Contacts of the helix formed by residues 116 - 140 (chain B) in PDB entry 2NP5
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 116 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B ASP* 2.8 27.4 + - - -
112B ARG* 3.2 17.0 + - - -
113B ALA 3.3 8.5 + - - +
115B THR* 1.3 78.4 - - - +
117B PRO* 1.3 69.0 - - - +
118B SER* 3.4 1.9 + - - -
119B LEU* 3.2 28.5 + - - +
120B ALA* 3.0 18.0 + - - +
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Residues in contact with PRO 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B ASP* 5.8 1.1 - - - +
115B THR 4.0 6.5 - - - +
116B SER* 1.3 83.1 - - - +
118B SER* 1.3 58.2 + - - +
120B ALA* 3.3 8.0 + - + +
121B GLU* 3.0 30.0 + - - +
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Residues in contact with SER 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B ASP* 2.8 35.2 + - - -
58B ALA* 3.8 17.8 - - - +
116B SER* 3.2 0.8 + - - -
117B PRO* 1.3 80.6 - - - +
119B LEU* 1.3 65.4 + - - +
121B GLU* 3.3 7.7 + - - +
122B ILE* 3.2 28.7 + - - +
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Residues in contact with LEU 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B ASP* 4.4 2.5 - - - +
57B PHE* 3.9 10.1 - - + +
58B ALA* 3.6 37.0 - - + +
61B LEU* 3.9 22.1 - - + +
109B PHE* 3.8 16.6 - - + +
112B ARG* 3.5 42.4 - - + +
113B ALA* 3.9 12.8 - - + +
116B SER* 3.2 22.5 + - - +
118B SER* 1.3 82.8 + - - +
120B ALA* 1.3 62.8 + - - +
122B ILE* 3.3 2.6 + - - +
123B ARG* 3.0 28.1 + - - +
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Residues in contact with ALA 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B ALA* 3.7 12.9 - - - +
116B SER 3.0 13.8 + - - +
117B PRO* 3.6 11.9 - - + +
119B LEU* 1.3 73.7 - - - +
121B GLU* 1.3 53.5 + - - +
123B ARG* 3.4 1.9 + - - +
124B ARG* 2.8 36.3 + - - +
166D GLY 3.3 24.7 - - - +
167D SER* 3.7 1.2 + - - -
168D PRO* 5.1 8.5 - - + -
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Residues in contact with GLU 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B PRO 3.0 17.2 + - - +
118B SER* 3.5 7.9 - - - +
120B ALA* 1.3 80.2 - - - +
122B ILE* 1.3 65.0 - - + +
124B ARG* 3.0 41.4 + - - +
125B LYS* 3.0 36.9 + - - +
204B LMT 5.7 0.7 - - - +
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Residues in contact with ILE 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B ALA* 3.5 42.4 - - + +
61B LEU* 3.7 26.5 - - + -
62B ARG* 3.6 21.3 - - + -
65B VAL* 4.1 22.2 - - + -
118B SER* 3.2 18.9 + - - +
119B LEU* 3.3 4.9 + - - +
121B GLU* 1.3 80.2 - - + +
123B ARG* 1.3 62.3 + - - +
125B LYS* 3.4 2.6 + - - +
126B THR* 2.9 28.4 + - - +
204B LMT 4.1 17.2 - - - +
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Residues in contact with ARG 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B LEU* 4.2 16.4 - - + -
65B VAL* 6.0 0.9 - - + -
106B MSE 3.8 35.3 + - + +
109B PHE* 4.2 2.5 - - - -
110B ALA* 3.4 44.8 - - - +
113B ALA* 4.0 10.3 - - - -
119B LEU 3.0 19.5 + - - +
120B ALA 3.6 4.3 - - - +
122B ILE* 1.3 75.3 - - - +
124B ARG* 1.3 65.2 + - - +
126B THR* 3.3 6.8 + - - -
127B LEU* 2.9 48.5 + - - +
158B ASP* 4.4 4.2 + - - -
162D LEU* 5.1 2.8 - - - +
163D ASP* 3.1 33.3 + - - +
166D GLY* 3.8 10.8 + - - +
167D SER* 3.5 9.3 + - - +
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Residues in contact with ARG 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B ALA 2.8 22.0 + - - +
121B GLU* 3.0 39.2 + - - +
123B ARG* 1.3 73.8 - - - +
125B LYS* 1.3 87.8 + - - +
128B PHE* 2.8 43.3 + - - +
167D SER* 3.1 16.5 + - - +
169D ALA* 5.1 13.0 - - + -
170D LEU* 3.3 38.7 - - + +
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Residues in contact with LYS 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 GLU* 3.0 27.9 + - - +
122B ILE 3.8 3.8 - - - +
124B ARG* 1.3 101.7 - - - +
126B THR* 1.3 57.6 + - - +
128B PHE* 3.3 6.7 + - + +
129B THR* 2.9 35.4 + - - +
204B LMT 3.1 63.6 + - - +
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Residues in contact with THR 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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65B VAL* 3.6 42.1 - - + +
68B LEU* 6.2 2.5 - - + -
69B LEU* 4.6 11.7 - - + +
106B MSE 4.9 10.3 - - + -
122B ILE 2.9 21.0 + - - -
123B ARG* 3.3 7.6 + - - -
125B LYS* 1.3 77.6 - - - +
127B LEU* 1.3 58.4 - - + +
129B THR* 3.2 4.1 + - - -
130B ILE* 2.9 47.8 + - + +
204B LMT 4.2 11.5 + - - -
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Residues in contact with LEU 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B ARG* 2.9 37.1 + - - +
124B ARG 3.8 2.7 - - - +
126B THR* 1.3 76.5 - - + +
128B PHE* 1.3 63.9 + - - +
130B ILE* 4.8 4.0 - - + -
131B ARG* 2.9 31.3 + - - +
154B LEU* 3.6 26.6 - - + +
158B ASP* 3.8 18.2 - - - +
163D ASP* 4.0 10.5 - - + +
167D SER* 3.8 22.4 - - - +
170D LEU* 4.0 7.0 - - + -
171D TYR* 3.9 28.9 - - + +
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Residues in contact with PHE 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 ARG* 2.8 34.9 + - - +
125B LYS* 3.5 11.7 - - + +
126B THR 3.3 0.2 - - - -
127B LEU* 1.3 73.0 - - - +
129B THR* 1.3 67.2 + - - +
131B ARG* 3.8 4.6 - - + +
132B THR* 2.8 57.7 + - + -
170D LEU* 4.0 22.2 - - + +
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Residues in contact with THR 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B LEU* 4.2 7.4 - - + -
125B LYS* 2.9 16.7 + - - +
126B THR* 3.5 5.2 - - - -
128B PHE* 1.3 87.0 - - - +
130B ILE* 1.3 63.3 + - - +
132B THR* 3.6 5.0 - - - -
133B GLY* 3.1 17.7 + - - -
204B LMT 2.6 77.4 + - + +
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Residues in contact with ILE 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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68B LEU* 6.3 1.8 - - + -
69B LEU* 3.8 12.1 - - + -
72B LEU* 3.8 23.6 - - + -
89B MSE 4.3 9.4 - - + -
92B LEU* 4.4 15.3 - - + -
126B THR* 2.9 38.9 + - + +
127B LEU* 4.9 2.9 - - + -
129B THR* 1.3 74.6 - - - +
131B ARG* 1.3 61.3 + - - +
133B GLY* 3.1 2.8 + - - -
134B LEU* 2.9 41.3 + - + +
154B LEU* 3.8 30.1 - - + -
204B LMT 3.7 16.5 - - + +
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Residues in contact with ARG 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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127B LEU* 2.9 22.7 + - - +
128B PHE* 3.8 5.2 - - - +
130B ILE* 1.3 76.5 - - - +
132B THR* 1.3 56.6 + - - +
134B LEU* 3.8 6.6 - - - +
135B SER* 2.8 38.2 + - - +
147B GLU* 4.9 12.7 + - - +
150B ALA* 4.5 1.3 - - + +
151B ALA* 3.6 31.3 - - - +
154B LEU* 3.7 16.8 - - + -
170D LEU* 3.7 29.7 + - - +
171D TYR* 3.2 45.7 - - - -
175D TYR* 3.0 28.7 + - - -
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Residues in contact with THR 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B PHE* 2.8 52.6 + - + -
129B THR* 3.6 6.1 - - - -
130B ILE 3.2 0.2 - - - -
131B ARG* 1.3 76.8 - - - +
133B GLY* 1.3 58.3 + - - +
135B SER* 3.6 5.9 - - - -
136B ALA* 3.0 28.4 + - + +
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Residues in contact with GLY 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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77B ARG* 4.6 7.3 + - - -
129B THR 3.1 11.5 + - - -
130B ILE 3.1 3.3 + - - -
132B THR* 1.3 76.7 - - - +
134B LEU* 1.3 61.3 + - - +
136B ALA* 3.3 8.6 + - - +
137B VAL* 3.1 27.5 + - - +
204B LMT 3.9 24.7 - - - -
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Residues in contact with LEU 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B LEU* 3.7 26.0 - - + +
89B MSE 3.8 26.9 - - + -
130B ILE* 2.9 39.3 + - + +
131B ARG* 3.8 2.0 - - - +
133B GLY* 1.3 75.3 - - - +
135B SER* 1.3 63.1 + - - +
137B VAL* 3.3 6.7 + - - +
138B LEU* 3.1 27.8 + - + +
150B ALA* 3.7 34.5 - - + +
153B LEU* 4.2 11.4 - - + -
154B LEU* 4.1 14.4 - - + +
204B LMT 4.0 11.8 - - + +
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Residues in contact with SER 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B ARG* 2.8 29.0 + - - +
132B THR* 3.6 7.2 - - - -
134B LEU* 1.3 69.2 - - - +
136B ALA* 1.3 56.4 + - - +
138B LEU* 3.2 4.0 + - - +
139B ILE* 2.8 53.4 + - - +
146B ALA 4.8 1.6 - - - -
147B GLU* 3.6 26.3 + - - +
150B ALA* 3.2 19.6 - - - +
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Residues in contact with ALA 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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77B ARG* 5.3 5.4 - - - +
132B THR* 3.0 16.4 + - + +
133B GLY* 3.5 12.3 - - - +
134B LEU 3.3 0.2 - - - -
135B SER* 1.3 75.2 - - - +
137B VAL* 1.3 63.9 + - + +
139B ILE* 3.9 7.3 - - - +
140B GLY* 2.9 21.3 + - - -
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Residues in contact with VAL 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B ARG* 3.8 27.1 - - - +
81B PRO* 4.4 19.7 - - + -
84B ALA* 5.8 3.1 - - + -
85B LEU* 3.9 30.5 - - + -
133B GLY 3.1 14.1 + - - +
134B LEU 3.3 8.3 + - - +
136B ALA* 1.3 76.3 - - - +
138B LEU* 1.3 64.3 + - + +
140B GLY* 3.2 11.3 + - - -
141B ILE* 3.6 14.0 + - - +
204B LMT 4.0 19.7 - - + -
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Residues in contact with LEU 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B LEU* 4.0 17.3 - - + -
134B LEU* 3.1 17.6 + - + +
135B SER 3.2 2.9 + - - +
137B VAL* 1.3 75.7 - - + +
139B ILE* 1.3 64.8 + - - +
141B ILE* 3.2 8.3 + - + -
143B THR* 2.9 48.8 + - + +
146B ALA* 3.6 13.7 - - + +
149B ARG* 4.0 4.7 - - + -
150B ALA* 3.6 35.4 - - + +
153B LEU* 5.8 2.5 - - + -
187B ILE* 3.8 31.9 - - + -
188B LEU* 3.9 16.8 - - + -
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Residues in contact with ILE 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B SER* 2.8 37.2 + - - +
136B ALA* 4.0 6.1 - - - +
138B LEU* 1.3 71.0 - - - +
140B GLY* 1.3 64.4 + - - +
141B ILE 3.0 1.6 + - - -
142B GLY* 3.0 13.9 + - - +
143B THR 4.8 1.3 - - - +
146B ALA* 3.6 20.0 - - + -
147B GLU* 5.5 8.3 - - + +
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Residues in contact with GLY 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B ALA 2.9 18.3 + - - -
137B VAL* 3.2 4.0 + - - -
138B LEU 3.2 1.0 - - - -
139B ILE* 1.3 76.5 - - - +
141B ILE* 1.3 64.7 + - - +
142B GLY 3.6 0.2 - - - -
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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
------------------------------------------------------------
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