Contacts of the helix formed by residues 105 - 124 (chain F) in PDB entry 2NOQ
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 LYS 105 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101F ARG* 4.0 5.1 - - - +
102F ASN* 3.2 27.7 + - - +
103F ASN* 3.0 27.7 + - + +
104F GLY* 1.3 74.7 - - - +
106F LYS* 1.3 62.8 + - - +
107F LEU* 3.2 8.7 + - - -
108F LYS* 3.3 43.4 + - + +
109F ALA* 3.2 20.1 + - - +
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Residues in contact with LYS 106 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83F LYS* 4.8 13.3 - - - +
97F MET* 3.3 33.6 - - + +
98F MET* 4.9 4.2 - - - +
101F ARG* 3.2 33.9 - - - +
104F GLY* 2.8 26.3 + - - +
105F LYS* 1.3 71.4 - - - +
107F LEU* 1.3 60.6 + - + +
109F ALA* 3.3 7.4 + - - +
110F VAL* 2.9 35.7 + - + +
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Residues in contact with LEU 107 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104F GLY 4.9 0.9 - - - +
105F LYS* 3.6 11.7 - - - -
106F LYS* 1.3 78.4 - - + +
108F LYS* 1.3 111.7 - - + +
110F VAL* 2.7 30.1 - - + +
111F ARG* 3.0 21.9 + - - +
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Residues in contact with LYS 108 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105F LYS* 3.3 44.0 + - + +
107F LEU* 1.3 113.8 - - + +
109F ALA* 1.3 63.0 + - - +
111F ARG* 3.2 13.5 + - - +
112F ILE* 2.9 24.3 + - - +
188F THR* 5.8 7.8 - - + +
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Residues in contact with ALA 109 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97F MET* 3.3 30.7 - - - +
100F GLY 4.4 1.8 - - - -
101F ARG* 3.3 33.9 - - + +
105F LYS 3.2 3.5 + - - +
106F LYS 3.4 3.1 - - - +
107F LEU 3.1 0.2 - - - -
108F LYS* 1.3 79.8 - - - +
110F VAL* 1.3 58.9 + - - +
112F ILE* 2.7 29.8 - - + +
113F ILE* 2.7 11.4 - - + +
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Residues in contact with VAL 110 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85F GLN* 5.1 9.0 - - - +
97F MET* 3.6 30.1 - - + -
106F LYS* 2.9 21.2 + - + +
107F LEU* 2.7 30.3 - - + +
109F ALA* 1.3 75.8 - - - +
111F ARG* 1.3 69.1 + - + +
113F ILE* 3.2 6.0 + - - +
114F LYS* 2.9 23.6 + - - +
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Residues in contact with ARG 111 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107F LEU* 3.0 24.2 + - + +
108F LYS* 3.2 13.8 + - - +
110F VAL* 1.3 86.8 - - + +
112F ILE* 1.4 59.5 + - - +
114F LYS* 3.0 6.0 + - - -
115F HIS* 2.7 56.6 + - + +
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Residues in contact with ILE 112 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100F GLY* 5.8 3.4 - - - -
108F LYS 2.9 10.3 + - - +
109F ALA* 2.7 32.8 - - - +
111F ARG* 1.4 74.4 - - - +
113F ILE* 1.3 78.3 + - + +
115F HIS* 3.4 1.1 + - - -
116F THR* 2.7 30.0 + - - +
188F THR* 3.9 10.3 - - + +
189F ILE* 3.0 44.9 - - + +
190F ALA* 3.0 32.7 - - + +
193F LEU* 3.3 19.3 - - + -
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Residues in contact with ILE 113 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85F GLN* 5.7 2.5 - - - +
93F THR* 4.6 16.4 - - + +
96F LEU* 4.1 28.3 - - + +
97F MET* 4.1 24.7 - - + +
100F GLY* 5.1 4.5 - - - -
109F ALA* 2.7 28.0 - - - +
110F VAL* 3.2 7.8 + - - +
112F ILE* 1.3 102.3 - - + +
114F LYS* 1.3 59.8 + - - +
116F THR* 2.6 27.1 + - - +
117F LEU* 2.7 31.6 - - + +
193F LEU* 3.8 16.8 - - + -
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Residues in contact with LYS 114 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87F PRO* 5.0 23.8 - - + +
110F VAL 2.9 13.8 + - - +
111F ARG* 3.6 9.9 - - - +
113F ILE* 1.3 75.3 - - - +
115F HIS* 1.3 75.2 + - + +
117F LEU* 2.9 25.3 + - + +
118F ASP* 2.9 42.1 + - - +
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Residues in contact with HIS 115 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111F ARG* 2.7 58.3 + - + +
112F ILE* 3.9 3.8 - - - +
114F LYS* 1.3 77.4 - - + +
116F THR* 1.3 63.1 + - - +
118F ASP* 3.0 18.3 + - - +
119F ILE* 3.0 26.1 + - + +
186F ILE* 3.7 32.0 - - + +
190F ALA* 4.0 1.6 - - + -
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Residues in contact with THR 116 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112F ILE 2.7 27.8 + - - +
113F ILE* 2.6 20.9 + - - +
115F HIS* 1.3 76.8 - - - +
117F LEU* 1.4 60.2 + - - +
119F ILE* 2.7 32.2 + - - +
120F ILE* 2.8 18.7 + - - +
190F ALA* 2.7 26.5 - - - +
193F LEU* 3.2 23.2 - - + +
194F ALA* 3.7 14.1 - - - +
197F LEU* 4.6 4.3 - - - +
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Residues in contact with LEU 117 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87F PRO* 6.4 2.2 - - + -
88F ILE* 5.4 7.9 - - + -
93F THR* 6.0 3.8 - - + -
113F ILE* 2.7 41.9 + - + +
114F LYS* 2.9 19.3 + - + +
116F THR* 1.4 87.5 + - - +
118F ASP* 1.3 63.9 + - - +
120F ILE* 3.2 12.5 + - + +
121F ASN* 2.9 27.6 + - - +
128F PRO* 3.3 35.9 - - + +
129F ILE* 4.7 14.6 - - + +
132F VAL* 4.7 11.4 - - + -
197F LEU* 5.3 0.7 - - + -
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Residues in contact with ASP 118 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114F LYS* 2.9 44.4 + - - +
115F HIS* 3.0 16.9 + - - +
117F LEU* 1.3 77.2 - - - +
119F ILE* 1.3 62.3 + - + +
121F ASN* 3.2 15.5 + - - +
122F VAL* 3.2 26.6 + - - +
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Residues in contact with ILE 119 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115F HIS* 3.0 22.1 + - + +
116F THR* 2.7 9.8 + - - +
118F ASP* 1.3 74.4 - - + +
120F ILE* 1.3 60.5 + - - +
122F VAL* 3.9 6.5 - - - -
123F LEU* 2.7 55.6 + - + +
186F ILE* 5.4 4.5 - - + -
190F ALA* 3.6 20.2 - - + +
191F GLU* 3.7 22.9 - - + +
194F ALA* 3.3 29.2 - - + -
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Residues in contact with ILE 120 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116F THR* 2.8 20.6 + - - +
117F LEU* 3.4 18.2 - - + +
119F ILE* 1.3 78.1 - - - +
121F ASN* 1.3 50.8 + - - +
123F LEU* 5.3 1.1 - - - -
124F THR* 2.6 42.0 + - - +
126F GLN 3.8 3.3 - - - +
128F PRO* 3.7 18.8 - - + +
131F VAL* 3.5 35.2 - - + -
132F VAL* 4.2 8.5 - - + -
194F ALA* 4.4 16.6 - - + +
197F LEU* 4.0 31.2 - - + -
198F ILE* 5.9 3.1 - - + +
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Residues in contact with ASN 121 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117F LEU* 2.9 26.3 + - - +
118F ASP* 3.2 20.3 + - - +
120F ILE* 1.3 74.4 - - - +
122F VAL* 1.3 67.4 + - + +
124F THR 2.5 18.8 - - - +
125F ASP* 4.3 3.9 - - - +
126F GLN 3.9 5.2 - - - +
127F ASN* 4.2 5.4 - - - +
128F PRO* 3.1 30.4 - - - +
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Residues in contact with VAL 122 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117A A 4.3 7.3 + - - -
118F ASP 3.2 12.3 + - - +
119F ILE* 3.2 7.6 - - - +
121F ASN* 1.3 79.5 - - + +
123F LEU* 1.3 98.7 + - + +
124F THR* 3.2 1.6 + - - -
125F ASP* 4.7 0.5 + - - -
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Residues in contact with LEU 123 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A C 3.6 16.8 - - - +
117A A 3.5 17.6 + - - -
119F ILE* 2.7 45.5 + - + +
120F ILE* 5.3 0.4 - - - -
122F VAL* 1.3 105.8 - - + +
124F THR* 1.3 66.2 + - - +
191F GLU* 5.9 4.3 - - + +
195F GLU* 6.5 1.1 - - - -
198F ILE* 5.5 4.9 - - + -
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Residues in contact with THR 124 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A C 4.5 12.0 - - - +
117A A 5.0 1.3 - - - -
120F ILE* 2.6 30.4 + - - +
121F ASN 2.5 23.8 - - - +
122F VAL 4.1 1.1 - - - -
123F LEU* 1.3 84.4 + - - +
125F ASP* 1.3 61.3 + - - +
126F GLN* 3.0 48.1 + - + +
131F VAL* 5.1 2.7 - - + -
198F ILE* 3.0 33.0 - - + +
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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
------------------------------------------------------------
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