Contacts of the helix formed by residues 133 - 149 (chain A) in PDB entry 3NT7
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 HIS 133 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A LEU* 4.0 11.7 + - + -
40A ASP* 3.2 27.7 + - - -
42A THR* 3.5 22.9 - - + +
122A TYR* 4.9 1.8 - - - -
124A SER* 3.3 37.5 + - - +
125A CYS* 3.5 16.6 - - - -
126A LYS* 3.5 14.0 + - + -
131A LYS 3.3 0.6 - - - -
132A SER* 1.3 87.1 + - - +
134A ALA* 1.3 65.5 + - - +
135A ILE 3.2 3.4 - - - -
136A TYR* 3.1 39.1 + + + -
137A TRP* 3.2 24.2 + - + +
36C TRP* 5.6 0.7 - - - -
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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
----------------------------------------------------------
122A TYR* 3.5 44.2 + - + +
131A LYS* 3.7 15.9 + - + +
132A SER 3.7 2.4 - - - -
133A HIS* 1.3 74.6 - - - +
135A ILE* 1.3 68.5 + - + +
138A ASP* 3.1 26.7 + - - +
36C TRP* 5.0 3.1 - - + -
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Residues in contact with ILE 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A VAL* 5.7 0.2 - - - +
133A HIS 3.2 0.6 - - - -
134A ALA* 1.3 80.1 - - + +
136A TYR* 1.3 75.4 + - + +
138A ASP* 3.8 13.3 - - - +
32C GLU* 4.3 15.0 - - + +
33C VAL* 4.0 26.2 - - + -
36C TRP* 3.7 35.9 - - + -
135C ILE* 4.5 24.8 - - + +
136C TYR* 4.5 15.3 - - + -
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Residues in contact with TYR 136 (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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33A VAL* 3.2 47.2 - - + +
36A TRP* 3.7 27.4 + + + -
37A LEU* 3.8 25.1 - - + -
40A ASP* 5.0 1.9 + - - -
132A SER 4.5 0.9 - - - -
133A HIS* 3.1 47.6 + + + +
135A ILE* 1.3 85.1 - - + +
137A TRP* 1.3 62.3 + - - +
138A ASP* 3.7 0.5 + - - +
139A LYS* 5.0 2.4 + - - +
140A ILE* 4.6 8.5 - - - +
36C TRP* 3.0 29.0 - + - -
39C ARG* 4.0 7.1 + - - -
135C ILE* 4.3 8.1 - - + -
136C TYR* 2.8 33.9 + + - -
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Residues in contact with TRP 137 (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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30A TYR* 3.8 11.7 - + - -
37A LEU* 3.5 20.8 - - + +
49A PHE* 4.3 12.6 - + - -
50A PHE* 3.8 34.5 - + - -
122A TYR* 3.6 13.5 - - + -
123A LEU* 3.7 37.7 - - + -
124A SER* 2.6 40.3 + - - +
133A HIS* 3.2 29.7 + - + +
136A TYR* 1.3 76.7 - - - +
138A ASP* 1.3 65.9 + - - +
139A LYS 3.3 1.8 - - - -
140A ILE* 2.8 39.8 + - + -
141A SER* 2.7 38.2 + - - +
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Residues in contact with ASP 138 (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 TYR* 4.5 1.3 + - - -
122A TYR* 4.5 7.7 + - - -
134A ALA 3.1 18.4 + - - +
135A ILE* 3.8 13.0 - - - +
136A TYR 3.4 0.8 - - - +
137A TRP* 1.3 76.0 - - - +
139A LYS* 1.3 85.8 + - + +
141A SER* 3.4 5.5 + - - -
142A LYS* 3.2 55.8 + - - +
166A ILE 5.3 0.7 - - - +
139C LYS* 5.2 5.5 + - - -
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Residues in contact with LYS 139 (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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29A PHE* 3.7 43.9 - - + -
32A GLU* 5.3 4.0 - - - +
33A VAL* 6.4 1.6 - - + -
136A TYR 5.0 2.2 + - - +
137A TRP 3.0 1.8 + - - -
138A ASP* 1.3 92.4 + - + +
140A ILE* 1.3 65.0 + - + +
142A LYS* 3.6 9.7 + - - +
143A LEU* 3.1 23.4 + - - +
138C ASP* 4.5 12.2 + - - -
139C LYS* 4.5 19.0 - - - +
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Residues in contact with ILE 140 (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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26A LEU* 3.3 27.1 - - + -
29A PHE* 3.6 25.1 - - + +
30A TYR* 3.9 34.8 - - + +
33A VAL* 5.7 2.0 - - + -
50A PHE* 5.1 0.2 - - + -
123A LEU* 5.2 1.1 - - + -
136A TYR 4.6 10.3 - - - +
137A TRP* 2.8 44.1 + - + +
139A LYS* 1.3 75.1 - - + +
141A SER* 1.3 60.6 + - - +
143A LEU* 3.1 9.0 + - - +
144A LEU* 2.9 41.8 + - + +
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Residues in contact with SER 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A TRP* 5.3 1.5 + - - +
121A TYR* 2.6 53.0 + - - +
122A TYR* 3.2 17.5 - - - -
123A LEU* 5.2 1.2 - - - +
137A TRP* 2.7 24.3 + - - +
138A ASP 3.5 5.4 - - - -
140A ILE* 1.3 74.0 - - - +
142A LYS* 1.3 62.1 + - - +
144A LEU* 3.4 4.0 + - - +
145A LEU* 3.0 27.0 + - - +
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Residues in contact with LYS 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A TYR* 3.3 18.2 - - - +
138A ASP* 3.2 43.0 + - - +
139A LYS* 3.8 10.1 - - - +
140A ILE 3.3 0.2 - - - -
141A SER* 1.3 75.0 - - - +
143A LEU* 1.3 64.0 + - - +
145A LEU* 4.2 1.2 - - - +
146A GLN* 3.0 46.2 + - - +
166A ILE 3.8 10.8 - - - -
167A ARG* 3.3 38.8 + - - +
168A ALA 4.1 3.8 - - - +
169A LYS* 5.8 1.8 - - + -
139C LYS* 5.5 6.7 - - - +
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Residues in contact with LEU 143 (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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22A VAL* 3.5 47.0 - - + +
25A GLN* 3.4 30.7 - - + +
26A LEU* 3.9 23.8 - - + +
29A PHE* 4.6 11.0 - - + -
139A LYS 3.1 14.4 + - - +
140A ILE* 3.3 7.0 - - - +
142A LYS* 1.3 77.2 - - - +
144A LEU* 1.3 64.2 + - + +
146A GLN* 3.7 13.3 - - - +
147A HIS* 3.3 21.8 + - - +
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Residues in contact with LEU 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A TRP* 4.3 11.7 - - + -
22A VAL* 3.8 28.5 - - + -
26A LEU* 4.3 19.7 - - + -
50A PHE* 5.4 0.4 - - + -
53A LEU* 4.4 10.8 - - + -
119A TRP* 3.7 33.9 - - + +
123A LEU* 4.4 16.6 - - + -
140A ILE* 2.9 40.2 + - + +
141A SER* 4.1 4.0 - - - +
143A LEU* 1.3 73.6 - - + +
145A LEU* 1.3 60.0 + - - +
147A HIS* 3.2 5.6 + - - +
148A ILE* 2.9 33.9 + - - +
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Residues in contact with LEU 145 (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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63A CYS* 4.7 5.2 - - - -
65A CYS* 4.3 9.6 - - - -
119A TRP* 4.2 23.4 - - + +
121A TYR* 4.1 19.1 - - + -
141A SER 3.0 17.2 + - - +
142A LYS* 4.2 2.2 - - - +
144A LEU* 1.3 74.9 - - - +
146A GLN* 1.3 63.7 + - - +
148A ILE* 3.0 9.2 + - + +
149A THR* 2.9 37.0 + - + +
155A LEU* 4.1 38.4 - - + -
157A CYS* 5.7 2.9 - - - -
163A PHE* 6.1 1.3 - - + -
166A ILE* 5.6 0.9 - - + -
168A ALA* 3.9 27.4 - - + -
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Residues in contact with GLN 146 (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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142A LYS* 3.0 31.5 + - - +
143A LEU* 3.7 14.2 - - - +
145A LEU* 1.3 76.1 - - - +
147A HIS* 1.3 60.8 + - - +
149A THR* 3.2 18.3 + - - -
150A LYS* 3.6 22.8 - - - +
168A ALA* 2.7 28.2 + - + +
169A LYS* 3.5 29.0 - - - +
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Residues in contact with HIS 147 (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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18A ASP 2.7 28.2 + - - -
19A TRP* 3.9 17.0 - + - -
21A PRO* 4.0 26.5 - - + +
22A VAL* 3.8 23.0 - - + +
57A LEU* 3.7 22.4 - - + -
143A LEU 3.3 11.5 + - - +
144A LEU* 3.2 9.8 + - - +
145A LEU 3.2 0.4 - - - -
146A GLN* 1.3 77.2 - - - +
148A ILE* 1.3 66.4 + - - +
150A LYS* 3.3 26.4 + - + +
151A HIS* 3.1 39.2 + + - -
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Residues in contact with ILE 148 (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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19A TRP* 3.6 23.6 - - + -
57A LEU* 4.2 12.1 - - + -
63A CYS* 3.9 30.3 - - + -
117A ILE* 4.3 9.0 - - + -
119A TRP* 3.4 52.3 - - + +
144A LEU 2.9 19.5 + - - +
145A LEU* 3.0 9.2 + - + +
147A HIS* 1.3 75.5 - - - +
149A THR* 1.3 60.0 + - + +
150A LYS 3.0 0.2 - - - -
151A HIS* 2.9 22.2 + - - +
152A VAL* 3.2 19.5 + - + -
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Residues in contact with THR 149 (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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145A LEU* 2.9 26.8 + - + +
146A GLN* 3.2 16.3 + - - -
147A HIS 3.4 0.2 - - - -
148A ILE* 1.3 75.0 - - + +
150A LYS* 1.3 60.1 + - - +
151A HIS 3.3 1.1 + - - -
152A VAL* 3.8 21.2 - - + +
155A LEU* 4.0 26.9 - - + -
173A PRO 5.4 4.3 - - - -
174A VAL* 3.8 37.7 - - + +
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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