Contacts of the helix formed by residues 114 - 128 (chain C) in PDB entry 4I6J
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 GLY 114 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61C TRP* 5.4 5.5 - - - -
112C ILE* 2.5 9.4 + - - +
113C LYS* 1.3 76.6 - - - +
115C LEU* 1.3 64.5 + - - +
116C LEU 3.5 0.9 - - - -
117C ASP* 3.4 5.0 - - - +
118C VAL* 2.8 34.2 + - - +
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Residues in contact with LEU 115 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54C ILE* 5.3 1.1 - - + +
57C LYS* 3.5 8.1 - - + -
58C VAL* 3.3 36.6 - - + +
61C TRP* 3.1 63.0 - - + -
62C CYS* 4.7 4.9 - - - -
92C PHE* 5.2 1.8 - - + -
107C ALA* 4.1 5.8 - - - +
112C ILE* 2.3 53.7 - - + +
114C GLY* 1.3 69.0 - - - -
116C LEU* 1.3 57.3 + - - +
118C VAL* 4.0 6.9 - - + +
119C THR* 3.1 27.4 + - - +
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Residues in contact with LEU 116 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B ILE* 3.7 27.6 - - + -
46B GLN* 3.9 21.8 - - + -
104C ILE* 4.1 6.3 - - + +
107C ALA* 3.5 33.0 - - + +
108C ASN* 4.6 7.4 - - + +
112C ILE* 2.8 16.2 + - - +
113C LYS* 6.3 0.4 - - - -
115C LEU* 1.3 74.6 - - - +
117C ASP* 1.3 72.7 + - + +
118C VAL 3.1 1.3 - - - -
119C THR* 3.0 10.5 + - - +
120C CYS* 2.9 44.1 + - - -
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Residues in contact with ASP 117 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B GLN* 5.7 4.3 - - - +
50B TYR* 1.9 35.1 + - - -
112C ILE 3.5 2.0 + - - -
113C LYS* 3.0 32.4 - - + +
114C GLY* 3.4 7.6 - - - +
116C LEU* 1.3 88.1 - - + +
118C VAL* 1.3 60.6 + - - +
120C CYS* 3.4 5.1 - - - +
121C LYS* 2.7 37.4 + - - +
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Residues in contact with VAL 118 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61C TRP* 4.3 18.4 - - + -
85C ILE* 4.8 15.9 - - + -
86C PRO* 5.1 7.9 - - + -
89C ASP* 3.9 17.7 - - + +
92C PHE* 6.3 0.2 - - + -
93C LEU* 4.0 17.5 - - + -
114C GLY 2.8 22.3 + - - +
115C LEU* 4.0 11.0 - - - +
117C ASP* 1.3 80.0 + - - +
119C THR* 1.3 72.3 + - + +
120C CYS 3.1 1.3 - - - -
121C LYS* 3.6 12.7 - - + +
122C THR* 3.1 25.3 + - - -
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Residues in contact with THR 119 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92C PHE* 6.2 0.9 - - + -
93C LEU* 4.1 24.0 - - + -
100C LEU* 4.3 6.1 - - + +
103C LEU* 4.3 21.1 - - + +
104C ILE* 2.9 32.9 - - + +
115C LEU 3.1 18.1 + - - +
116C LEU* 3.0 17.7 + - - +
118C VAL* 1.3 84.9 - - + +
120C CYS* 1.3 59.3 + - - +
122C THR* 3.2 18.7 - - - +
123C VAL* 3.3 15.2 + - - +
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Residues in contact with CYS 120 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B ILE* 4.3 4.9 - - - -
46B GLN* 3.5 28.5 - - + -
47B VAL* 3.9 29.9 - - + +
50B TYR* 4.1 8.7 - - + -
104C ILE* 4.5 7.9 - - - -
116C LEU* 2.9 39.5 + - - +
117C ASP* 3.4 5.8 - - - +
119C THR* 1.3 74.4 + - - +
121C LYS* 1.3 56.2 + - - +
122C THR 2.6 16.0 + - - -
123C VAL* 3.0 3.6 + - - +
124C ALA* 2.9 22.5 + - - +
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Residues in contact with LYS 121 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B TYR* 3.5 40.5 - - + +
85C ILE* 3.3 61.1 - - + +
86C PRO* 5.0 3.2 - - + +
117C ASP* 2.7 27.2 + - - +
118C VAL* 3.3 13.9 + - + +
120C CYS* 1.3 71.8 - - - +
122C THR* 1.3 62.7 + - - +
124C ALA* 3.5 3.3 - - - +
125C ASN* 3.3 25.8 + - - +
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Residues in contact with THR 122 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85C ILE* 6.1 0.5 - - - +
93C LEU* 3.4 23.4 - - + +
100C LEU* 4.3 12.6 - - + -
118C VAL 3.1 12.6 + - - -
119C THR* 3.2 13.2 - - - +
120C CYS 2.6 4.6 + - - -
121C LYS* 1.3 69.5 - - - +
123C VAL* 1.3 56.6 + - - +
124C ALA 2.5 5.1 + - - -
125C ASN* 2.5 40.0 + - + +
126C MET* 3.2 30.7 + - + -
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Residues in contact with VAL 123 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B TRP* 3.9 25.4 - - + -
47B VAL* 4.0 17.3 - - + -
66B TRP* 5.1 5.8 - - + -
100C LEU* 4.1 11.0 - - + -
104C ILE* 3.9 18.8 - - + -
119C THR 3.3 12.5 + - - +
120C CYS 3.0 8.1 + - - +
122C THR* 1.3 78.5 - - - +
124C ALA* 1.3 62.2 + - - +
126C MET* 3.1 20.2 + - - +
127C ILE* 3.1 29.4 + - + +
139C PHE* 4.0 16.6 - - + -
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Residues in contact with ALA 124 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B VAL* 4.1 10.7 - - + +
50B TYR* 3.6 21.3 - - + -
51B LEU* 3.5 24.8 - - + +
120C CYS 2.9 10.2 + - - +
121C LYS 3.5 11.9 - - - +
122C THR 2.5 4.0 + - - -
123C VAL* 1.3 70.8 - - - +
125C ASN* 1.3 58.3 + - - +
127C ILE* 2.6 25.4 + - - +
128C LYS* 2.9 20.8 + - - +
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Residues in contact with ASN 125 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85C ILE* 4.0 24.3 - - - +
121C LYS* 3.3 17.1 + - - +
122C THR* 2.5 18.1 + - + +
124C ALA* 1.3 73.7 - - - +
126C MET* 1.3 61.9 + - + +
127C ILE 3.4 0.2 + - - -
128C LYS* 2.7 47.8 + - + +
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Residues in contact with MET 126 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97C GLN* 6.0 5.8 - - + -
100C LEU* 4.0 24.7 - - + -
122C THR* 3.2 19.0 + - + +
123C VAL* 3.1 16.3 + - - +
124C ALA 2.9 1.0 + - - -
125C ASN* 1.3 78.5 - - + +
127C ILE* 1.3 60.9 + - - +
128C LYS 4.8 1.2 - - - +
130C LYS* 3.4 28.5 + - - +
138C THR 5.6 0.9 - - - +
139C PHE* 4.0 31.2 - - + -
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Residues in contact with ILE 127 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B VAL* 3.9 23.3 - - + -
48B PHE* 5.9 0.2 - - + -
51B LEU* 3.6 26.5 - - + -
55B ASP* 4.5 10.2 - - + +
59B ALA* 4.5 2.0 - - + -
66B TRP* 3.9 25.8 - - + -
123C VAL* 3.1 21.5 + - + +
124C ALA 2.6 12.0 + - - +
126C MET* 1.3 72.3 - - - +
128C LYS* 1.3 68.2 + - - +
129C GLY 2.9 4.2 + - - -
130C LYS* 2.9 23.0 + - - +
135C ILE* 4.1 24.4 - - + +
139C PHE* 4.0 17.3 - - + -
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Residues in contact with LYS 128 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B TYR* 4.1 16.2 + - - +
51B LEU* 4.5 4.9 - - + -
52B PRO* 5.0 7.4 - - + -
55B ASP* 3.1 21.8 - - - +
124C ALA* 2.9 19.3 + - - +
125C ASN* 2.7 57.4 + - + +
126C MET 3.6 1.4 - - - +
127C ILE* 1.3 75.3 - - - +
129C GLY* 1.3 56.7 + - - +
130C LYS* 4.0 0.9 + - - +
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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