Contacts of the helix formed by residues 116 - 135 (chain A) in PDB entry 3NUI
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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114A THR* 2.9 8.5 + - - -
115A ASN* 1.3 78.8 - - - +
117A GLY* 1.3 59.1 + - - +
118A SER* 3.4 6.5 + - - -
119A GLU* 3.0 16.7 + - - +
120A ALA* 2.9 26.3 + - - +
284A SER* 4.3 2.2 - - - -
294A MET 4.3 2.5 - - - +
295A GLY* 3.6 10.9 - - - +
115B ASN* 3.8 14.4 - - - -
119B GLU* 2.6 28.0 + - - -
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Residues in contact with GLY 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A SER* 1.3 73.3 - - - +
118A SER* 1.3 54.7 + - - +
120A ALA* 3.2 6.7 + - - +
121A ASN* 2.9 35.8 + - - +
151A HIS 4.3 4.9 - - - -
258A VAL* 3.9 27.6 - - - -
282A ILE* 4.3 0.2 - - - +
284A SER* 3.5 16.6 + - - -
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Residues in contact with SER 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A SER* 3.3 9.4 + - - -
117A GLY* 1.3 73.9 - - - +
119A GLU* 1.3 59.3 + - - +
121A ASN 3.4 0.2 + - - -
122A ASP* 3.0 32.9 + - - +
150A TYR* 4.8 0.9 + - - -
151A HIS 3.8 7.5 + - - -
152A GLY* 3.0 7.0 - - - -
153A VAL* 2.8 33.7 + - - +
154A THR* 4.0 16.6 - - - -
157A SER* 3.6 16.9 - - - -
119B GLU* 4.6 2.2 - - - -
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Residues in contact with GLU 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A THR* 3.6 11.6 - - + -
115A ASN* 3.0 35.0 + - - -
116A SER* 3.0 11.4 + - - +
118A SER* 1.3 80.5 - - - +
120A ALA* 1.3 56.4 + - - +
122A ASP* 3.6 7.9 - - - +
123A THR* 2.8 37.0 + - - +
154A THR* 5.3 2.2 - - + -
323A ALA* 6.1 0.7 - - - -
116B SER* 2.5 31.5 + - - -
118B SER* 4.0 12.3 - - - +
119B GLU* 3.4 26.2 - - + +
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Residues in contact with ALA 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114A THR* 3.3 18.0 + - + +
116A SER 2.9 17.7 + - - +
117A GLY* 3.2 4.2 + - - +
119A GLU* 1.3 75.4 - - - +
121A ASN* 1.3 55.9 + - - +
124A MET* 2.9 30.7 + - - +
282A ILE* 3.5 25.1 - - + -
295A GLY* 4.6 0.2 - - - -
296A ALA 4.3 9.9 - - - +
297A VAL* 3.7 19.3 - - + +
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Residues in contact with ASN 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117A GLY 2.9 20.4 + - - +
118A SER 3.9 3.4 - - - +
120A ALA* 1.3 69.1 - - - +
122A ASP* 1.3 67.1 + - - +
124A MET* 3.2 4.7 + - - +
125A VAL* 2.9 28.5 + - - +
151A HIS* 3.0 28.3 + - - +
157A SER* 4.2 5.8 - - - -
160A MET* 4.0 11.4 - - + +
221A PHE* 3.3 21.2 - - - -
256A ASP* 2.8 26.1 + - - +
258A VAL* 4.7 1.7 - - - +
282A ILE* 3.3 29.2 - - - +
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Residues in contact with ASP 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118A SER 3.0 13.4 + - - +
119A GLU* 3.6 7.8 - - - +
121A ASN* 1.3 75.4 - - - +
123A THR* 1.3 61.2 + - - +
125A VAL* 3.4 2.8 + - - +
126A LYS* 2.9 44.8 + - - +
154A THR* 2.5 32.0 + - - +
156A VAL* 3.4 21.3 + - + +
157A SER* 2.9 30.3 + - - -
122B ASP* 4.8 2.4 - - - +
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Residues in contact with THR 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A PHE* 3.3 28.9 - - + -
114A THR* 4.1 6.4 - - - +
119A GLU* 2.8 19.9 + - - +
120A ALA 3.9 3.1 - - - -
122A ASP* 1.3 75.9 - - - +
124A MET* 1.3 60.1 + - - +
126A LYS* 3.3 7.4 + - - +
127A MET* 2.9 28.5 + - - +
321A PHE* 3.7 22.7 - - + -
323A ALA* 4.1 9.1 - - + +
169B PHE* 4.2 8.4 - - + -
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Residues in contact with MET 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A PHE* 4.5 3.9 - - - -
120A ALA 2.9 18.8 + - - +
121A ASN 3.5 4.3 - - - +
123A THR* 1.3 72.8 - - - +
125A VAL* 1.3 65.9 + - - +
127A MET* 3.2 9.9 + - - +
128A LEU* 3.0 28.2 + - + +
221A PHE* 3.7 22.4 - - + -
254A ILE* 4.0 12.6 - - + -
280A ALA* 3.0 32.5 - - + -
281A ILE 4.6 0.7 - - - +
282A ILE* 3.7 19.3 - - + -
297A VAL* 2.7 38.6 - - + -
299A LEU* 3.7 14.6 - - + -
303A LEU* 5.1 2.2 - - - -
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Residues in contact with VAL 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121A ASN 2.9 18.4 + - - +
122A ASP 3.5 7.0 - - - +
124A MET* 1.3 73.4 - - - +
126A LYS* 1.3 60.4 + - + +
128A LEU* 3.0 10.8 + - - +
129A TRP* 3.0 64.6 + - + +
143A ILE* 4.0 15.9 - - + -
156A VAL* 4.1 13.0 - - + -
160A MET* 3.6 26.9 - - - -
176A PHE* 4.9 0.4 - - + -
221A PHE* 3.7 19.7 - - + -
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Residues in contact with LYS 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122A ASP* 2.9 34.7 + - - +
123A THR* 3.9 4.0 - - - +
124A MET 3.3 0.4 - - - -
125A VAL* 1.3 75.7 - - + +
127A MET* 1.3 57.4 + - - +
129A TRP* 3.2 30.1 + - + -
130A PHE* 2.8 27.4 + - - +
156A VAL* 5.0 12.3 - - + +
168B VAL* 3.3 25.5 + - + +
169B PHE* 3.6 40.0 + - + +
171B LEU 4.6 12.0 + - - -
173B LEU* 6.1 2.8 - - - +
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Residues in contact with MET 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A PHE* 3.5 33.4 - - + -
123A THR 2.9 15.0 + - - +
124A MET* 3.5 12.6 - - - +
126A LYS* 1.3 76.9 - - - +
128A LEU* 1.3 60.5 + - + +
130A PHE* 3.3 5.1 + - - +
131A LEU* 2.7 31.1 + - + +
299A LEU* 4.8 5.8 - - + -
307A LEU* 3.6 42.0 - - + -
311A ILE* 6.5 0.2 - - - -
318A PRO* 5.4 5.4 - - + -
321A PHE* 3.7 25.8 - - + -
169B PHE* 3.7 17.2 - - + -
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Residues in contact with LEU 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124A MET* 3.0 22.7 + - + +
125A VAL* 3.0 10.3 + - - +
127A MET* 1.3 74.4 - - + +
129A TRP* 1.3 67.6 + - - +
131A LEU* 4.2 5.4 - - + -
132A HIS* 2.8 37.9 + - + +
143A ILE* 4.4 3.1 - - + -
218A ALA* 3.8 30.7 - - + +
219A GLY* 4.3 6.3 - - - -
221A PHE* 4.1 28.0 - - + -
252A PRO* 4.1 21.1 - - + -
254A ILE* 4.6 7.9 - - + -
303A LEU* 4.5 21.3 - - + -
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Residues in contact with TRP 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125A VAL* 3.0 36.7 + - + +
126A LYS* 3.5 39.0 - - + +
128A LEU* 1.3 77.2 - - - +
130A PHE* 1.3 62.8 + - - +
132A HIS* 4.0 0.9 - - - +
133A ALA* 2.9 27.7 + - - +
138A PRO* 5.6 0.3 - - - +
140A LYS 4.0 6.2 - - - +
141A ARG* 2.8 87.4 + - + +
143A ILE* 5.1 0.2 - - + -
156A VAL* 4.5 17.0 - - + -
173A LEU* 6.5 0.2 - - + -
176A PHE* 4.3 15.9 - + - -
218A ALA* 4.0 7.7 - - + +
168B VAL* 3.8 17.5 - - + -
171B LEU* 6.1 3.4 - - + -
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Residues in contact with PHE 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126A LYS 2.8 20.6 + - - +
127A MET* 3.5 4.3 - - - +
129A TRP* 1.3 74.1 - - - +
131A LEU* 1.3 64.3 + - - +
133A ALA* 3.4 2.8 + - - +
134A ALA* 3.0 28.4 + - + +
307A LEU* 3.8 26.7 - - + -
310A ALA* 4.5 12.3 - - + -
311A ILE* 4.3 16.2 - - + -
314A ILE* 4.4 11.4 - - + -
318A PRO* 3.8 41.1 - - + -
165B TYR* 3.6 39.6 - + + +
168B VAL* 3.9 11.6 - - + +
169B PHE* 3.6 20.0 - + + -
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Residues in contact with LEU 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127A MET* 2.7 20.8 + - + +
128A LEU* 3.2 9.2 + - + +
130A PHE* 1.3 77.6 - - - +
132A HIS* 1.3 63.6 + - + +
134A ALA* 3.1 5.0 + - - +
135A GLU* 2.9 46.3 + - - +
303A LEU* 3.9 28.5 - - + -
306A ARG* 3.5 55.0 - - + +
307A LEU* 4.0 18.4 - - + +
310A ALA* 3.9 13.5 - - + -
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Residues in contact with HIS 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A LEU* 2.8 35.5 + - + +
129A TRP 4.1 0.9 - - - +
131A LEU* 1.3 77.2 - - + +
133A ALA* 1.3 59.9 + - - +
135A GLU* 3.2 14.9 + - - +
136A GLY 3.3 0.2 + - - -
137A LYS* 2.8 41.6 + - + +
140A LYS* 3.4 52.3 - - + +
218A ALA* 2.9 36.9 + - + -
252A PRO* 4.0 16.3 - - + +
306A ARG* 4.0 20.2 + - - -
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Residues in contact with ALA 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129A TRP 2.9 19.1 + - - +
130A PHE 3.6 3.8 - - - +
132A HIS* 1.3 76.5 - - - +
134A ALA* 1.3 60.3 + - - +
136A GLY* 3.1 14.4 + - - -
137A LYS 4.0 0.6 + - - -
138A PRO* 3.9 28.8 - - + +
164B PRO* 4.1 9.6 - - + +
165B TYR* 3.9 31.9 - - + +
168B VAL* 5.1 2.5 - - + -
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Residues in contact with ALA 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A PHE* 3.0 19.0 + - + +
131A LEU* 3.6 8.1 - - - +
133A ALA* 1.3 76.2 - - - +
135A GLU* 1.3 57.1 + - - +
136A GLY 3.3 2.7 + - - -
310A ALA* 3.8 26.8 - - + +
314A ILE* 4.3 19.4 - - + +
165B TYR* 4.0 17.7 - - + +
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Residues in contact with GLU 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131A LEU* 2.9 28.3 + - + +
132A HIS* 3.6 11.4 + - - +
133A ALA 3.1 0.8 - - - -
134A ALA* 1.3 78.2 - - + +
136A GLY* 1.3 60.0 + - - +
137A LYS* 3.3 19.5 + - + -
306A ARG* 3.0 57.1 + - - +
309A THR* 5.4 1.4 + - - -
310A ALA* 5.5 3.4 - - + -
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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