Contacts of the helix formed by residues 120 - 136 (chain L) in PDB entry 2ONM
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 VAL 120 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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116L ILE* 2.8 46.5 + - + +
119L LEU* 1.3 79.6 - - + +
121L ASP* 1.3 71.2 + - - +
122L LEU 3.5 0.2 - - - -
123L ASP* 3.2 2.9 + - - +
124L MET* 2.9 47.9 + - + +
170L PHE* 6.1 0.7 - - + -
296L PHE* 4.2 24.5 - - + -
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Residues in contact with ASP 121 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106L GLU* 4.1 12.5 - - + +
112L LYS* 2.8 43.2 + - - +
116L ILE* 3.1 15.3 + - - +
117L SER* 3.4 16.6 - - - +
120L VAL* 1.3 82.9 - - - +
122L LEU* 1.3 60.6 + - + +
124L MET* 3.2 5.5 + - - +
125L VAL* 2.9 35.3 + - + +
170L PHE* 3.5 22.9 - - - +
172L LEU* 5.5 2.2 - - + -
173L LEU* 4.4 11.6 + - - +
296L PHE* 5.4 0.2 - - - -
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Residues in contact with LEU 122 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95L ILE* 3.7 30.1 - - + -
99L ARG* 3.7 24.7 - - + +
102L LEU* 3.8 20.2 - - + -
103L ALA* 3.3 43.1 - - + +
117L SER* 3.0 19.3 + - - +
118L TYR 3.8 7.4 + - - +
120L VAL 3.5 0.2 - - - -
121L ASP* 1.3 79.5 - - + +
123L ASP* 1.3 61.8 + - - +
125L VAL* 3.3 6.5 + - + +
126L LEU* 3.1 30.4 + - + +
172L LEU* 3.9 18.2 - - + -
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Residues in contact with ASP 123 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99L ARG* 3.7 19.5 + - - +
118L TYR 3.8 3.8 + - - -
119L LEU 3.2 25.8 - - - +
120L VAL* 3.2 3.3 + - - +
122L LEU* 1.3 77.9 - - - +
124L MET* 1.3 63.5 + - - +
126L LEU* 3.5 7.7 + - - +
127L LYS* 3.1 59.8 + - - +
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Residues in contact with MET 124 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120L VAL* 2.9 39.7 + - + +
121L ASP 3.7 1.1 - - - +
123L ASP* 1.3 82.5 - - - +
125L VAL* 1.3 54.6 + - - +
127L LYS* 3.7 9.4 - - + +
128L CYS* 2.8 36.2 + - - +
173L LEU* 3.4 39.3 - - + +
177L TRP* 4.5 11.6 + - + +
459L PHE* 4.5 29.2 - - + +
461L ALA* 5.6 0.2 - - - +
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Residues in contact with VAL 125 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95L ILE* 4.2 20.2 - - + -
121L ASP 2.9 22.8 + - - +
122L LEU* 3.3 11.6 + - + +
124L MET* 1.3 77.6 - - - +
126L LEU* 1.3 55.8 + - - +
128L CYS* 3.3 1.6 + - - +
129L LEU* 3.0 42.4 + - + +
172L LEU* 3.8 18.8 - - + +
173L LEU* 3.6 33.2 - - - +
175L GLN* 6.3 0.7 - - - +
176L ALA* 3.7 21.1 - - + -
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Residues in contact with LEU 126 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92L ALA* 3.1 33.0 - - - +
95L ILE* 3.7 23.6 - - + -
96L GLU* 3.7 37.0 - - + +
99L ARG* 4.5 18.2 - - + +
122L LEU* 3.1 21.6 + - + +
123L ASP* 3.7 8.5 - - - +
125L VAL* 1.3 76.8 - - - +
127L LYS* 1.3 58.5 + - + +
129L LEU* 3.5 4.1 + - - +
130L ARG* 2.9 52.7 + - - +
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Residues in contact with LYS 127 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80J ASP* 5.1 4.4 + - - -
82J SER* 5.2 6.7 - - - +
147K ASP* 3.9 29.5 + - - +
123L ASP* 3.1 45.8 + - - +
124L MET* 3.9 9.9 - - + +
126L LEU* 1.3 74.5 - - + +
128L CYS* 1.3 60.5 + - - +
130L ARG* 4.2 5.5 - - - +
131L TYR* 3.0 30.0 + - - +
461L ALA* 3.9 9.0 - - + +
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Residues in contact with CYS 128 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124L MET 2.8 19.0 + - - +
125L VAL* 3.7 6.3 - - - +
127L LYS* 1.3 78.9 - - - +
129L LEU* 1.3 62.2 - - - +
131L TYR* 3.3 0.9 + - - +
132L TYR* 3.1 43.7 + - - -
176L ALA* 3.6 22.7 - - + -
177L TRP* 3.6 35.7 - - + +
180L GLY* 5.1 0.2 - - - -
461L ALA* 3.9 13.0 - - + +
477L LEU* 4.5 2.5 - - - -
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Residues in contact with LEU 129 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88L LEU* 4.0 33.2 - - + +
91L LEU* 4.3 20.0 - - + -
92L ALA* 4.2 17.5 - - + -
95L ILE* 3.6 31.4 - - + -
125L VAL* 3.0 25.8 + - + +
126L LEU* 4.0 3.1 - - - +
128L CYS* 1.3 75.1 - - - +
130L ARG* 1.3 59.3 + - - +
132L TYR* 3.3 5.2 + - - +
133L ALA* 2.9 29.0 + - - +
176L ALA* 4.3 25.6 - - + +
179L LEU* 5.0 4.9 - - + -
180L GLY* 4.5 7.6 - - - +
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Residues in contact with ARG 130 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86J ARG* 3.7 47.7 - - - +
89J ASN* 6.4 0.2 - - - +
134J GLY* 6.0 0.3 - - - -
138J LYS* 4.9 1.0 + - - -
89L ASN* 3.7 21.4 + - - +
92L ALA* 3.5 35.2 + - + +
93L ASP* 3.2 23.8 + - - +
96L GLU* 2.9 30.9 + - - -
126L LEU* 2.9 43.4 + - - +
127L LYS* 4.2 4.7 - - - +
129L LEU* 1.3 72.5 - - - +
131L TYR* 1.3 67.4 + - - +
133L ALA* 3.5 3.1 + - - +
134L GLY* 3.5 13.3 + - - -
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Residues in contact with TYR 131 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137J ASP* 3.5 15.2 + - - +
138J LYS* 3.1 52.5 + - + +
140J HIS* 4.6 4.2 + - - -
127L LYS 3.0 21.0 + - - +
128L CYS 3.5 3.6 - - - +
129L LEU 3.2 0.2 - - - -
130L ARG* 1.3 77.6 - - - +
132L TYR* 1.3 78.0 + + - +
134L GLY 3.1 5.0 + - - -
135L TRP* 2.9 36.5 + + - -
461L ALA* 3.3 26.2 - - + -
462L GLN* 3.4 47.0 + - + +
478L GLY* 3.4 22.8 - - - -
479L GLU 3.9 1.4 + - - -
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Residues in contact with TYR 132 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88L LEU* 4.4 2.2 - - + -
128L CYS* 3.1 36.5 + - - +
129L LEU 3.3 3.1 + - - +
131L TYR* 1.3 88.9 - + - +
133L ALA* 1.3 63.5 + - - +
134L GLY 3.1 2.0 - - - -
135L TRP* 3.0 17.2 + + - +
136L ALA 3.3 8.1 + - - -
177L TRP 5.1 1.1 - - - -
180L GLY* 3.5 31.2 - - - +
181L PRO* 3.7 30.4 - - + +
184L ALA* 3.3 13.1 - - + +
477L LEU* 3.0 46.0 + - + -
478L GLY 3.2 12.7 + - - -
481L GLY* 4.0 5.4 - - - -
482L LEU* 3.7 28.0 - - + -
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Residues in contact with ALA 133 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85L GLY* 3.4 20.9 - - - +
88L LEU* 3.7 15.7 - - + +
89L ASN* 3.3 35.4 - - - +
129L LEU 2.9 16.5 + - - +
130L ARG 3.5 7.4 - - - +
132L TYR* 1.3 77.3 - - - +
134L GLY* 1.3 62.5 + - - +
136L ALA* 3.3 18.2 + - - +
137L ASP* 4.8 1.9 - - - +
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Residues in contact with GLY 134 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130J ARG 6.0 0.2 - - - -
134J GLY* 3.9 23.3 - - - -
138J LYS* 3.8 7.6 - - - -
89L ASN* 5.2 0.6 - - - +
130L ARG 3.5 4.1 + - - -
131L TYR 3.1 9.8 + - - -
132L TYR 3.1 0.8 - - - -
133L ALA* 1.3 80.6 - - - +
135L TRP* 1.3 58.4 + - - +
137L ASP* 3.6 1.8 - - - +
138L LYS* 2.9 34.4 + - - +
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Residues in contact with TRP 135 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135J TRP* 4.9 7.6 - + - -
138J LYS* 3.3 41.3 - - + +
140J HIS* 4.1 7.2 - + - -
131L TYR* 2.9 40.8 + + - -
132L TYR* 3.0 19.0 + + - +
134L GLY* 1.3 74.7 - - - +
136L ALA* 1.3 67.1 + - - +
137L ASP 3.2 2.7 - - - -
138L LYS* 3.0 51.5 + - + -
139L TYR* 3.7 15.5 + - - +
184L ALA* 4.7 1.6 - - + -
479L GLU* 3.5 49.1 - - + +
482L LEU* 3.5 37.1 - - + +
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Residues in contact with ALA 136 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145I PRO* 4.7 2.1 - - - +
81L ALA* 3.2 24.2 - - - +
82L SER* 5.0 0.2 - - - -
84L ARG* 3.3 24.3 + - + -
85L GLY* 3.7 13.7 - - - +
88L LEU* 5.3 0.2 - - + -
132L TYR 3.3 6.9 + - - +
133L ALA* 3.3 17.9 + - - +
135L TRP* 1.3 77.0 - - - +
137L ASP* 1.3 59.1 + - - +
138L LYS 3.9 0.5 + - - -
139L TYR* 5.0 2.6 + - - +
184L ALA* 3.5 24.5 - - - +
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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