Contacts of the helix formed by residues 103 - 118 (chain C) in PDB entry 1QNN
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 SER 103 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97C ILE* 4.4 3.8 - - - -
98C ASP* 3.3 13.8 + - - +
101C PHE* 3.2 5.5 + - - +
102C GLY* 1.3 80.0 - - - +
104C PHE* 1.3 63.8 + - - +
105C GLU* 3.7 7.6 + - - +
106C LYS* 3.2 24.6 + - - +
107C PHE* 3.1 21.5 + - - +
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Residues in contact with PHE 104 (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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87C GLY 3.3 26.5 - - - -
88C ALA* 3.6 18.8 - - + -
89C PRO* 3.6 28.7 - - + -
97C ILE* 4.1 9.9 - - + -
98C ASP* 3.4 9.7 + - - +
103C SER* 1.3 73.9 - - - +
105C GLU* 1.3 62.8 + - + +
107C PHE* 3.1 24.8 + + - +
108C LYS* 2.9 60.9 + - + +
179C TRP* 4.2 4.9 - + + -
184C TRP* 3.6 24.5 - + - -
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Residues in contact with GLU 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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103C SER* 3.3 7.3 + - - +
104C PHE* 1.3 82.9 - - + +
106C LYS* 1.3 61.3 + - - +
108C LYS* 3.3 33.8 + - - +
109C GLU* 3.2 24.6 + - - +
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Residues in contact with LYS 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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101C PHE 3.0 25.1 + - - +
102C GLY* 4.4 10.5 - - - -
103C SER* 3.2 19.1 + - - +
105C GLU* 1.3 75.8 - - - +
107C PHE* 1.3 66.8 + - - +
109C GLU* 3.2 22.0 - - - +
110C GLU* 2.9 46.2 + - + +
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Residues in contact with PHE 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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97C ILE* 3.7 25.6 - - + -
101C PHE* 4.0 33.6 - + + +
103C SER 3.1 13.6 + - - +
104C PHE* 3.1 29.8 + + - +
106C LYS* 1.3 76.9 - - - +
108C LYS* 1.3 58.2 + - - +
110C GLU* 3.3 3.3 + - - +
111C PHE* 2.8 59.6 + + - +
126C LEU* 3.8 34.3 - - + -
136C ILE* 4.3 5.6 - - + -
154C LEU* 4.7 1.6 - - + -
179C TRP* 3.6 24.7 - + - -
184C TRP* 4.4 5.4 - + - -
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Residues in contact with LYS 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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87C GLY 5.2 1.8 + - - -
104C PHE* 2.9 45.9 + - + +
105C GLU* 3.6 36.9 + - - +
106C LYS 3.2 0.4 - - - -
107C PHE* 1.3 73.1 - - - +
109C GLU* 1.3 56.4 + - - +
111C PHE* 3.1 0.9 + - - +
112C ASN* 2.6 44.5 + - - +
179C TRP* 3.4 59.1 - - + +
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Residues in contact with GLU 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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105C GLU 3.2 9.4 + - - +
106C LYS* 3.2 37.1 - - - +
108C LYS* 1.3 79.4 - - - +
110C GLU* 1.3 60.4 + - + +
112C ASN* 3.9 8.9 - - - +
113C THR* 2.9 35.8 + - - +
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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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101C PHE* 3.7 27.5 - - - +
106C LYS* 2.9 41.2 + - + +
107C PHE* 3.5 4.7 - - - +
108C LYS 3.1 0.4 - - - -
109C GLU* 1.3 81.4 - - + +
111C PHE* 1.3 62.7 + - - +
113C THR* 3.6 5.3 + - - +
114C ALA* 3.2 22.9 + - - +
136C ILE* 4.1 13.9 - - + +
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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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107C PHE* 2.8 39.2 + + + +
108C LYS 3.6 3.1 - - - +
110C GLU* 1.3 75.8 - - - +
112C ASN* 1.3 64.9 + - - +
114C ALA* 3.3 5.5 + - - +
115C GLY* 3.1 18.7 + - - -
124C VAL* 3.5 36.4 - - + +
125C TRP 3.7 6.3 - - - -
126C LEU* 3.5 27.8 - - + -
136C ILE* 4.0 15.9 - - + +
154C LEU* 3.7 20.2 - - + -
156C PHE* 3.6 41.0 - + - -
179C TRP* 3.8 17.0 - + + -
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Residues in contact with ASN 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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108C LYS* 2.6 29.2 + - - +
109C GLU* 3.9 8.1 - - - +
111C PHE* 1.3 74.4 - - - +
113C THR* 1.3 57.0 + - - +
115C GLY* 3.1 3.2 + - - +
116C THR* 2.9 37.1 + - + +
156C PHE* 4.8 2.8 - - - -
175C LEU* 3.7 24.5 - - + +
176C LYS* 4.2 21.2 - - + +
179C TRP* 2.8 33.7 + - - +
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Residues in contact with THR 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 GLU* 2.9 23.2 + - - +
110C GLU* 3.9 6.7 - - - +
111C PHE 3.3 0.2 - - - -
112C ASN* 1.3 73.8 - - - +
114C ALA* 1.3 65.7 + - - +
116C THR* 3.0 19.7 + - - +
117C THR* 3.0 26.2 + - + +
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Residues in contact with ALA 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 GLU 3.2 15.5 + - - +
111C PHE 3.6 4.9 - - - +
112C ASN 3.3 0.2 - - - -
113C THR* 1.3 80.1 - - - +
115C GLY* 1.3 62.5 + - - +
117C THR* 3.4 8.4 + - - -
118C LEU* 3.3 21.3 + - - +
124C VAL* 4.0 18.4 - - + -
136C ILE* 4.1 12.3 - - + -
138C LYS* 3.5 24.9 + - + +
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Residues in contact with GLY 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 PHE 3.1 13.0 + - - -
112C ASN 3.1 4.0 + - - -
114C ALA* 1.3 80.5 - - - +
116C THR* 1.3 57.2 + - - +
118C LEU* 3.6 6.6 + - - +
124C VAL* 4.3 18.4 - - - +
158C VAL* 3.9 7.9 - - - +
171C ARG* 2.9 26.0 + - - -
175C LEU* 3.7 15.0 - - - -
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Residues in contact with THR 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 ASN* 2.9 16.5 + - + +
113C THR* 3.0 18.2 + - - +
115C GLY* 1.3 77.1 - - - +
117C THR* 1.3 64.1 + - - +
118C LEU 3.4 1.6 + - - +
171C ARG* 4.0 14.1 + - + +
172C ALA* 3.9 29.6 - - + +
175C LEU* 3.6 15.0 - - + -
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Residues in contact with THR 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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113C THR* 3.0 31.0 + - + +
114C ALA* 3.4 1.9 + - - -
115C GLY 3.4 0.2 - - - -
116C THR* 1.3 81.7 - - - +
118C LEU* 1.3 63.9 + - - +
119C PHE* 3.1 7.2 + - - +
138C LYS* 2.7 30.2 + - - -
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Residues in contact with LEU 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 ALA 3.3 16.0 + - - +
115C GLY* 3.8 8.3 - - - +
116C THR 3.4 2.1 - - - +
117C THR* 1.3 75.5 - - - +
119C PHE* 1.3 73.4 + - - +
120C GLY 3.6 4.3 + - - +
121C SER 3.6 26.7 - - - +
122C GLY* 3.9 6.3 - - - +
123C TRP 3.4 38.1 - - - +
124C VAL* 4.8 2.2 - - + +
138C LYS* 4.1 20.2 - - + +
139C GLU 4.0 12.6 - - - +
140C PRO* 4.7 9.9 - - + -
158C VAL* 4.1 5.6 - - + -
171C ARG* 2.8 27.6 + - - +
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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