Contacts of the helix formed by residues 104 - 116 (chain C) in PDB entry 4I6N
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 LEU 104 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23C PHE 4.0 1.0 - - - +
24C GLY 3.6 0.9 - - - -
25C CYS* 3.4 26.9 + - - +
94C LEU* 3.6 36.1 - - + +
95C LEU* 3.6 30.7 - - + -
97C CYS* 5.9 3.1 - - + +
102C VAL* 4.1 7.5 + - + +
103C ASP* 1.3 71.9 - - - +
105C GLY* 1.3 67.0 + - - +
108C LEU* 3.6 32.9 - - + +
109C LYS* 4.1 30.3 - - + +
112C LYS* 4.3 10.5 - - + +
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Residues in contact with GLY 105 (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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23C PHE 5.0 0.2 - - - -
24C GLY 3.3 13.9 - - - -
103C ASP* 3.4 6.3 + - - +
104C LEU* 1.3 77.4 - - - +
106C PRO* 1.3 70.6 - - - +
107C THR 3.5 1.3 - - - -
109C LYS* 2.9 31.4 + - - +
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Residues in contact with PRO 106 (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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23C PHE 4.8 0.2 - - - +
24C GLY* 4.5 12.8 - - - +
105C GLY* 1.3 82.6 - - - +
107C THR* 1.3 73.0 + - - +
109C LYS* 4.6 3.1 - - + +
110C GLU* 3.2 25.8 + - - +
132C LYS* 5.5 2.0 + - - +
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Residues in contact with THR 107 (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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23C PHE* 3.9 16.6 + - + -
106C PRO* 1.3 85.0 - - - +
108C LEU* 1.3 58.8 + - + +
110C GLU* 3.7 6.4 - - - +
111C PHE* 3.0 28.2 + - + +
130C SER* 4.8 2.7 - - - +
132C LYS* 3.5 55.4 + - + +
133C ILE* 4.5 17.9 - - + -
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Residues in contact with LEU 108 (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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23C PHE* 3.6 36.5 + - + +
25C CYS* 4.3 2.2 - - + -
91C ILE* 4.0 28.9 - - + -
94C LEU* 3.8 27.1 - - + -
95C LEU* 4.1 14.8 - - + +
104C LEU* 3.6 34.3 - - + +
105C GLY 3.7 1.2 + - - -
107C THR* 1.3 78.9 - - + +
109C LYS* 1.3 60.8 + - - +
111C PHE* 3.7 5.5 - - + +
112C LYS* 2.8 31.2 + - - +
133C ILE* 4.7 13.7 - - + -
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Residues in contact with LYS 109 (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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104C LEU* 4.1 21.0 - - + +
105C GLY 2.9 21.2 + - - +
106C PRO* 4.6 2.7 - - + +
108C LEU* 1.3 76.4 - - - +
110C GLU* 1.3 59.3 + - - +
112C LYS* 3.4 28.1 + - + +
113C ASP* 2.9 51.6 + - - +
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Residues in contact with GLU 110 (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 PRO 3.2 18.9 + - - +
107C THR* 3.7 5.9 - - - +
109C LYS* 1.3 77.7 - - - +
111C PHE* 1.3 58.3 - - - +
113C ASP* 3.2 9.0 + - - +
114C PHE* 2.8 35.0 + - + +
132C LYS* 3.8 22.7 + - - -
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Residues in contact with PHE 111 (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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75C TYR* 3.2 24.9 - + - -
77C SER* 5.5 1.8 - - - -
91C ILE* 4.4 15.7 - - + -
95C LEU* 3.9 13.0 - - + -
107C THR* 3.0 20.9 + - + +
108C LEU* 3.3 11.0 + - + +
110C GLU* 1.3 78.7 - - - +
112C LYS* 1.3 57.8 + - - +
114C PHE* 3.4 4.7 + + - -
115C THR* 2.7 42.7 + - + +
123C ARG 3.6 11.7 - - - -
126C CYS* 3.7 15.5 - - + -
127C LEU* 3.5 45.8 - - + -
130C SER* 5.1 3.4 - - - -
133C ILE* 4.1 17.7 - - + -
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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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75C TYR* 4.5 11.2 - - + -
95C LEU* 2.9 49.6 + - + +
96C ASN* 5.1 0.4 - - - +
97C CYS 4.6 9.9 + - - -
104C LEU* 4.3 10.7 - - + +
108C LEU 2.8 17.6 + - - +
109C LYS* 3.6 31.2 - - + +
111C PHE* 1.3 77.1 - - - +
113C ASP* 1.3 59.3 + - - +
115C THR* 3.8 4.7 - - - -
116C TYR* 2.9 56.2 + - + +
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Residues in contact with ASP 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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109C LYS* 2.9 45.8 + - - +
110C GLU* 3.5 7.8 - - - +
112C LYS* 1.3 80.7 - - - +
114C PHE* 1.3 61.0 + - - +
116C TYR* 4.0 10.7 + - - +
117C ASP 5.4 0.2 + - - -
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Residues in contact with PHE 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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61A ARG* 5.8 8.3 - - + -
110C GLU* 2.8 23.6 + - + +
111C PHE* 3.9 5.4 - + - +
113C ASP* 1.3 74.8 - - - +
115C THR* 1.3 70.8 + - + +
116C TYR 3.5 0.4 + - - -
117C ASP 5.0 1.0 + - - -
118C LEU* 3.8 18.6 - - + +
126C CYS* 4.4 18.2 - - + -
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Residues in contact with THR 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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75C TYR* 2.7 28.4 + - - -
111C PHE* 2.7 34.2 + - + +
112C LYS 3.5 0.5 + - - -
114C PHE* 1.3 86.1 - - + +
116C TYR* 1.3 62.5 + - - +
117C ASP 3.3 3.1 - - - -
118C LEU* 3.1 22.3 + - + -
123C ARG* 2.9 35.4 + - - +
126C CYS* 3.9 29.2 - - + -
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Residues in contact with TYR 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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66A ASP* 4.7 12.0 + - - -
75C TYR* 4.3 17.5 - + + -
112C LYS* 2.9 39.3 + - - +
113C ASP* 4.1 10.3 - - - +
114C PHE 3.5 1.4 - - - -
115C THR* 1.3 78.0 - - - +
117C ASP* 1.3 86.7 + - - +
123C ARG* 2.9 21.0 + - - -
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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