Contacts of the helix formed by residues 109 - 124 (chain C) in PDB entry 4H7Y
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 ASN 109 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80C ARG* 3.5 13.9 - - - +
104C GLU* 2.8 41.6 + - - +
105C LEU* 4.7 0.7 - - - -
107C GLN* 3.6 22.8 + - - +
108C GLY* 1.3 76.8 - - - +
110C VAL* 1.3 59.5 + - - +
111C LYS 3.5 2.5 - - - -
112C LYS* 4.0 11.2 - - + -
113C SER* 3.1 24.1 + - - -
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Residues in contact with VAL 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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105C LEU* 4.1 18.4 - - + +
108C GLY* 3.1 15.4 + - - +
109C ASN* 1.3 70.7 - - - +
111C LYS* 1.3 71.1 + - + +
113C SER* 3.4 7.0 + - - -
114C LYS* 3.0 23.6 + - + +
138C LEU* 4.4 17.6 - - + +
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Residues in contact with LYS 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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110C VAL* 1.3 80.7 - - + +
112C LYS* 1.3 57.3 - - - +
114C LYS* 3.2 7.2 + - - +
115C GLN* 2.8 41.2 + - + +
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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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81B ASP* 4.0 24.9 + - - -
84B GLN* 5.2 3.2 + - - -
100C PHE* 5.7 3.6 - - - -
104C GLU* 3.9 26.0 - - + +
109C ASN* 3.7 22.0 + - + +
110C VAL 3.3 0.2 - - - -
111C LYS* 1.3 76.6 - - - +
113C SER* 1.3 64.8 + - - +
115C GLN* 3.1 25.9 + - + +
116C LEU* 2.9 51.5 + - + +
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Residues in contact with SER 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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101C ALA* 2.7 42.6 + - - +
104C GLU* 4.0 2.6 - - - +
105C LEU* 3.7 15.3 - - - +
109C ASN 3.1 19.0 + - - -
110C VAL* 3.5 8.5 - - - -
112C LYS* 1.3 76.7 - - - +
114C LYS* 1.3 62.8 + - - +
116C LEU 3.4 0.3 + - - -
117C LEU* 3.3 26.1 + - - +
138C LEU* 4.0 11.1 - - - +
145C LEU* 4.0 6.6 - - - +
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Residues in contact with LYS 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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110C VAL* 3.0 15.0 + - + +
111C LYS* 3.6 7.2 - - - +
112C LYS 3.2 0.2 - - - -
113C SER* 1.3 75.6 - - - +
115C GLN* 1.3 59.0 + - + +
117C LEU* 3.4 4.5 + - - +
118C GLN* 3.0 60.0 + - + +
135C LEU* 4.3 10.3 - - + -
138C LEU* 3.6 25.5 - - + +
139C ASN* 5.7 6.9 - - - +
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Residues in contact with GLN 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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111C LYS* 2.8 29.9 + - + +
112C LYS* 3.1 34.1 + - + +
114C LYS* 1.3 73.6 - - + +
116C LEU* 1.3 58.0 + - - +
118C GLN* 3.9 12.7 - - - +
119C LYS* 3.0 30.1 + - - +
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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
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81B ASP* 5.1 0.2 - - - +
87C ARG* 3.8 36.7 + - - +
97C HIS* 4.6 10.1 + - + +
100C PHE* 3.7 43.1 - - + -
101C ALA* 3.7 20.6 - - + +
104C GLU* 3.8 17.7 - - + -
112C LYS* 2.9 35.4 + - + +
113C SER 3.6 4.0 - - - +
114C LYS 3.2 0.2 - - - -
115C GLN* 1.3 74.3 - - - +
117C LEU* 1.3 65.6 + - - +
119C LYS* 3.3 6.2 + - - +
120C ALA* 3.0 22.9 + - - +
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Residues in contact with LEU 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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97C HIS 4.6 1.8 - - - +
98C ILE* 3.8 30.1 - - + -
101C ALA* 3.6 17.3 - - + -
113C SER 3.3 16.2 + - - +
114C LYS 3.7 1.8 - - - +
116C LEU* 1.3 76.9 - - - +
118C GLN* 1.3 63.5 + - - +
120C ALA* 3.2 8.2 + - - +
121C VAL* 3.0 26.3 + - - +
131C LEU* 4.4 8.6 - - + +
134C ALA* 4.0 26.9 - - + +
135C LEU* 3.6 35.2 - - + -
138C LEU* 4.2 13.5 - - + -
145C LEU* 4.3 10.3 - - + -
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Residues in contact with GLN 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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114C LYS* 3.0 54.1 + - + +
115C GLN* 4.0 10.9 - - - +
117C LEU* 1.3 75.5 - - - +
119C LYS* 1.3 57.6 + - - +
121C VAL* 3.3 8.4 + - - +
122C GLU* 2.9 30.3 + - - +
135C LEU* 4.3 14.9 - - + +
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Residues in contact with LYS 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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77B ASP 4.2 6.1 + - - -
78B ASP* 2.9 25.9 + - - +
87C ARG* 4.3 18.7 - - - +
97C HIS* 5.8 1.8 - - + +
115C GLN 3.0 19.7 + - - +
116C LEU* 3.6 6.5 - - - +
118C GLN* 1.3 76.3 - - - +
120C ALA* 1.3 57.9 + - - +
122C GLU* 3.3 19.8 + - - +
123C ARG* 2.8 74.0 + - + +
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Residues in contact with ALA 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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97C HIS* 3.5 45.4 + - + -
116C LEU 3.0 10.9 + - - +
117C LEU* 3.2 9.2 + - - +
119C LYS* 1.3 77.2 - - - +
121C VAL* 1.3 61.8 + - - +
123C ARG* 3.4 2.8 + - - -
124C GLY 3.0 17.8 + - - -
125C ALA* 3.0 13.8 + - + +
131C LEU* 3.7 19.3 - - + -
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Residues in contact with VAL 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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117C LEU 3.0 15.3 + - - +
118C GLN* 3.7 7.6 - - - +
120C ALA* 1.3 74.8 - - - +
122C GLU* 1.3 64.7 + - - +
124C GLY* 3.1 13.1 + - - -
128C LEU* 4.0 23.4 - - + +
131C LEU* 3.8 29.2 - - + -
132C GLU* 5.3 2.2 - - + +
135C LEU* 4.3 16.8 - - + -
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Residues in contact with GLU 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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118C GLN 2.9 17.1 + - - +
119C LYS* 3.5 25.2 - - - +
121C VAL* 1.3 79.1 - - - +
123C ARG* 1.3 87.8 + - - +
124C GLY 3.6 0.2 + - - -
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Residues in contact with ARG 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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75B GLU* 5.9 0.6 - - - +
77B ASP* 3.8 19.8 + - - +
78B ASP* 2.5 41.8 + - - +
91C LYS* 6.5 0.9 - - + -
97C HIS* 5.8 5.8 - - + -
119C LYS* 2.8 45.0 + - + +
120C ALA* 4.0 4.9 - - - +
121C VAL 3.2 0.2 - - - -
122C GLU* 1.3 108.3 + - - +
124C GLY* 1.3 60.8 + - - +
125C ALA* 4.9 1.8 - - + +
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Residues in contact with GLY 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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92C LYS* 4.7 1.0 - - - +
120C ALA 3.0 4.5 + - - -
121C VAL* 3.1 11.3 + - - -
122C GLU 3.3 0.8 + - - -
123C ARG* 1.3 80.6 - - - +
125C ALA* 1.3 67.1 + - - +
126C VAL* 3.5 13.8 - - - +
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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