Contacts of the helix formed by residues 139 - 162 (chain A) in PDB entry 3P1S
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 ASP 139 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A GLY 3.2 1.0 - - - -
138A ASP* 1.3 75.9 - - - +
140A LYS* 1.3 64.8 - - - +
141A LYS 3.3 3.4 - - - -
142A ARG* 3.1 37.3 + - - +
143A ILE* 2.9 39.4 + - + +
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Residues in contact with LYS 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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132A ALA 4.8 6.8 + - - +
135A ALA* 4.1 41.7 + - + +
136A THR* 4.7 8.1 - - - +
137A GLY 3.2 19.1 + - - +
138A ASP 3.5 0.4 - - - -
139A ASP* 1.3 77.5 - - - +
141A LYS* 1.3 70.2 + - + +
143A ILE* 3.2 2.8 + - - +
144A ILE* 2.9 48.5 + - + +
183A ILE* 5.2 3.6 + - - +
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Residues in contact with LYS 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A ASP 4.9 3.6 + - - +
139A ASP 3.3 1.0 - - - -
140A LYS* 1.3 83.3 - - + +
142A ARG* 1.3 58.2 + - - +
144A ILE* 3.3 11.3 + - + +
145A ASP* 2.9 29.2 + - - +
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Residues in contact with ARG 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A ASP* 3.6 23.5 + - - +
139A ASP* 3.1 28.2 + - - +
141A LYS* 1.3 75.9 - - + +
143A ILE* 1.3 60.7 + - + +
145A ASP* 3.3 12.4 + - + +
146A SER* 3.0 32.8 + - - +
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Residues in contact with ILE 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A TYR* 3.3 36.5 - - + +
131A LEU* 3.7 18.8 - - + +
132A ALA* 3.6 16.8 - - - +
135A ALA* 3.9 21.5 - - + -
139A ASP* 2.9 32.8 + - + +
140A LYS* 3.6 5.8 - - - +
142A ARG* 1.3 72.9 - - + +
144A ILE* 1.3 65.9 + - - +
146A SER* 3.1 8.5 + - - -
147A ALA* 3.0 22.0 + - - +
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Residues in contact with ILE 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A ALA* 3.8 11.7 - - + -
140A LYS* 2.9 51.7 + - + +
141A LYS* 3.6 9.0 - - + +
143A ILE* 1.3 75.4 - - - +
145A ASP* 1.3 58.2 + - - +
147A ALA* 3.2 3.2 + - - +
148A ARG* 2.9 26.2 + - + +
179A PHE* 3.5 27.8 - - + -
183A ILE* 3.6 31.2 - - + +
184A ALA* 4.9 8.5 - - + -
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Residues in contact with ASP 145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A LYS 2.9 15.0 + - - +
142A ARG* 3.4 16.5 - - + +
144A ILE* 1.3 77.3 - - - +
146A SER* 1.3 65.2 + - - +
148A ARG* 3.4 28.4 + - - +
149A SER* 2.8 31.9 + - - -
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Residues in contact with SER 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A LYS* 5.3 2.4 - - - -
128A TYR* 3.6 38.8 + - - -
142A ARG* 3.0 15.8 + - - +
143A ILE* 3.1 8.2 + - - -
145A ASP* 1.3 82.3 + - - +
147A ALA* 1.3 64.9 + - - +
149A SER* 3.9 4.4 - - - -
150A ALA* 3.1 24.6 + - - +
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Residues in contact with ALA 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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125A GLY* 3.6 17.8 - - - +
128A TYR* 3.6 23.5 - - + +
129A ARG* 3.8 7.9 - - - +
132A ALA* 5.7 0.4 - - + -
143A ILE 3.0 9.6 + - - +
144A ILE* 3.5 8.5 - - - +
146A SER* 1.3 74.8 - - - +
148A ARG* 1.3 65.6 + - - +
150A ALA* 3.3 1.7 + - - +
151A TYR* 3.0 30.4 + - + -
179A PHE* 3.6 20.0 - - + -
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Residues in contact with ARG 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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144A ILE* 2.9 18.1 + - + +
145A ASP* 3.5 27.7 + - - +
147A ALA* 1.3 75.3 - - - +
149A SER* 1.3 74.8 + - - +
151A TYR* 3.3 2.1 + - - +
152A GLN* 2.8 63.9 + - - +
176A PHE* 4.3 15.5 - - + -
179A PHE* 3.8 25.7 - - + -
180A HIS* 5.7 2.0 - - + -
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Residues in contact with SER 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 ASP* 2.8 25.8 + - - -
146A SER* 3.9 5.8 - - - -
147A ALA 3.2 0.2 - - - -
148A ARG* 1.3 94.8 + - - +
150A ALA* 1.3 58.2 + - - +
152A GLN* 3.4 2.4 + - - +
153A GLU* 3.0 29.6 + - - +
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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
----------------------------------------------------------
121A LEU* 3.7 21.5 - - + +
124A LYS* 3.8 23.3 - - + -
125A GLY 3.6 25.1 - - - +
146A SER 3.1 17.9 + - - +
147A ALA 3.7 1.1 - - - +
149A SER* 1.3 74.5 - - - +
151A TYR* 1.3 66.9 + - - +
153A GLU* 3.3 3.7 + - - +
154A ALA* 3.0 22.5 + - - +
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Residues in contact with TYR 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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122A LYS* 3.6 17.5 - - + -
125A GLY* 3.4 20.4 - - - -
126A ASP* 2.5 34.5 + - - -
129A ARG* 2.9 22.6 + - - -
147A ALA 3.0 25.7 + - - +
148A ARG 3.7 0.2 - - - +
150A ALA* 1.3 76.1 - - - +
152A GLN* 1.3 53.6 + - - +
154A ALA* 3.3 6.0 + - - +
155A MET* 2.8 39.5 + - - +
172A LEU* 3.6 20.8 - - + +
175A ASN* 3.8 15.6 - - + +
176A PHE* 3.5 37.5 - + + -
179A PHE* 3.8 27.6 - + + -
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Residues in contact with GLN 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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148A ARG* 2.8 36.8 + - - +
149A SER* 3.7 4.5 - - - +
150A ALA 3.2 0.2 - - - -
151A TYR* 1.3 77.8 - - - +
153A GLU* 1.3 57.0 + - - +
155A MET* 3.2 11.9 + - - +
156A ASP* 2.9 64.6 + - - +
159A LYS* 4.7 4.4 - - - +
176A PHE* 3.7 22.3 - - + -
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Residues in contact with GLU 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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117A ARG* 3.6 26.2 + - - -
121A LEU* 3.6 27.6 - - + +
149A SER 3.0 17.4 + - - +
150A ALA* 3.9 3.9 - - - +
152A GLN* 1.3 75.4 - - - +
154A ALA* 1.3 61.8 + - - +
156A ASP* 3.2 9.5 + - + +
157A ILE* 3.0 32.6 + - + +
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Residues in contact with ALA 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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118A VAL* 3.8 19.3 - - + +
121A LEU* 3.6 25.5 - - + +
122A LYS 4.1 1.8 - - - +
150A ALA 3.0 14.4 + - - +
151A TYR 3.5 6.3 - - - +
153A GLU* 1.3 77.4 - - - +
155A MET* 1.4 56.4 + - - +
157A ILE 3.4 0.5 + - - -
158A SER* 2.9 31.0 + - - -
172A LEU* 3.4 27.2 - - + +
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Residues in contact with MET 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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151A TYR 2.8 24.3 + - - +
152A GLN* 3.5 11.9 - - - +
154A ALA* 1.4 68.7 - - - +
156A ASP* 1.3 66.6 + - - +
158A SER* 3.0 8.0 + - - +
159A LYS* 2.9 66.1 + - + +
169A ARG* 5.3 4.0 - - + +
172A LEU* 3.7 22.4 - - + -
173A ALA* 4.3 17.3 - - + -
176A PHE* 3.4 30.3 - - + -
193A LEU* 4.2 19.3 - - + -
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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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152A GLN* 2.9 48.7 + - - +
153A GLU* 3.2 8.9 + - + +
155A MET* 1.3 75.7 - - - +
157A ILE* 1.3 65.5 + - + +
159A LYS* 3.5 8.7 + - - +
160A LYS* 3.3 28.2 + - - +
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Residues in contact with ILE 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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114A ALA* 4.0 21.3 - - + -
117A ARG* 3.8 25.1 - - + +
118A VAL* 3.6 21.3 - - + -
121A LEU* 3.8 23.1 - - + -
153A GLU* 3.0 28.0 + - + +
156A ASP* 1.3 78.2 - - + +
158A SER* 1.3 56.8 - - - +
160A LYS* 3.1 4.8 + - - -
161A GLU* 2.8 37.3 + - + +
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Residues in contact with SER 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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118A VAL* 3.8 15.0 - - - +
154A ALA 2.9 16.5 + - - -
155A MET* 3.0 19.9 + - - +
157A ILE* 1.3 77.3 - - - +
159A LYS* 1.3 58.9 + - - +
162A MET* 2.9 56.9 + - - +
169A ARG* 3.7 23.0 + - - +
172A LEU* 3.7 6.5 - - - +
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Residues in contact with LYS 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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152A GLN* 4.7 3.8 - - - +
155A MET* 2.9 60.5 + - + +
156A ASP* 4.0 12.6 + - - +
158A SER* 1.3 79.7 + - - +
160A LYS* 1.3 63.4 + - + +
162A MET 4.3 2.1 - - - +
169A ARG* 3.9 34.1 + - - +
193A LEU* 5.9 1.3 - - - -
200A GLU* 6.1 0.4 - - - +
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Residues in contact with LYS 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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156A ASP 3.3 16.5 + - - +
157A ILE* 3.1 5.8 + - - +
159A LYS* 1.3 82.8 - - + +
161A GLU* 1.3 75.9 + - + +
162A MET 5.1 0.2 - - - -
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Residues in contact with GLU 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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114A ALA* 3.5 27.7 - - + +
115A GLU* 4.6 1.7 - - - +
157A ILE* 2.8 23.9 + - + +
160A LYS* 1.3 91.6 - - + +
162A MET* 1.3 59.2 + - + +
251A MG 2.3 31.5 - - - -
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Residues in contact with MET 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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114A ALA* 3.7 14.1 - - + +
115A GLU* 3.6 45.5 - - + +
118A VAL* 3.9 11.0 - - + -
158A SER* 2.9 34.5 + - - +
159A LYS 4.3 2.9 - - - +
160A LYS 3.8 0.4 - - - -
161A GLU* 1.3 82.4 - - - +
163A PRO* 1.4 74.3 - - + +
166A HIS* 4.1 10.3 - - + +
168A ILE* 3.9 18.8 - - + -
169A ARG* 2.9 42.2 + - - -
251A MG 4.3 0.2 - - - -
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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
------------------------------------------------------------
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