Contacts of the helix formed by residues 143 - 156 (chain A) in PDB entry 3SN6
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 PRO 143 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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130A TYR* 4.1 13.7 - - - +
140A PHE* 3.6 19.3 - - + -
141A ASP* 3.5 15.8 - - + +
142A PHE* 1.3 93.1 - - - +
144A PRO* 1.3 69.8 - - + +
145A GLU* 3.0 15.0 - - + +
146A PHE* 2.8 27.8 + - + +
147A TYR* 3.8 4.4 - - - -
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Residues in contact with PRO 144 (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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141A ASP* 5.5 0.9 - - - +
142A PHE 4.5 1.1 - - - +
143A PRO* 1.3 86.3 - - + +
145A GLU* 1.3 60.9 + - - +
147A TYR* 3.8 21.5 + - + +
148A GLU* 3.7 18.1 + - - +
186A LYS* 5.0 5.2 + - - +
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Residues in contact with GLU 145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A TYR* 4.7 14.1 + - + -
143A PRO* 2.9 12.3 + - + +
144A PRO* 1.3 79.6 - - - +
146A PHE* 1.3 65.3 + - - +
148A GLU* 3.2 27.6 + - - +
149A HIS* 3.5 33.4 + - + +
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Residues in contact with PHE 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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96A LYS 5.7 0.2 - - - -
99A LEU* 4.2 15.3 - - + -
100A LYS* 3.9 27.1 - - + -
103A ILE* 3.2 36.1 - - + -
130A TYR* 3.1 38.5 + + - +
131A ILE* 3.8 7.4 - - + -
134A VAL* 4.7 6.3 - - + -
140A PHE* 4.3 9.2 - + - -
142A PHE* 3.9 20.0 - + + -
143A PRO* 2.8 21.6 + - + +
145A GLU* 1.3 80.6 - - - +
147A TYR* 1.3 77.5 + + - +
148A GLU 3.2 0.3 + - - -
149A HIS* 3.3 3.8 + - - +
150A ALA* 2.9 31.5 + - + +
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Residues in contact with TYR 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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96A LYS* 3.0 34.7 + - + +
99A LEU* 5.1 5.2 - - + -
142A PHE* 3.6 29.6 + + + +
143A PRO 3.8 9.4 - - - -
144A PRO* 4.1 13.2 - - + +
145A GLU 3.3 0.6 - - - -
146A PHE* 1.3 95.3 - + - +
148A GLU* 1.3 57.7 + - - +
150A ALA* 3.9 4.0 - - - -
151A LYS* 2.9 33.6 + - - +
182A ILE* 4.1 18.7 - - + +
185A ILE* 4.4 23.4 + - + -
186A LYS* 3.2 48.9 - - + +
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Residues in contact with GLU 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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127A ARG* 5.3 2.5 - - - +
144A PRO 3.7 16.3 - - - +
145A GLU* 3.2 14.9 + - - +
146A PHE 3.2 0.6 - - - -
147A TYR* 1.3 75.1 - - - +
149A HIS* 1.3 71.6 + - + +
151A LYS* 4.1 4.4 - - - +
152A ALA* 2.9 33.6 + - - +
186A LYS* 4.8 11.6 + - - +
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Residues in contact with HIS 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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126A PHE* 4.3 13.6 - + - -
127A ARG* 3.4 48.8 - - + +
130A TYR* 3.2 42.4 - + + +
131A ILE* 4.8 0.9 - - + -
145A GLU* 3.5 38.1 + - + +
146A PHE 3.3 5.9 + - - +
148A GLU* 1.3 84.7 + - + +
150A ALA* 1.3 57.4 + - - +
152A ALA* 3.8 0.9 - - - +
153A LEU* 2.9 36.1 + - - +
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Residues in contact with ALA 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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99A LEU* 4.7 1.8 - - + -
103A ILE* 3.7 39.2 - - + +
131A ILE* 4.8 1.5 - - - +
146A PHE* 2.9 27.6 + - + +
147A TYR* 4.0 4.5 - - - +
149A HIS* 1.3 74.4 - - - +
151A LYS* 1.3 61.2 + - - +
153A LEU* 3.1 9.8 + - - +
154A TRP* 2.9 28.2 + - - +
182A ILE* 4.3 10.8 - - + +
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Residues in contact with LYS 151 (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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147A TYR 2.9 24.0 + - - +
148A GLU* 4.7 3.6 - - - +
150A ALA* 1.3 71.9 - - - +
152A ALA* 1.3 68.4 + - + +
154A TRP* 3.0 5.1 + - - +
155A GLU* 2.9 57.8 + - + +
182A ILE* 4.0 23.4 - - + +
183A ASP* 2.7 44.8 + - - +
186A LYS* 6.1 1.3 - - + -
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Residues in contact with ALA 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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124A ASN* 4.0 12.1 + - - +
127A ARG* 3.2 33.9 - - - +
148A GLU 2.9 20.4 + - - +
149A HIS 3.9 2.7 - - - +
151A LYS* 1.3 83.9 - - + +
153A LEU* 1.3 59.2 + - - +
155A GLU* 3.2 22.0 + - - +
156A ASP 3.3 5.7 + - - -
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Residues in contact with LEU 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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103A ILE* 5.7 4.3 - - + -
107A VAL* 3.5 24.2 - - + -
119A LEU* 4.7 0.7 - - + -
124A ASN* 4.3 15.3 - - + +
127A ARG* 3.7 13.2 - - + +
128A VAL* 3.6 26.0 - - + -
131A ILE* 3.6 29.4 - - + -
149A HIS 2.9 22.8 + - - +
150A ALA* 3.2 7.4 - - - +
152A ALA* 1.3 73.3 - - - +
154A TRP* 1.3 57.6 + - - +
155A GLU 2.9 4.9 - - - -
156A ASP* 2.8 28.6 + - + +
159A VAL* 3.5 33.5 - - + +
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Residues in contact with TRP 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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106A ILE* 3.8 14.8 - - + -
150A ALA 2.9 12.3 + - - +
151A LYS* 3.0 8.2 + - - +
153A LEU* 1.3 76.4 - - - +
155A GLU* 1.3 58.0 + - + +
156A ASP 3.4 0.7 - - - -
159A VAL* 4.5 10.8 - - + -
160A ARG* 2.8 64.5 + - + +
163A TYR* 3.9 31.9 - + + -
176A GLN* 3.8 28.3 - - + -
179A LEU* 3.2 63.5 + - + -
180A ASP* 3.0 20.5 + - - -
182A ILE* 4.3 4.7 - - + -
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Residues in contact with GLU 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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121A ASN* 5.5 1.1 + - - -
151A LYS* 2.9 50.0 + - + +
152A ALA* 3.2 15.5 - - - +
153A LEU 2.9 0.8 - - - -
154A TRP* 1.3 78.9 - - + +
156A ASP* 1.3 62.8 + - - +
157A GLU* 3.3 16.3 + - - +
160A ARG* 4.6 15.2 + - - +
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Residues in contact with ASP 156 (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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119A LEU* 3.5 10.2 - - - +
120A ALA 3.5 5.6 + - - -
121A ASN* 3.1 30.7 + - - +
124A ASN* 2.9 30.1 + - - +
152A ALA 3.3 5.0 + - - -
153A LEU* 2.8 16.8 + - + +
155A GLU* 1.3 76.7 - - - +
157A GLU* 1.3 65.1 + - - +
158A GLY* 2.7 30.2 + - - -
159A VAL* 3.1 19.8 + - + +
160A ARG* 3.3 21.8 + - - +
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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