Contacts of the helix formed by residues 147 - 164 (chain A) in PDB entry 4EDZ
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 THR 147 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A LEU* 3.2 23.3 - - - +
78A ALA 4.2 11.4 - - - +
79A GLY* 4.4 4.5 - - - +
80A ASN* 5.8 1.8 - - - +
84A GLU* 5.4 0.9 - - - +
88A VAL* 3.9 21.4 - - + +
142A ILE* 3.9 17.7 - - + +
145A SER* 3.7 10.5 - - - +
146A VAL* 1.3 83.8 - - - +
148A TRP* 1.3 59.7 + - - +
149A ALA* 3.3 21.7 + - - +
150A ASP* 2.9 34.1 + - - +
151A PHE* 3.5 3.8 + - - -
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Residues in contact with TRP 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A ILE* 3.8 13.0 - - + +
21A ILE* 4.2 10.5 - - + -
65A LEU* 3.9 24.5 - - + -
68A ALA* 3.7 24.0 - - + -
69A ARG* 4.0 25.7 - - + +
72A THR* 3.5 37.2 + - + -
77A LEU* 3.0 33.9 + - + +
78A ALA* 4.5 3.6 - - - +
88A VAL* 3.5 21.0 - - + +
89A ASP* 3.9 19.7 + - - -
92A VAL* 3.7 34.5 - - + -
147A THR* 1.3 74.2 - - - +
149A ALA* 1.3 55.9 + - - +
150A ASP 3.3 0.2 - - - -
151A PHE* 3.4 12.7 - - + +
152A TYR* 3.0 29.0 + - + +
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Residues in contact with ALA 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A VAL* 3.8 21.9 - - + +
91A ILE* 4.2 9.6 - - + -
92A VAL* 3.9 12.8 - - + -
95A LEU* 4.4 3.3 - - - +
141A LEU* 3.8 5.5 - - + +
142A ILE* 3.7 23.3 - - + -
147A THR* 3.1 13.4 + - - +
148A TRP* 1.3 78.6 - - - +
150A ASP* 1.3 59.4 + - - +
152A TYR* 3.4 2.0 + - - +
153A TRP* 3.0 27.9 + - - +
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Residues in contact with ASP 150 (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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140A TRP* 3.6 18.6 - - + +
141A LEU* 2.9 38.8 + - - +
142A ILE 4.9 0.3 + - - -
145A SER 4.1 0.3 - - - +
146A VAL* 3.3 20.4 - - + -
147A THR* 2.9 34.1 + - - +
149A ALA* 1.3 72.5 - - - +
151A PHE* 1.3 65.3 - - - +
153A TRP* 3.4 5.6 + - - +
154A GLU 3.2 17.0 + - - -
177A LEU* 3.6 9.8 - - + +
181A VAL* 3.6 22.3 - - + +
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Residues in contact with PHE 151 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A ILE* 3.7 9.0 - - + -
20A TYR* 3.7 33.4 - + + -
21A ILE* 4.4 8.1 - - + -
24A TYR* 3.8 28.5 - + + -
77A LEU* 3.5 39.7 - - + -
146A VAL* 3.9 20.2 - - + -
147A THR 3.5 5.3 + - - -
148A TRP* 3.4 13.4 + - - +
150A ASP* 1.3 78.6 - - - +
152A TYR* 1.3 56.8 + - - +
154A GLU* 3.3 4.0 + - - +
155A ILE* 3.0 34.4 + - - +
181A VAL* 4.0 17.9 - - + -
184A ILE* 3.9 14.1 - - + -
187A VAL* 4.0 13.0 - - + -
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Residues in contact with TYR 152 (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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14A ARG* 5.5 5.6 - - - +
17A ILE* 3.7 35.7 - - + -
64A SER* 5.1 2.3 + - - -
65A LEU* 3.9 16.4 - - + +
92A VAL* 3.8 32.3 - - + -
95A LEU* 3.9 17.5 - - + -
96A ASP* 2.6 34.1 + - + -
148A TRP* 3.0 17.4 + - + +
149A ALA* 3.4 7.2 + - - +
150A ASP 3.3 0.2 - - - -
151A PHE* 1.3 74.1 - - - +
153A TRP* 1.3 61.0 + - - +
155A ILE* 4.3 10.8 - - + -
156A CYS* 2.9 59.3 + - - -
202A 0O5 3.5 17.4 - + + -
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Residues in contact with TRP 153 (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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95A LEU* 3.6 28.2 - - + +
128A MET* 3.7 28.7 - - + -
131A LEU* 3.8 21.3 - - + -
141A LEU* 3.9 14.6 - - + -
149A ALA 3.0 16.9 + - - +
150A ASP 3.6 4.7 - - - +
152A TYR* 1.3 76.3 - - - +
154A GLU* 1.3 53.9 + - + +
156A CYS 5.8 0.2 - - - -
157A SER* 2.6 63.2 + - - -
160A LEU* 5.8 2.7 - - + -
167A LEU* 5.0 0.7 - - + -
168A LEU* 3.8 22.2 - - + -
174A LEU* 3.2 41.2 + - + +
177A LEU* 3.6 29.8 - - + +
178A ARG* 3.5 11.2 - - + +
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Residues in contact with GLU 154 (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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20A TYR* 2.6 39.6 + - - -
150A ASP 3.2 10.6 + - - +
151A PHE 3.7 6.1 - - - +
153A TRP* 1.3 82.0 - - + +
155A ILE* 1.3 57.1 + - - +
157A SER* 3.2 5.7 + - - -
158A THR* 2.8 47.2 + - - +
178A ARG* 3.3 23.6 + - - +
181A VAL* 3.8 15.9 - - + -
182A GLN* 2.9 43.5 + - + +
191A ILE* 4.5 2.6 - - - +
194A ARG* 5.2 2.4 + - - -
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Residues in contact with ILE 155 (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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12A ARG* 5.3 5.0 + - + +
13A GLY 4.5 0.9 - - - +
16A GLU* 3.7 18.4 - - + +
17A ILE* 3.5 40.8 - - + +
20A TYR* 3.5 41.1 - - + +
151A PHE 3.0 21.3 + - - +
152A TYR* 3.9 12.3 - - + +
154A GLU* 1.3 79.9 - - - +
156A CYS* 1.3 62.4 + - - +
158A THR* 3.5 5.5 + - - -
159A THR* 3.5 20.1 + - - -
202A 0O5 3.4 24.2 - - + +
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Residues in contact with CYS 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A LEU* 4.4 17.3 - - + -
99A MET* 3.7 35.4 - - + +
152A TYR* 2.9 57.1 + - - +
153A TRP* 4.1 2.0 - - + +
155A ILE* 1.3 76.6 - - - +
157A SER* 1.3 58.4 + - - +
159A THR* 3.3 5.2 + - - -
160A LEU* 3.0 32.8 + - + +
202A 0O5 4.2 8.7 - - - -
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Residues in contact with SER 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A TRP* 2.6 52.7 + - - -
154A GLU* 3.2 2.8 + - - -
156A CYS* 1.3 73.5 - - - +
158A THR* 1.3 59.3 + - - +
160A LEU* 3.7 9.0 - - - +
161A LEU* 2.8 35.0 + - - +
167A LEU* 4.9 3.1 - - - -
168A LEU* 4.7 4.5 - - - -
178A ARG* 2.9 36.7 + - - +
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Residues in contact with THR 158 (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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12A ARG* 4.1 24.0 - - - +
154A GLU* 2.8 42.2 + - - +
155A ILE* 3.7 7.0 - - - -
157A SER* 1.3 76.6 - - - +
159A THR* 1.3 62.1 + - - +
161A LEU* 3.4 10.3 + - - +
162A VAL* 3.4 17.0 + - + +
178A ARG* 3.1 19.9 + - - +
182A GLN* 4.2 0.7 + - - -
194A ARG* 5.0 9.9 - - - +
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Residues in contact with THR 159 (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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12A ARG* 3.5 18.2 + - - +
99A MET* 4.2 10.3 - - + -
104A TRP* 3.6 30.7 - - + -
155A ILE 3.5 9.3 + - - -
156A CYS 3.3 8.6 + - - -
157A SER 3.2 0.8 - - - -
158A THR* 1.3 75.7 - - - +
160A LEU* 1.3 65.3 + - - +
162A VAL* 3.2 23.5 + - - +
163A PHE* 3.5 7.5 - - + -
199A LEU* 3.9 22.9 + - + -
202A 0O5 4.0 17.0 - - + +
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Residues in contact with LEU 160 (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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95A LEU* 6.5 1.6 - - + -
98A PHE* 3.8 23.1 - - + -
99A MET* 3.7 28.0 - - + -
102A PHE* 3.9 28.9 - - + -
104A TRP* 5.1 5.2 - - + -
120A LEU* 4.3 10.9 - - + +
128A MET* 4.5 10.5 - - + -
153A TRP* 5.8 1.8 - - + -
156A CYS* 3.0 22.5 + - + +
157A SER* 3.2 4.2 + - - +
159A THR* 1.3 75.7 - - - +
161A LEU* 1.3 58.5 + - - +
163A PHE* 3.2 8.2 + - + +
164A LYS* 2.9 29.8 + - - +
167A LEU* 3.7 26.5 - - + -
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Residues in contact with LEU 161 (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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157A SER 2.8 20.4 + - - +
158A THR* 3.7 5.4 - - - +
159A THR 3.2 0.4 - - - -
160A LEU* 1.3 69.1 - - - +
162A VAL* 1.3 65.5 + - - +
164A LYS 3.5 10.3 - - - +
165A PRO* 3.4 49.6 - - + +
167A LEU* 3.8 19.5 - - + +
168A LEU* 4.5 12.1 - - + +
175A VAL* 6.4 0.2 - - + -
178A ARG* 3.6 44.0 - - - +
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Residues in contact with VAL 162 (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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12A ARG* 4.7 2.5 - - - +
158A THR* 3.5 17.5 - - + +
159A THR* 3.2 13.4 + - - +
161A LEU* 1.3 79.9 - - - +
163A PHE* 1.3 73.6 + - + +
165A PRO* 4.6 5.7 - - - +
198A LYS* 4.1 47.3 - - + +
199A LEU* 4.9 0.9 - - + -
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Residues in contact with PHE 163 (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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104A TRP* 3.9 18.8 - + - -
112A LYS* 6.1 4.5 - - - -
116A PHE* 4.2 25.8 - + - -
120A LEU* 3.8 25.8 - - + +
159A THR 3.5 15.0 - - - -
160A LEU* 3.2 6.9 + - + +
162A VAL* 1.3 86.4 - - + +
164A LYS* 1.3 60.9 + - - +
165A PRO* 3.9 5.1 - - - +
198A LYS* 4.2 21.5 - - - -
199A LEU* 3.5 36.8 - - + -
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Residues in contact with LYS 164 (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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120A LEU* 3.2 54.4 + - + +
121A THR* 5.2 7.8 - - + +
125A PRO* 4.7 11.5 - - - +
160A LEU 2.9 9.7 + - - +
161A LEU* 3.5 9.9 - - - +
163A PHE* 1.3 79.5 - - - +
165A PRO* 1.3 67.7 - - - +
166A ASP* 3.1 31.0 + - - +
167A LEU* 3.1 45.2 + - + +
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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
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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