Contacts of the helix formed by residues 110 - 128 (chain F) in PDB entry 5N9G
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 ARG 110 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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108F ALA 3.8 19.4 + - - -
109F ALA* 1.4 77.5 - - - +
111F LEU* 1.3 61.0 + - - +
112F GLN* 3.1 11.2 - - + +
113F LYS* 2.9 24.3 + - + +
114F LYS* 3.1 9.7 + - - +
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Residues in contact with LEU 111 (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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68F SER* 3.5 13.7 - - - +
71F ARG* 3.5 32.1 - - - +
109F ALA 3.7 1.0 + - - -
110F ARG* 1.3 71.8 - - - +
112F GLN* 1.4 54.9 + - - +
114F LYS* 3.2 14.9 + - + +
115F GLU* 3.0 30.4 + - - +
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Residues in contact with GLN 112 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110F ARG* 3.1 7.5 - - + +
111F LEU* 1.4 75.3 - - - +
113F LYS* 1.4 58.8 + - - +
115F GLU* 3.2 8.9 + - + +
116F VAL* 3.0 30.3 + - + +
143F TYR 5.1 7.9 + - - -
144F ALA* 5.5 3.2 - - + +
145F ASP 5.8 0.6 - - - +
148F VAL* 4.1 30.5 - - + +
296H LYS* 5.9 0.4 - - - +
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Residues in contact with LYS 113 (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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105F GLY 5.4 0.4 - - - +
106F ILE* 4.8 8.3 - - + -
109F ALA* 3.8 24.2 - - + -
110F ARG* 2.9 16.5 + - + +
112F GLN* 1.4 76.4 - - - +
114F LYS* 1.3 52.7 + - + +
116F VAL* 3.3 7.2 + - - +
117F LEU* 2.8 35.6 + - + +
148F VAL* 6.5 0.2 - - - -
151F SER* 5.2 7.0 + - - -
152F THR* 3.4 34.8 - - + +
155F GLN* 2.8 31.7 + - - +
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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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68F SER* 3.8 16.8 + - - +
97F TYR* 3.3 24.8 + - - +
101F TYR* 3.1 32.8 + - + +
106F ILE* 3.2 24.9 - - + +
107F ARG 2.7 23.1 + - - -
108F ALA 4.2 0.6 - - - -
109F ALA* 2.8 25.6 + - + +
110F ARG 3.1 9.0 + - - +
111F LEU* 3.2 18.2 + - + +
113F LYS* 1.3 76.1 - - + +
115F GLU* 1.3 59.9 + - - +
117F LEU* 3.9 9.6 - - + -
118F VAL* 3.4 17.8 + - - +
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Residues in contact with GLU 115 (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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72F GLY* 5.9 0.2 - - - -
75F ARG* 3.1 54.9 + - - +
111F LEU 3.0 13.3 + - - +
112F GLN* 3.4 13.2 - - + +
113F LYS 3.2 0.2 - - - -
114F LYS* 1.3 74.9 - - - +
116F VAL* 1.3 65.2 + - + +
118F VAL* 3.2 24.4 - - - +
142F LEU* 3.5 39.1 - - + +
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Residues in contact with VAL 116 (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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112F GLN* 3.0 20.8 + - + +
113F LYS* 3.7 7.4 - - - +
115F GLU* 1.3 73.4 - - + +
117F LEU* 1.4 54.3 + - - +
119F GLY* 2.8 22.7 + - - -
120F CYS* 2.9 12.6 + - - -
142F LEU* 3.8 9.5 - - + +
144F ALA* 4.1 18.6 - - + -
148F VAL* 3.9 26.0 - - + +
149F PHE* 3.7 29.0 - - + -
152F THR* 3.4 32.1 - - + +
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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
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97F TYR* 3.8 25.6 - - + +
100F ALA* 3.8 13.9 - - + -
101F TYR* 4.6 4.0 - - + -
106F ILE* 3.5 33.7 - - + -
113F LYS* 2.8 22.9 + - + +
114F LYS* 3.7 9.6 - - - +
116F VAL* 1.4 69.4 - - - +
118F VAL* 1.4 63.6 + - - +
120F CYS* 3.1 5.1 + - + -
121F CYS* 3.0 37.3 + - - -
152F THR* 4.1 10.5 - - + +
156F ILE* 3.6 40.8 - - + -
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Residues in contact with VAL 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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72F GLY* 3.6 17.0 - - - +
75F ARG* 3.8 22.0 - - + +
76F VAL* 3.7 26.9 - - + +
79F LEU* 4.1 13.7 - - + -
97F TYR* 3.5 21.8 - - + +
114F LYS 3.4 16.4 + - - +
115F GLU* 3.2 17.7 + - - +
116F VAL 3.2 0.2 - - - -
117F LEU* 1.4 75.4 - - - +
119F GLY* 1.3 55.9 + - - +
121F CYS* 3.7 2.3 + - - +
122F VAL* 3.2 29.3 + - - +
142F LEU* 4.8 6.3 - - + -
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Residues in contact with GLY 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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79F LEU* 4.1 10.8 - - - -
115F GLU 3.7 1.8 + - - -
116F VAL 2.8 10.1 + - - -
118F VAL* 1.3 78.6 - - - +
120F CYS* 1.4 54.0 + - - +
122F VAL* 3.8 0.9 - - - +
123F LEU* 2.8 36.0 + - - +
138F ILE* 3.8 11.8 - - - +
142F LEU* 3.7 17.4 - - - +
149F PHE* 4.1 7.0 - - - -
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Residues in contact with CYS 120 (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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116F VAL* 2.9 19.2 + - - -
117F LEU* 3.1 10.5 + - + +
119F GLY* 1.4 74.0 - - - +
121F CYS* 1.4 58.0 + - - +
123F LEU* 3.3 2.5 + - - +
124F ILE* 2.9 38.7 + - + +
149F PHE* 3.9 16.4 - - - -
152F THR* 4.0 13.5 - - - -
153F TYR* 3.6 40.6 - - + -
156F ILE* 4.0 19.3 - - + -
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Residues in contact with CYS 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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76F VAL* 5.2 1.1 - - + -
93F ALA* 3.4 23.6 - - + +
96F TYR* 3.8 16.9 - - + -
97F TYR* 3.6 33.4 - - + -
100F ALA* 4.9 0.7 - - - -
117F LEU* 3.0 36.1 + - - +
118F VAL 4.1 3.1 - - - +
120F CYS* 1.4 76.2 - - - +
122F VAL* 1.3 54.2 + - - +
124F ILE* 3.6 8.2 + - - +
125F THR* 2.7 34.2 + - - -
156F ILE* 5.5 2.5 - - - -
160F LEU* 5.7 0.9 - - - -
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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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76F VAL* 3.9 20.0 - - + +
79F LEU* 3.7 27.8 - - + -
80F CYS* 3.7 24.0 - - - -
83F LEU* 3.8 21.5 - - + -
85F LEU* 4.2 12.4 - - + +
93F ALA* 4.0 6.1 - - + -
118F VAL 3.2 19.8 + - - +
119F GLY 3.9 1.1 - - - +
121F CYS* 1.3 71.4 - - - +
123F LEU* 1.4 63.8 - - - +
125F THR* 3.6 3.9 - - - -
126F CYS* 3.3 22.7 + - - -
133F LEU* 4.2 1.8 - - + -
138F ILE* 4.2 5.4 - - + -
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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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119F GLY 2.8 19.1 + - - +
120F CYS 3.6 4.7 - - - +
122F VAL* 1.4 73.9 - - - +
124F ILE* 1.4 65.6 + - - +
126F CYS* 2.9 15.4 + - - +
127F ARG* 2.9 29.6 + - + +
133F LEU* 3.2 46.9 - - + +
134F THR 4.6 2.7 - - - +
135F MET* 3.7 33.9 - - + -
138F ILE* 4.7 4.5 - - + -
149F PHE* 3.7 17.7 - - + -
153F TYR* 4.1 16.4 - - + -
286G GLU* 5.5 0.2 - - - +
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Residues in contact with ILE 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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96F TYR* 4.0 13.2 - - + -
120F CYS 2.9 27.3 + - - +
121F CYS* 4.0 8.3 - - - +
123F LEU* 1.4 73.0 - - - +
125F THR* 1.3 62.9 + - - +
127F ARG* 3.2 9.6 + - - +
128F GLN* 2.9 53.7 + - - +
153F TYR* 4.0 13.2 - - + -
156F ILE* 4.0 15.0 - - + -
157F VAL* 4.0 17.3 - - + -
160F LEU* 5.9 0.9 - - + -
162F LEU* 3.9 23.1 - - + -
164F VAL* 3.8 22.4 - - + -
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Residues in contact with THR 125 (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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85F LEU* 5.8 0.7 - - + -
89F PHE* 3.5 45.8 - - + +
92F THR* 3.7 19.5 - - + +
93F ALA* 3.4 19.9 + - + -
96F TYR* 3.8 2.8 - - - -
121F CYS 2.7 23.0 + - - -
122F VAL 3.6 6.3 - - - -
123F LEU 3.2 0.4 - - - -
124F ILE* 1.3 77.1 - - - +
126F CYS* 1.4 60.2 + - - +
128F GLN* 3.5 8.8 + - - +
129F HIS* 2.7 35.9 + - - +
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Residues in contact with CYS 126 (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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85F LEU* 3.4 38.8 - - - -
89F PHE* 3.8 4.3 - - - -
122F VAL 3.3 15.0 + - - -
123F LEU* 2.9 11.9 + - + +
125F THR* 1.4 73.0 - - - +
127F ARG* 1.3 52.7 + - - +
129F HIS 2.9 16.5 + - - -
131F TRP* 2.8 57.7 + - + +
133F LEU* 3.8 24.0 - - + -
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Residues in contact with ARG 127 (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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123F LEU* 2.9 33.0 + - + +
124F ILE 3.4 8.3 - - - +
126F CYS* 1.3 76.9 - - - +
128F GLN* 1.3 60.5 + - - +
129F HIS 3.1 1.1 + - - -
130F ASN* 3.5 12.7 + - - +
131F TRP 4.3 4.5 + - - +
133F LEU 4.7 1.9 + - - +
135F MET* 3.6 9.1 - - - +
153F TYR* 4.0 1.8 - - - -
164F VAL* 3.3 33.3 + - + +
165F PRO* 2.7 53.7 + - - +
166F SER* 4.0 15.1 - - - +
167F LEU* 4.3 24.4 - - - +
283G TYR 4.7 2.2 + - - -
284G GLU* 2.6 36.1 + - - +
285G PRO* 5.7 2.8 - - - +
286G GLU* 3.3 23.4 + - - +
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Residues in contact with GLN 128 (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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102A ARG* 3.6 38.5 + - - +
92F THR* 4.7 4.5 - - - +
96F TYR* 2.7 35.5 + - - -
124F ILE* 2.9 31.8 + - + +
125F THR* 3.9 5.9 - - - +
126F CYS 3.3 0.4 - - - -
127F ARG* 1.3 75.4 - - + +
129F HIS* 1.3 68.6 + - + +
130F ASN* 3.6 5.4 + - - -
162F LEU* 4.7 5.1 - - - +
163F ASP 3.1 20.8 + - - +
165F PRO* 3.6 23.2 - - + +
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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