Contacts of the helix formed by residues 152 - 167 (chain A) in PDB entry 3S51
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 ASN 152 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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141A LYS* 4.0 19.3 - - - +
142A GLU* 3.5 19.9 + - - -
143A VAL* 4.2 7.1 + - - +
144A LEU* 4.6 2.2 - - - -
151A LEU* 1.3 78.5 - - - +
153A GLY* 1.3 64.9 + - - +
154A GLU* 3.0 34.4 + - + +
155A GLU* 3.0 23.2 + - - +
156A TYR* 3.4 21.5 + - - +
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Residues in contact with GLY 153 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A LEU* 3.0 38.6 - - - +
140A LYS* 2.8 17.5 + - - -
142A GLU 4.2 1.4 + - - -
144A LEU* 4.4 14.3 - - - +
152A ASN* 1.3 72.7 - - - +
154A GLU* 1.3 61.0 + - - +
156A TYR* 3.8 0.7 + - - -
157A LYS* 3.3 24.1 + - - +
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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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138A ALA* 3.8 24.8 + - + +
140A LYS 4.3 1.0 + - - -
141A LYS* 3.9 29.8 + - + +
152A ASN* 3.0 28.1 + - + +
153A GLY* 1.3 78.3 - - - +
155A GLU* 1.3 72.9 + - + +
157A LYS* 3.5 8.9 + - + +
158A ARG* 3.0 26.2 + - - +
190A GLU* 4.4 1.2 - - - +
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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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150A ASP 3.7 4.0 - - - +
151A LEU* 3.3 29.1 - - + +
152A ASN* 3.0 38.6 + - - +
153A GLY 3.3 0.2 - - - -
154A GLU* 1.3 91.0 - - + +
156A TYR* 1.3 60.5 + - - +
157A LYS 3.2 0.2 - - - -
158A ARG* 3.6 6.6 - - - +
159A GLN* 2.8 36.8 + - + +
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Residues in contact with TYR 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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106A VAL* 3.8 36.1 - - + -
137A LEU* 4.5 3.4 - - + -
144A LEU* 3.9 26.0 - - + -
146A CYS* 3.4 34.4 + - + +
147A GLY* 5.1 1.0 - - - -
148A LYS 3.6 16.3 + - - -
149A GLY 4.2 4.7 - - - -
151A LEU* 3.5 42.9 - - + +
152A ASN 3.4 9.4 + - - +
153A GLY 4.3 3.4 - - - +
155A GLU* 1.3 77.5 - - - +
157A LYS* 1.3 57.4 - - - +
159A GLN* 3.8 10.2 - - + +
160A LEU* 2.9 36.8 + - + +
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Residues in contact with LYS 157 (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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134A LEU* 3.4 47.8 - - + +
135A THR* 5.7 1.1 - - - +
137A LEU* 4.0 7.6 - - + +
138A ALA* 4.4 16.2 - - + +
153A GLY 3.3 18.7 + - - +
154A GLU* 3.6 8.8 - - + +
155A GLU 3.2 0.4 - - - -
156A TYR* 1.3 79.2 - - - +
158A ARG* 1.3 58.9 + - - +
161A ILE* 3.3 31.6 + - + +
184A VAL* 4.5 5.6 - - - -
185A CYS* 3.0 29.9 + - - +
186A LEU* 4.2 2.6 - - - +
187A THR* 4.7 2.4 + - - -
190A GLU* 3.1 31.8 + - - +
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Residues in contact with ARG 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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154A GLU 3.0 17.4 + - - +
155A GLU* 3.6 7.9 - - - +
156A TYR 3.2 0.2 - - - -
157A LYS* 1.3 76.5 - - - +
159A GLN* 1.3 66.1 + - + +
161A ILE* 3.9 2.9 - - - +
162A ASP* 2.8 46.2 + - - +
187A THR* 5.1 0.9 - - - +
189A GLU* 4.0 23.4 - - - +
190A GLU* 3.3 33.8 - - + +
193A LEU* 4.0 26.7 - - - +
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Residues in contact with GLN 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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151A LEU* 4.0 29.9 - - - +
155A GLU* 2.8 20.7 + - + +
156A TYR* 4.2 11.1 - - + +
158A ARG* 1.3 79.6 - - - +
160A LEU* 1.3 57.2 + - - +
162A ASP* 3.4 12.4 - - - +
163A THR* 2.7 36.9 + - - -
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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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106A VAL* 4.2 14.6 - - + +
109A ALA* 3.6 37.7 - - + +
110A SER* 3.4 32.1 - - - +
113A VAL* 4.1 12.5 - - + +
130A LEU* 6.2 0.4 - - + -
134A LEU* 4.0 11.2 - - + -
137A LEU* 3.7 23.8 - - + -
156A TYR* 2.9 23.7 + - + +
157A LYS 3.9 4.3 - - - +
159A GLN* 1.3 73.4 - - - +
161A ILE* 1.3 67.2 + - - +
163A THR* 3.1 7.9 + - - -
164A LEU* 2.9 24.7 + - + +
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Residues in contact with ILE 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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134A LEU* 4.2 19.3 - - + -
157A LYS* 3.3 29.0 + - + +
158A ARG* 3.9 3.6 - - - +
160A LEU* 1.3 77.9 - - - +
162A ASP* 1.3 64.9 + - - +
164A LEU* 2.9 20.9 + - + +
165A CYS* 2.9 24.4 + - - -
181A PHE* 3.9 27.6 - - + -
184A VAL* 4.8 0.4 - - + -
186A LEU* 3.6 18.4 - - + -
190A GLU* 3.6 33.0 - - + +
193A LEU* 5.1 3.8 - - + -
194A VAL* 4.2 7.6 - - + -
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Residues in contact with ASP 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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158A ARG* 2.8 39.2 + - - +
159A GLN* 3.4 15.4 - - - +
161A ILE* 1.3 77.5 - - - +
163A THR* 1.3 60.5 + - - +
165A CYS* 3.5 4.8 + - - +
166A SER* 3.4 18.2 + - - -
193A LEU* 3.5 32.5 - - + +
197A LYS* 5.6 0.3 - - - -
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Residues in contact with THR 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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113A VAL* 4.1 17.5 - - + -
117A ARG* 5.7 5.2 - - - +
159A GLN 2.7 20.1 + - - -
160A LEU* 3.5 9.2 - - - -
162A ASP* 1.3 72.4 - - - +
164A LEU* 1.3 66.0 + - - +
165A CYS 3.0 1.8 - - - -
166A SER* 2.9 24.1 + - - +
167A VAL* 3.0 21.8 + - + +
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Residues in contact with LEU 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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113A VAL* 3.9 22.6 - - + +
116A VAL* 3.9 32.5 - - + -
130A LEU* 4.1 31.6 - - + -
134A LEU* 5.3 1.6 - - + -
160A LEU* 2.9 8.9 + - + +
161A ILE* 2.9 19.2 + - + +
163A THR* 1.3 76.2 - - - +
165A CYS* 1.3 59.1 + - - +
167A VAL* 3.1 24.7 - - + +
169A TRP* 3.6 16.3 + - + -
177A LEU* 4.7 12.1 - - + -
180A VAL* 6.4 0.4 - - + -
181A PHE* 4.2 26.7 - - + -
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Residues in contact with CYS 165 (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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161A ILE* 2.9 28.6 + - - -
162A ASP 3.7 8.5 - - - +
163A THR 3.0 0.2 - - - -
164A LEU* 1.3 79.3 - - - +
166A SER* 1.3 60.0 + - - +
167A VAL 3.7 5.2 + - - +
169A TRP* 4.0 15.6 + - - -
181A PHE* 5.0 2.2 - - - -
193A LEU* 3.9 24.2 - - + -
194A VAL* 4.1 11.2 - - - -
197A LYS* 3.2 51.4 + - + +
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Residues in contact with SER 166 (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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162A ASP 3.4 6.6 + - - -
163A THR* 2.9 27.6 + - - +
165A CYS* 1.3 77.6 - - - +
167A VAL* 1.3 63.2 + - - +
168A ARG* 4.0 3.1 + - - +
197A LYS* 4.1 11.9 - - - +
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Residues in contact with VAL 167 (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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113A VAL* 4.1 11.9 - - + -
116A VAL* 3.6 25.1 - - + -
117A ARG* 4.3 27.1 - - + +
163A THR* 3.0 29.6 + - + +
164A LEU* 3.1 25.2 - - - +
165A CYS 3.7 1.7 - - - +
166A SER* 1.3 80.8 - - - +
168A ARG* 1.3 59.5 + - - +
169A TRP* 3.2 22.7 + - - -
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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
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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