Contacts of the helix formed by residues 153 - 170 (chain A) in PDB entry 2P3L
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 153 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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151A SER* 3.1 9.5 + - - +
152A PRO* 1.3 78.2 - - - +
154A PRO* 1.4 69.2 - - - +
155A THR* 3.0 26.9 + - - -
156A VAL* 3.2 39.0 + - + +
157A GLU* 3.3 8.0 + - - +
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Residues in contact with PRO 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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11A GLU* 4.7 9.9 - - + +
14A LYS* 4.0 14.8 - - + -
18A ASN* 5.4 0.2 - - - +
152A PRO 3.5 9.6 - - - +
153A ASN* 1.4 87.5 - - - +
155A THR* 1.3 58.0 + - - +
157A GLU* 3.3 8.6 + - - +
158A ALA* 2.8 28.1 + - - +
184A ASN* 3.7 10.8 - - - +
186A TYR* 3.6 23.1 - - + +
187A MET* 3.7 26.3 - - + +
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Residues in contact with THR 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A ASN* 3.0 16.9 + - - -
154A PRO* 1.3 74.2 - - - +
156A VAL* 1.3 66.1 + - + +
158A ALA* 3.3 9.4 + - + +
159A GLY* 3.1 19.1 + - - -
187A MET* 4.0 15.7 - - + +
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Residues in contact with VAL 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A SER* 3.4 13.5 - - - +
153A ASN* 3.4 34.3 + - + +
155A THR* 1.3 77.7 - - - +
157A GLU* 1.3 61.3 + - - +
159A GLY* 3.2 4.6 + - - -
160A ARG* 3.1 57.4 + - + +
163A ARG* 5.7 0.2 + - - -
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Residues in contact with GLU 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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13A TRP* 6.0 0.7 - - - -
14A LYS* 3.5 19.6 + - - -
149A GLU 4.6 0.2 - - - +
150A SER* 3.5 12.2 + - - -
151A SER* 3.0 46.9 + - - +
153A ASN 3.3 5.6 + - - +
154A PRO* 3.5 6.9 - - - +
155A THR 3.3 0.2 - - - -
156A VAL* 1.3 72.6 - - - +
158A ALA* 1.3 60.6 + - - +
160A ARG* 3.3 6.6 + - - +
161A THR* 2.8 35.1 + - - -
183A LEU* 3.6 26.0 - - + +
184A ASN* 2.9 28.8 + - + +
186A TYR* 4.0 2.1 + - - -
1002A G3A 5.6 0.2 - - - +
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Residues in contact with ALA 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 PRO 2.8 18.2 + - - +
155A THR* 3.3 13.7 + - + +
157A GLU* 1.3 71.7 - - - +
159A GLY* 1.3 56.3 + - - +
161A THR* 3.3 2.0 + - - -
162A LEU* 2.9 37.5 + - + +
184A ASN* 4.5 1.7 - - - +
187A MET* 3.9 20.9 - - + -
189A SER* 3.7 21.3 - - - +
190A VAL* 4.0 10.7 - - + +
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Residues in contact with GLY 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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155A THR 3.1 13.5 + - - -
156A VAL 3.2 4.2 + - - -
158A ALA* 1.3 75.2 - - - +
160A ARG* 1.3 61.7 + - - +
162A LEU* 3.8 10.3 - - - +
163A ARG* 3.2 44.2 + - - +
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Residues in contact with ARG 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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148A GLY* 5.6 2.2 - - - -
149A GLU* 2.9 67.3 + - - +
150A SER 3.1 16.4 + - - -
151A SER* 3.6 11.5 - - - -
156A VAL* 3.1 34.6 + - + +
157A GLU* 3.6 8.1 - - - +
159A GLY* 1.3 73.7 - - - +
161A THR* 1.3 65.1 + - - +
163A ARG* 3.4 15.9 + - - +
164A VAL* 3.1 27.3 + - - +
183A LEU* 5.0 4.3 - - + -
1003A CIT 4.6 18.2 + - - +
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Residues in contact with THR 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 GLU 2.8 23.0 + - - -
158A ALA 3.7 3.4 - - - -
160A ARG* 1.3 69.6 - - - +
162A LEU* 1.3 59.7 + - - +
164A VAL* 3.1 9.8 + - + +
165A LEU* 2.8 33.7 + - + +
181A LYS 5.4 0.7 - - - +
182A VAL* 3.7 32.5 - - + -
183A LEU* 3.3 16.6 - - - +
184A ASN* 3.1 20.9 + - - +
190A VAL* 3.7 22.9 - - + -
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Residues in contact with LEU 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 ALA* 2.9 24.1 + - + +
159A GLY* 3.8 8.7 - - - +
161A THR* 1.3 75.0 - - - +
163A ARG* 1.3 55.4 + - - +
165A LEU* 3.3 4.7 + - + +
166A ASN* 2.7 46.5 + - - +
189A SER* 3.6 44.6 - - - +
190A VAL* 4.2 7.9 - - + -
193A LYS* 3.8 23.6 - - + -
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Residues in contact with ARG 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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133A PHE* 3.3 20.6 - - + -
159A GLY* 3.2 31.9 + - - +
160A ARG* 3.6 14.4 - - - +
161A THR 3.3 0.2 - - - -
162A LEU* 1.3 76.7 - - - +
164A VAL* 1.3 58.7 + - - +
166A ASN* 3.8 5.4 - - - +
167A LEU* 2.9 28.8 + - - +
1003A CIT 4.0 30.2 + - - +
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Residues in contact with VAL 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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133A PHE* 4.3 9.9 - - + -
145A CYS* 4.1 22.7 - - - -
147A ILE* 3.8 37.9 - - + +
148A GLY* 5.0 2.7 - - - -
160A ARG* 3.1 15.4 + - + +
161A THR* 3.1 11.8 + - + +
163A ARG* 1.3 76.2 - - - +
165A LEU* 1.3 58.8 + - + +
167A LEU* 3.0 8.5 - - - +
168A VAL* 3.0 27.0 + - - +
180A VAL* 4.1 18.2 - - + -
181A LYS 4.1 11.0 - - - +
183A LEU* 6.4 0.2 - - + -
1003A CIT 5.9 0.9 - - - +
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Residues in contact with LEU 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 THR* 2.8 28.3 + - + +
162A LEU* 3.3 6.7 + - + +
164A VAL* 1.3 72.4 - - + +
166A ASN* 1.3 59.8 + - - +
168A VAL* 3.2 8.6 - - + +
169A GLU* 3.0 29.9 + - - +
180A VAL* 4.8 6.7 - - + -
181A LYS 5.4 0.7 - - - +
182A VAL* 4.7 11.7 - - + -
190A VAL* 4.1 17.7 - - + -
193A LYS* 3.7 27.4 - - + -
194A MET* 3.8 32.5 - - + -
197A LEU* 3.8 24.5 - - + +
220A TRP* 4.5 11.2 - - + -
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Residues in contact with ASN 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 LEU* 2.7 42.5 + - - +
163A ARG* 4.0 4.6 - - - +
165A LEU* 1.3 69.8 - - - +
167A LEU* 1.3 66.7 + - - +
169A GLU* 3.7 10.4 - - - +
170A ASN* 3.5 26.8 + - - +
193A LYS* 3.3 28.7 + - - +
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Residues in contact with LEU 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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80A LEU* 4.1 16.4 - - + -
132A VAL* 3.7 38.1 - - + +
133A PHE* 3.5 31.0 - - + +
135A ILE 6.0 0.2 - - - +
145A CYS* 4.7 10.5 - - - -
147A ILE* 5.0 0.9 - - + -
163A ARG 2.9 15.8 + - - +
164A VAL* 3.0 15.3 - - - +
166A ASN* 1.3 76.8 - - - +
168A VAL* 1.3 54.6 + - - +
170A ASN* 3.0 25.0 + - + +
171A TRP* 3.3 30.3 - - + +
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Residues in contact with VAL 168 (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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80A LEU* 4.6 4.5 - - + -
143A LEU* 3.7 24.2 - - + +
145A CYS* 3.9 20.2 - - + -
164A VAL 3.0 15.8 + - - +
165A LEU* 3.2 18.2 - - + +
167A LEU* 1.3 75.6 - - + +
169A GLU* 1.3 63.6 + - - +
171A TRP* 2.9 19.6 + - - +
172A LEU* 3.1 19.8 + - + +
180A VAL* 3.9 28.9 - - + -
220A TRP* 4.2 23.6 - - + -
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Residues in contact with GLU 169 (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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165A LEU 3.0 16.4 + - - +
166A ASN* 3.7 12.5 - - - +
168A VAL* 1.3 78.0 - - - +
170A ASN* 1.3 62.6 + - - +
171A TRP 3.4 0.7 + - - -
172A LEU* 3.6 23.2 + - - +
193A LYS* 2.7 31.6 + - - -
197A LEU* 3.5 21.3 - - + +
200A LYS* 3.7 24.9 - - + +
201A HIS* 4.7 11.6 - - + -
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Residues in contact with ASN 170 (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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137A PRO* 3.4 32.3 - - + +
166A ASN* 3.5 16.8 + - - +
167A LEU* 3.0 16.5 + - + +
169A GLU* 1.3 79.7 - - - +
171A TRP* 1.3 60.5 + - + +
172A LEU 3.5 0.9 - - - -
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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