALA 108 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2059A C 5.9 1.3 - - - +
2060A A 4.0 24.9 - - - +
104Z PRO 3.0 17.3 + - - +
105Z SER 3.7 6.3 - - - +
106Z VAL 3.3 0.2 - - - -
107Z ASN* 1.3 76.5 - - - +
109Z LYS* 1.3 64.7 + - + +
111Z LYS* 3.3 14.4 + - - +
112Z VAL* 3.2 24.5 + - - +
56o ARG* 5.4 1.3 - - - +
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Residues in contact with LYS 109 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2058A C 3.0 41.6 + - + +
2059A C 6.0 0.6 - - - -
2060A A 6.0 0.4 + - - -
2080A U 5.0 1.4 + - - -
2081A U 2.8 25.1 + - - -
2082A G 3.6 37.1 - - - +
85Z ILE* 3.5 29.7 - - + +
88Z MET* 4.9 6.5 - - + -
89Z LEU* 4.2 17.0 - - + -
105Z SER* 3.7 20.9 + - - -
106Z VAL* 3.4 8.0 + - - +
107Z ASN 3.3 0.4 - - - -
108Z ALA* 1.3 79.3 - - + +
110Z LEU* 1.3 64.1 - - - +
112Z VAL* 2.9 22.8 + - - +
113Z VAL 3.4 4.2 + - - -
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Residues in contact with LEU 110 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67Z HIS* 3.5 32.8 - - + +
69Z VAL* 4.1 25.6 - - + -
89Z LEU* 3.4 37.0 - - + -
100Z HIS* 4.5 2.9 - - + -
106Z VAL* 3.2 31.0 + - + +
107Z ASN* 3.7 7.2 - - - +
109Z LYS* 1.3 79.0 - - - +
111Z LYS* 1.3 61.3 + - - +
113Z VAL* 3.4 4.1 + - - -
114Z LYS* 3.0 24.1 + - - +
117Z ILE* 3.8 16.0 - - + +
119Z ILE* 4.4 4.5 - - + -
49o LEU* 3.9 11.6 - - + +
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Residues in contact with LYS 111 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41Z ILE* 4.3 10.0 - - + +
43Z GLU* 5.5 6.9 + - - +
46Z PHE* 3.5 57.9 - - + +
104Z PRO 5.7 0.4 - - - -
107Z ASN* 2.9 42.4 + - - +
108Z ALA* 3.6 11.0 - - - +
109Z LYS 3.1 0.6 - - - -
110Z LEU* 1.3 71.9 - - - +
112Z VAL* 1.3 64.4 + - - +
114Z LYS* 3.3 32.3 + - - +
49o LEU* 3.9 12.2 + - + +
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Residues in contact with VAL 112 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2059A C 4.4 17.7 - - - +
222N ASN* 5.3 3.5 + - - -
38Z ARG* 6.1 2.9 - - + -
41Z ILE* 5.7 1.6 - - - -
81Z TRP* 4.2 13.2 - - + +
82Z GLU* 4.1 19.2 - - + +
85Z ILE* 3.8 25.6 - - + -
108Z ALA 3.2 13.9 + - - +
109Z LYS* 2.9 13.4 + - - +
111Z LYS* 1.3 78.8 - - - +
113Z VAL* 1.3 56.5 + - + +
114Z LYS* 5.6 0.2 - - - -
115Z HIS* 3.3 19.4 + - - -
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Residues in contact with VAL 113 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82Z GLU* 3.6 32.5 - - + +
85Z ILE* 3.6 30.1 - - + -
86Z ILE* 4.0 21.5 - - + -
89Z LEU* 4.0 14.4 - - + -
109Z LYS 3.7 5.8 - - - +
110Z LEU 3.9 4.5 - - - +
111Z LYS 3.3 0.2 - - - -
112Z VAL* 1.3 76.9 - - + +
114Z LYS* 1.3 59.3 + - - +
115Z HIS* 3.1 8.7 - - - -
116Z LEU* 2.8 30.6 + - + -
117Z ILE* 3.4 19.0 + - + +
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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