Contacts of the helix formed by residues 157 - 169 (chain A) in PDB entry 1P4X
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 SER 157 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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150A ILE* 3.9 1.8 - - - -
155A THR 4.0 0.6 + - - -
156A LEU* 1.3 76.4 - - - +
158A PHE* 1.3 60.0 + - - +
159A VAL* 3.3 8.8 + - - +
160A GLU* 2.5 42.4 + - - +
161A PHE* 3.0 26.5 + - - +
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Residues in contact with PHE 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 PHE* 3.9 24.5 - + + -
16A GLU* 3.9 11.7 - - + -
146A PHE* 5.6 0.4 - - - -
147A LYS* 3.7 51.8 - - + +
150A ILE* 4.0 22.8 - - + +
151A LYS* 6.1 1.8 - - - -
157A SER* 1.3 75.7 - - - +
159A VAL* 1.3 72.2 + - + +
161A PHE* 3.5 4.4 + - - +
162A THR* 3.0 31.5 + - - -
186A HIS* 3.9 25.1 - + - -
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Residues in contact with VAL 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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157A SER* 3.2 7.5 + - - +
158A PHE* 1.3 95.9 - - + +
160A GLU* 1.3 65.9 + - - +
162A THR* 3.1 6.9 + - - -
163A ILE* 3.0 29.8 + - + +
186A HIS* 3.7 41.5 - - + +
190A GLN* 4.5 16.4 - - + +
194A ALA* 4.2 17.0 - - + -
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Residues in contact with GLU 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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155A THR 4.6 1.0 - - - +
156A LEU* 3.3 17.7 - - + +
157A SER* 2.5 45.1 + - - +
159A VAL* 1.3 76.1 - - + +
161A PHE* 1.3 58.0 + - - +
163A ILE* 3.3 1.5 + - - -
164A LEU* 2.9 29.7 + - - +
194A ALA* 3.7 30.5 - - + +
197A ASN* 3.4 32.1 + - - +
198A LEU* 3.6 23.1 - - + +
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Residues in contact with PHE 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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9A ILE* 4.1 18.8 - - + -
12A PHE* 6.1 0.2 - + - -
146A PHE* 3.8 32.3 - + - -
150A ILE* 4.0 11.4 - - + -
154A LEU* 3.8 14.1 - - + -
156A LEU* 4.6 8.4 - - + +
157A SER 3.0 18.1 + - - +
158A PHE* 3.7 7.9 - - - +
159A VAL 3.1 0.2 - - - -
160A GLU* 1.3 74.9 - - - +
162A THR* 1.3 69.3 + - - +
164A LEU* 3.3 11.7 + - + +
165A ALA* 2.9 22.7 + - + +
231A LEU* 3.3 28.9 - - + -
232A LEU* 3.7 24.5 - - + -
235A VAL* 3.5 28.7 - - + -
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Residues in contact with THR 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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9A ILE* 6.3 0.4 - - - -
12A PHE* 4.0 19.8 - - - -
13A ILE* 4.4 22.1 - - + +
158A PHE* 3.0 19.0 + - - -
159A VAL* 3.1 12.1 + - - -
161A PHE* 1.3 80.5 - - - +
163A ILE* 1.3 60.1 + - + +
165A ALA* 3.5 5.0 - - - +
166A ILE* 2.9 48.4 + - + +
184A ILE* 5.1 1.8 - - + -
185A HIS* 6.1 0.7 - - + -
186A HIS* 4.4 21.3 + - + +
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Residues in contact with ILE 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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159A VAL* 3.0 20.1 + - + +
160A GLU 3.6 6.3 - - - +
162A THR* 1.3 80.5 - - + +
164A LEU* 1.3 61.7 + - - +
166A ILE* 3.9 6.4 - - - +
167A ILE* 3.1 26.2 + - + +
180A LEU* 4.9 13.2 - - + -
184A ILE* 4.5 16.2 - - + -
186A HIS* 5.6 0.4 - - + -
191A THR* 3.8 31.2 - - + +
194A ALA* 3.5 29.4 - - + -
195A LEU* 3.5 28.9 - - + -
198A LEU* 3.8 10.1 - - + -
204A LEU* 5.0 2.0 - - + -
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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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156A LEU* 4.1 22.4 - - + -
160A GLU 2.9 18.1 + - - +
161A PHE* 3.6 16.8 - - + +
163A ILE* 1.3 75.9 - - - +
165A ALA* 1.3 51.6 + - - +
167A ILE* 3.7 4.0 - - - +
168A THR* 2.7 50.6 + - - +
198A LEU* 4.1 10.3 - - + +
203A TYR* 3.8 44.6 - - + +
204A LEU* 4.7 7.4 - - + -
220A MET* 4.7 4.3 - - - -
228A ALA* 4.4 13.7 - - + -
231A LEU* 4.7 12.6 - - + -
232A LEU* 4.9 3.8 - - + -
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Residues in contact with ALA 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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3A TYR* 3.4 28.9 - - + -
9A ILE* 4.2 15.9 - - + -
13A ILE* 4.4 3.8 - - + -
161A PHE* 2.9 18.8 + - + +
162A THR* 3.5 4.5 - - - +
164A LEU* 1.3 77.4 - - - +
166A ILE* 1.3 62.0 + - - +
168A THR* 3.2 2.6 + - - -
169A SER 3.1 18.4 + - - -
232A LEU* 4.0 25.5 - - + +
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Residues in contact with ILE 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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1A MET* 4.5 18.8 - - + +
2A LYS* 4.7 7.6 - - - -
3A TYR* 4.2 14.1 - - + +
13A ILE* 4.5 18.6 - - + -
162A THR* 2.9 35.1 + - + +
163A ILE* 3.9 7.0 - - - +
165A ALA* 1.3 75.1 - - - +
167A ILE* 1.3 65.5 + - + +
169A SER* 2.7 24.3 + - - -
170A GLN* 3.1 14.3 + - - +
180A LEU* 4.4 17.0 - - + -
183A THR* 5.7 4.5 - - + -
184A ILE* 3.5 30.5 - - + -
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Residues in contact with ILE 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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163A ILE* 3.1 20.8 + - + +
164A LEU 4.0 2.9 - - - +
166A ILE* 1.3 81.1 - - + +
168A THR* 1.3 64.5 + - - +
170A GLN* 3.1 21.8 + - - +
172A LYS 5.2 0.7 + - - -
175A VAL* 3.9 31.6 - - + -
180A LEU* 4.1 27.4 - - + -
204A LEU* 4.1 15.3 - - + -
218A ILE* 3.7 27.8 - - + +
219A HIS* 5.0 4.7 - - - -
220A MET* 3.5 34.3 - - + +
225A GLN* 4.3 1.0 + - - -
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Residues in contact with THR 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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5A ASN* 5.9 0.9 - - - +
164A LEU* 2.7 26.5 + - - +
165A ALA 3.5 5.2 - - - -
166A ILE 3.2 0.4 - - - -
167A ILE* 1.3 78.1 - - - +
169A SER* 1.3 58.2 + - - +
170A GLN 3.1 3.9 + - - -
171A ASN* 3.4 6.6 + - - +
220A MET* 3.1 15.2 - - + +
225A GLN* 3.1 18.2 + - - +
228A ALA* 3.1 31.9 - - + +
229A GLU* 3.3 24.9 - - - +
232A LEU* 3.5 25.7 - - + +
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Residues in contact with SER 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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2A LYS 3.3 10.4 + - - -
3A TYR* 3.7 4.7 - - - -
4A ASN* 3.0 32.0 + - - +
5A ASN* 3.4 29.1 - - - +
165A ALA 3.1 10.0 + - - -
166A ILE 2.7 20.5 + - - -
168A THR* 1.3 73.9 - - - +
170A GLN* 1.3 65.8 + - - +
171A ASN* 3.2 18.6 + - - +
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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