Contacts of the helix formed by residues 111 - 125 (chain C) in PDB entry 5JLH
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 111 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74C ILE* 3.5 24.9 - - + -
106C GLU* 4.1 3.5 - - - +
109C LEU 3.8 4.9 - - - +
110C ASN* 1.3 102.6 - - - +
112C LYS* 1.3 66.3 + - - +
113C ALA* 3.2 9.4 - - + +
114C ASN* 3.3 18.1 + - - +
115C ARG* 3.8 3.5 + - - -
176C ARG* 3.9 5.4 - - - +
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Residues in contact with LYS 112 (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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110C ASN 3.5 3.1 + - - +
111C PRO* 1.3 72.9 - - - +
113C ALA* 1.3 63.7 + - - +
115C ARG* 2.8 17.2 + - - +
116C GLU* 2.9 29.0 + - - +
370C HIS* 3.1 55.9 + - + +
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Residues in contact with ALA 113 (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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78C TRP* 5.1 1.1 - - + -
111C PRO* 3.2 7.8 - - + -
112C LYS* 1.3 79.6 - - - +
114C ASN* 1.3 55.4 + - - +
116C GLU* 3.8 9.6 - - - -
117C LYS* 2.7 39.9 + - + +
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Residues in contact with ASN 114 (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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73C GLY 3.6 3.9 + - - +
74C ILE* 3.3 35.2 - - - +
75C VAL* 3.5 32.5 + - - +
78C TRP* 3.8 10.9 - - + -
106C GLU* 4.3 6.5 - - + +
110C ASN* 2.7 26.2 + - - +
111C PRO* 3.3 11.5 + - - +
112C LYS 3.1 0.8 - - - -
113C ALA* 1.3 77.9 - - - +
115C ARG* 1.3 60.8 + - - +
118C MET* 2.8 42.8 + - + +
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Residues in contact with ARG 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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106C GLU* 3.1 43.5 + - + +
107C ALA 4.1 2.0 + - - -
108C PRO* 4.9 1.8 - - - +
109C LEU 5.2 2.0 - - - +
110C ASN* 3.9 17.4 + - - +
111C PRO 3.8 2.0 + - - -
112C LYS 2.8 8.6 + - - +
114C ASN* 1.3 77.4 - - - +
116C GLU* 1.3 64.5 + - - +
118C MET* 3.2 8.8 + - - +
119C THR* 3.0 27.4 + - - +
133C VAL* 4.1 19.2 + - + +
134C ALA 6.1 1.2 - - - -
135C ILE* 3.6 24.4 - - - +
369C VAL* 3.7 27.1 - - + -
370C HIS* 3.9 27.0 + - + +
373C CYS* 5.0 0.9 - - - -
374C PHE* 3.7 29.7 + - - -
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Residues in contact with GLU 116 (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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112C LYS* 2.9 32.2 + - - +
113C ALA* 3.8 7.0 + - - +
115C ARG* 1.3 76.6 - - - +
117C LYS* 1.3 58.2 + - - +
119C THR* 2.4 27.6 + - - -
120C GLN* 2.9 14.5 + - - +
366C PRO* 3.8 24.8 - - + +
367C SER* 4.2 14.9 - - - -
369C VAL* 4.2 4.5 - - + -
370C HIS* 3.2 35.1 + - + +
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Residues in contact with LYS 117 (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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78C TRP* 3.4 46.2 - - + +
113C ALA* 2.7 24.7 + - + +
116C GLU* 1.3 74.9 - - - +
118C MET* 1.3 62.3 + - - +
120C GLN* 3.1 40.9 + - - +
121C ILE* 2.9 38.3 + - - +
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Residues in contact with MET 118 (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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11C ASN* 5.9 7.2 - - + +
75C VAL* 5.0 16.6 - - + -
78C TRP* 3.8 12.0 - - + -
81C MET* 6.4 0.4 - - - -
85C TRP* 3.8 20.5 - - + -
104C LEU* 3.3 43.1 - - + -
105C THR 4.3 10.1 - - - +
106C GLU* 4.6 19.7 - - + -
114C ASN* 2.8 29.5 + - + +
115C ARG* 3.3 7.2 - - - +
117C LYS* 1.3 73.9 - - - +
119C THR* 1.3 62.1 + - - +
121C ILE* 3.2 6.9 + - - +
122C MET* 3.0 23.0 + - - +
133C VAL* 4.2 11.4 - - + -
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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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115C ARG 3.0 10.3 + - - +
116C GLU* 2.4 24.3 + - - -
118C MET* 1.3 70.4 - - - +
120C GLN* 1.3 65.5 + - - +
122C MET* 3.1 1.4 + - - -
123C PHE* 3.0 37.4 + - + -
131C MET* 3.4 35.9 - - + -
133C VAL* 4.4 3.6 - - + -
356C ILE* 4.8 6.1 - - + -
361C TYR* 5.3 0.9 - - - -
366C PRO* 3.9 9.4 + - - +
369C VAL* 3.2 37.2 - - + +
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Residues in contact with GLN 120 (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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116C GLU 2.9 7.6 + - - +
117C LYS* 3.1 44.9 + - + +
119C THR* 1.3 83.6 + - - +
121C ILE* 1.3 56.6 + - + +
123C PHE* 3.9 0.3 - - - -
124C GLU* 2.8 50.6 + - + +
361C TYR* 4.1 16.6 - - - +
366C PRO* 4.7 16.5 - - + +
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Residues in contact with ILE 121 (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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78C TRP* 3.4 49.4 - - + +
82C GLU* 4.8 10.3 - - + +
85C TRP* 3.7 28.5 - - + -
117C LYS* 2.9 27.1 + - - +
118C MET 3.2 8.0 + - - +
120C GLN* 1.3 74.0 - - + +
122C MET* 1.3 62.5 + - - +
124C GLU 4.9 0.2 - - - -
125C THR* 2.7 55.1 + - + +
126C PHE* 4.6 4.3 - - + -
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Residues in contact with MET 122 (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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9C ILE* 5.1 0.4 - - + -
85C TRP* 3.9 28.9 - - + -
89C PHE* 4.2 20.4 - - + -
97C PRO* 6.3 0.7 - - - -
102C VAL* 3.9 21.3 - - + -
104C LEU* 3.8 42.8 - - + -
118C MET 3.0 11.7 + - - +
119C THR 3.1 1.1 + - - +
121C ILE* 1.3 77.3 - - - +
123C PHE* 1.3 56.0 + - - +
126C PHE* 2.5 48.1 - - + +
128C THR* 3.1 15.0 - - + +
131C MET* 3.7 26.0 - - + -
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Residues in contact with PHE 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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119C THR* 3.0 27.1 + - - +
122C MET* 1.3 79.4 - - - +
124C GLU* 1.3 60.9 + - - +
125C THR 3.6 1.0 + - - -
127C ASN* 3.7 25.5 - - - +
128C THR* 3.8 21.5 - - + -
130C ALA* 4.4 0.4 - - - -
131C MET* 3.5 40.4 - - + -
356C ILE* 4.0 23.3 - - + -
357C SER 4.3 1.1 - - - -
358C LYS* 3.6 36.6 - - + +
361C TYR* 3.2 59.7 - + + -
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Residues in contact with GLU 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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120C GLN* 2.8 38.8 + - + +
121C ILE 3.5 0.4 - - - -
123C PHE* 1.3 75.0 - - - +
125C THR* 1.3 63.7 + - - +
358C LYS* 6.0 1.6 - - - +
361C TYR* 3.5 31.9 + - + +
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Residues in contact with THR 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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82C GLU* 3.8 24.3 - - + +
121C ILE* 2.7 40.6 + - - +
124C GLU* 1.3 78.0 + - - +
126C PHE* 1.3 85.4 + - + +
127C ASN* 3.5 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