Contacts of the helix formed by residues 119 - 136 (chain B) in PDB entry 3N2N
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 TYR 119 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85B PHE* 3.8 10.3 - - - +
86B SER 2.8 15.6 + - - +
87B THR* 3.5 21.8 - - + +
88B ARG 4.9 0.2 - - - +
89B GLY 4.8 0.3 + - - -
117B ASP* 3.5 33.6 - - + -
118B THR* 1.3 71.0 - - - +
120B MET* 1.3 65.1 + - - +
121B HIS* 3.2 28.7 - + + -
122B GLU* 3.2 28.0 + - + +
123B GLY 3.9 1.4 + - - -
157B LEU* 3.7 30.1 - - + -
160B TYR* 6.1 1.1 - + - -
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Residues in contact with MET 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B ILE* 4.8 0.7 - - + -
85B PHE* 3.5 41.1 - - + -
118B THR 3.1 5.3 + - - -
119B TYR* 1.3 72.8 - - - +
121B HIS* 1.3 66.2 + - - +
123B GLY* 2.9 14.3 + - - -
124B PHE* 3.2 26.8 + - + -
147B ALA* 4.6 7.9 - - - -
149B THR* 4.0 23.8 - - + -
153B LEU* 3.7 24.2 - - + +
157B LEU* 5.5 0.6 + - - +
158B PHE* 5.1 0.4 - - + -
161B SER* 3.4 27.0 + - - +
188B LEU* 5.1 2.0 - - + -
191B ILE* 4.0 28.7 - - + -
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Residues in contact with HIS 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B TYR* 3.5 37.0 - + + +
120B MET* 1.3 74.7 - - - +
122B GLU* 1.3 72.3 + - + +
124B PHE* 3.2 6.9 + - - +
125B GLU* 2.9 46.6 + - - +
157B LEU* 4.5 4.8 + - + +
160B TYR* 3.5 57.2 - + + +
161B SER* 3.3 13.4 + - - +
163B ARG* 4.2 17.0 + - - -
164B GLU* 3.6 8.1 - - + +
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Residues in contact with GLU 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87B THR 4.7 3.6 - - - +
88B ARG* 3.4 25.8 + - - +
89B GLY* 2.9 35.3 + - - +
119B TYR* 3.2 15.4 + - + +
120B MET 3.1 0.6 - - - -
121B HIS* 1.3 97.6 + - + +
123B GLY* 1.3 63.9 + - - +
125B GLU* 3.2 17.3 + - - +
126B ARG* 3.0 36.8 + - - +
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Residues in contact with GLY 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48B ILE* 3.6 23.6 - - - +
83B ILE* 3.6 21.7 - - - +
85B PHE* 4.3 9.1 - - - +
89B GLY* 4.1 3.1 - - - -
119B TYR 3.9 2.2 + - - -
120B MET 2.9 10.2 + - - -
122B GLU* 1.3 78.3 - - - +
124B PHE* 1.3 60.1 + - - +
126B ARG* 3.3 6.2 + - - +
127B ALA 3.2 15.6 + - - -
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Residues in contact with PHE 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B ILE* 3.8 16.4 - - + -
120B MET* 3.2 37.3 + - + -
121B HIS* 3.2 7.6 + - - +
123B GLY* 1.3 71.5 - - - +
125B GLU* 1.3 59.5 + - - +
127B ALA* 3.1 2.9 + - - +
128B SER* 2.8 33.7 + - - -
145B ILE* 4.0 15.9 - - + -
147B ALA* 4.1 14.1 - - + -
161B SER* 4.8 6.1 - - - -
164B GLU* 3.7 19.1 - - + +
165B ALA* 3.7 19.5 - - + -
168B SER* 3.5 18.5 + - - -
175B VAL* 3.7 25.4 - - + -
191B ILE* 3.6 30.7 - - + -
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Residues in contact with GLU 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121B HIS* 2.9 39.6 + - - +
122B GLU* 3.2 21.4 + - - +
124B PHE* 1.3 75.9 - - - +
126B ARG* 1.3 76.1 + - - +
128B SER* 3.4 6.2 + - - -
129B GLU* 3.0 40.3 + - - +
163B ARG* 5.6 1.1 - - - -
164B GLU* 3.7 25.1 + - - +
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Residues in contact with ARG 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83B ILE* 3.8 13.9 - - + -
89B GLY 2.9 38.2 + - - +
90B THR* 3.9 4.5 - - - +
91B THR* 3.4 27.8 + - - +
122B GLU* 3.0 37.3 + - - +
123B GLY 3.5 7.4 - - - +
124B PHE 3.2 0.2 - - - -
125B GLU* 1.3 94.8 + - - +
127B ALA* 1.3 61.7 + - - +
129B GLU* 2.7 45.0 + - - +
130B GLN* 3.4 27.5 + - - +
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Residues in contact with ALA 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B TYR* 4.2 12.3 - - + -
48B ILE* 3.9 19.3 - - + -
83B ILE* 3.5 18.3 - - + +
123B GLY 3.2 4.4 + - - -
124B PHE 3.1 8.8 + - - +
126B ARG* 1.3 74.6 - - - +
128B SER* 1.3 59.9 + - - +
130B GLN* 3.1 5.7 + - - +
131B ILE* 2.8 33.5 + - + +
145B ILE* 4.0 21.3 - - + -
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Residues in contact with SER 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124B PHE 2.8 17.0 + - - -
125B GLU* 3.8 7.2 - - - -
127B ALA* 1.3 69.4 - - - +
129B GLU* 1.3 60.2 + - - +
131B ILE* 4.3 5.4 - - - -
132B TYR* 2.8 33.1 + - - +
164B GLU* 4.2 5.0 + - - -
167B ARG* 4.2 8.8 - - - +
168B SER* 2.9 36.9 + - - -
171B LEU* 3.4 18.3 - - - +
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Residues in contact with GLU 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B GLU* 3.0 24.1 + - - +
126B ARG* 2.7 48.6 + - - +
127B ALA 3.3 0.2 - - - -
128B SER* 1.3 76.1 - - - +
130B GLN* 1.3 63.9 + - + +
132B TYR* 3.5 7.8 + - - +
133B TYR* 3.2 21.5 + - - +
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Residues in contact with GLN 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B TYR* 3.7 15.9 - - + +
81B SER* 3.0 22.8 + - - -
83B ILE* 3.7 10.7 - - - +
91B THR* 3.6 20.3 - - - +
94B LYS* 3.6 14.9 - - + +
95B LEU* 3.0 34.0 + - + +
126B ARG 3.4 16.8 + - - +
127B ALA 3.1 7.0 + - - +
129B GLU* 1.3 76.8 - - + +
131B ILE* 1.3 59.4 + - - +
133B TYR* 3.3 8.2 + - - +
134B GLU* 2.9 34.6 + - + +
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Residues in contact with ILE 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B TYR* 3.5 34.8 - - + +
127B ALA 2.8 30.0 + - - +
128B SER* 3.8 8.3 - - - +
130B GLN* 1.3 71.0 - - - +
132B TYR* 1.3 53.9 + - - +
134B GLU* 3.2 3.9 + - + +
135B ASN* 2.8 44.1 + - - +
143B SER* 4.4 15.0 - - - +
145B ILE* 4.3 12.1 - - + -
168B SER* 4.8 4.0 - - - +
171B LEU* 3.6 34.3 - - + +
173B ALA* 3.8 26.9 - - + +
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Residues in contact with TYR 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128B SER 2.8 18.7 + - - +
129B GLU* 3.6 7.9 - - - +
131B ILE* 1.3 76.7 - - - +
133B TYR* 1.3 68.1 + - + +
135B ASN* 3.3 23.5 + - + +
136B ARG* 3.4 41.3 + - + +
171B LEU* 4.1 12.1 - - + +
156D ASP* 4.1 16.1 + - - -
159D PHE* 3.7 47.6 - + - -
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Residues in contact with TYR 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129B GLU 3.2 10.3 + - - +
130B GLN* 3.3 9.2 + - - +
132B TYR* 1.3 82.8 - - + +
134B GLU* 1.3 92.5 + - + +
136B ARG* 3.1 22.8 + - + +
137B GLN* 3.4 37.6 + - + +
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Residues in contact with GLU 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B ASP* 3.9 9.4 - - - +
46B TYR* 3.8 5.2 - - - +
79B ARG* 2.7 33.6 + - - -
95B LEU* 3.6 26.8 - - + +
130B GLN* 2.9 21.5 + - + +
131B ILE* 3.7 5.6 - - + +
133B TYR* 1.3 100.5 - - - +
135B ASN* 1.3 63.9 + - - +
137B GLN* 3.0 30.7 + - - +
138B GLY 4.0 1.2 + - - -
139B TYR* 5.0 3.3 + - - +
141B THR* 6.0 1.6 - - - +
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Residues in contact with ASN 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131B ILE* 2.8 30.6 + - - +
132B TYR* 3.4 10.9 - - + +
134B GLU* 1.3 72.8 - - - +
136B ARG* 1.3 57.2 + - + +
138B GLY* 2.9 19.9 + - - -
139B TYR 5.5 2.9 - - - +
141B THR* 6.2 0.2 - - - -
171B LEU* 2.9 42.9 + - - +
38E ALA* 3.4 32.1 - - + +
39E CYS* 3.2 18.8 - - - +
220E CYS* 3.4 1.0 - - - -
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Residues in contact with ARG 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132B TYR* 3.4 45.8 + - + +
133B TYR* 3.1 17.5 + - + +
135B ASN* 1.3 75.1 - - + +
137B GLN* 1.3 68.0 + - - +
138B GLY 3.3 0.4 - - - -
155D GLU* 5.5 5.1 + - - -
39E CYS* 3.9 12.6 - - - -
220E CYS* 3.4 23.9 - - + +
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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