Contacts of the helix formed by residues 157 - 170 (chain A) in PDB entry 1PT6
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 157 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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156A TYR* 1.3 111.7 + - + +
158A TRP* 1.3 61.7 + - - +
159A ASP* 4.3 13.0 - - + +
160A SER* 2.3 47.7 + - - +
161A VAL* 3.9 1.7 + - - +
317A GLU* 4.4 3.5 - - + +
318A LEU* 4.7 20.4 - - + -
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Residues in contact with TRP 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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149A LEU* 4.3 17.0 - - + -
150A ASP 3.6 25.6 - - - -
151A GLY* 4.0 7.9 - - - -
155A ILE* 4.0 9.4 - - + -
156A TYR* 4.0 4.4 - - - +
157A PRO* 1.3 67.8 - - - +
159A ASP* 1.3 62.5 + - - +
160A SER 3.0 2.0 - - - -
161A VAL* 2.8 53.1 + - + +
162A THR* 3.0 22.9 + - + +
165A LEU* 6.1 0.2 - - + -
185A GLN* 3.9 24.2 - - - -
212A ILE* 3.0 32.1 + - + -
213A VAL* 4.6 0.9 - - - -
214A GLN* 3.4 51.5 - - + +
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Residues in contact with ASP 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 PRO* 4.8 11.5 - - + +
158A TRP* 1.3 79.1 - - - +
160A SER* 1.3 56.2 + - - +
162A THR* 3.1 12.0 + - - -
163A ALA* 2.8 31.5 + - - +
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Residues in contact with SER 160 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A PRO* 2.3 35.1 + - - +
159A ASP* 1.3 76.9 - - - +
161A VAL* 1.3 60.7 + - - +
163A ALA* 3.7 7.0 - - - +
164A PHE* 3.1 24.8 + - - +
317A GLU* 3.2 44.0 - - - +
318A LEU* 4.2 13.5 - - - -
320A LEU* 4.3 4.7 - - - +
321A VAL* 4.6 3.4 - - - +
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Residues in contact with VAL 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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149A LEU* 4.0 32.1 - - + -
150A ASP 5.7 0.4 - - - +
155A ILE* 3.7 30.7 - - + -
157A PRO 4.5 0.4 - - - +
158A TRP* 2.8 37.7 + - + +
160A SER* 1.3 81.0 + - - +
162A THR* 1.3 60.7 + - - +
164A PHE* 3.1 9.5 + - + +
165A LEU* 3.0 28.2 + - + +
251A VAL* 5.9 2.0 - - + -
281A ILE* 5.4 2.9 - - + -
317A GLU* 5.3 1.1 - - + -
320A LEU* 4.3 16.6 - - + -
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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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158A TRP* 3.0 33.2 + - + +
159A ASP* 3.1 23.2 + - - -
161A VAL* 1.3 75.5 - - - +
163A ALA* 1.3 56.0 + - - +
165A LEU* 3.3 11.8 + - + +
166A ASN* 2.8 30.5 + - - +
209A ALA* 4.0 17.1 - - - +
210A LYS* 4.4 17.4 + - - +
212A ILE* 3.9 11.2 - - + +
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Residues in contact with ALA 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 ASP 2.8 20.8 + - - +
160A SER* 3.7 8.7 - - - +
162A THR* 1.3 72.6 + - - +
164A PHE* 1.3 60.0 + - - +
166A ASN* 3.3 5.7 + - - +
167A ASP* 2.9 38.2 + - - +
321A VAL* 3.8 16.4 - - + -
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Residues in contact with PHE 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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147A ILE* 5.3 1.6 - - + -
149A LEU* 5.3 1.1 - - + -
160A SER 3.1 15.6 + - - +
161A VAL* 3.1 13.4 + - + +
163A ALA* 1.3 74.1 - - - +
165A LEU* 1.3 82.6 + - + +
167A ASP* 3.2 2.1 + - - +
168A LEU* 3.0 37.2 + - + +
249A VAL* 4.9 2.2 - - + -
251A VAL* 4.2 18.8 - - + -
279A ILE* 3.9 13.5 - - + -
320A LEU* 3.6 45.5 - - + -
321A VAL* 3.8 8.2 - - - +
323A ILE* 4.0 20.2 - - + -
324A VAL* 3.6 20.2 - - + -
327A LEU* 3.8 24.5 - - + -
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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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147A ILE* 3.8 40.8 - - + -
149A LEU* 3.8 26.7 - - + -
158A TRP* 6.1 0.2 - - + -
161A VAL* 3.0 19.1 + - + +
162A THR* 3.6 13.5 - - + +
164A PHE* 1.3 87.8 - - + +
166A ASN* 1.3 57.7 + - - +
168A LEU* 4.6 2.7 - - - -
169A LEU* 2.9 45.9 + - + +
183A ILE* 4.3 7.9 - - + -
209A ALA* 4.3 15.0 - - + +
212A ILE* 4.0 21.8 - - + -
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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 THR 2.8 17.9 + - - +
163A ALA* 3.6 6.7 - - - +
165A LEU* 1.3 77.4 - - - +
167A ASP* 1.3 76.2 + - - +
169A LEU* 5.2 0.2 - - - -
170A LYS* 3.0 53.1 + - - +
206A LEU* 3.5 22.5 - - - +
209A ALA* 5.0 3.5 - - + +
210A LYS* 3.4 36.5 + - + -
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Residues in contact with ASP 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 ALA* 2.9 21.5 + - - +
164A PHE* 3.9 3.1 - - - +
166A ASN* 1.3 83.6 + - - +
168A LEU* 1.3 61.6 + - - +
170A LYS* 3.1 33.5 + - - +
171A ARG* 3.3 26.2 - - - +
321A VAL* 3.6 21.3 - - - +
324A VAL* 3.5 19.3 - - + -
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Residues in contact with LEU 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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147A ILE* 4.3 25.6 - - + -
164A PHE* 3.0 28.8 + - + +
165A LEU* 3.9 3.1 - - - +
167A ASP* 1.3 76.8 - - - +
169A LEU* 1.3 65.2 + - + +
171A ARG* 3.3 18.6 + - + +
172A MET* 3.7 26.7 - - + +
249A VAL* 5.3 4.3 - - + -
324A VAL* 3.5 28.6 - - + +
327A LEU* 3.8 33.7 - - + -
328A GLY* 4.2 14.4 - - - +
331A ILE* 4.6 6.5 - - + -
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Residues in contact with LEU 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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147A ILE* 4.3 11.2 - - + -
165A LEU* 2.9 30.5 + - + +
168A LEU* 1.3 77.9 - - + +
170A LYS* 1.3 57.6 + - - +
171A ARG 3.1 0.4 - - - -
172A MET* 3.0 36.3 + - + +
174A ILE* 4.6 2.4 - - + +
181A VAL* 3.6 39.5 - - + -
183A ILE* 4.4 12.3 - - + -
202A THR* 3.4 10.3 - - - +
205A VAL* 3.6 25.4 - - + -
206A LEU* 3.8 11.7 - - + -
209A ALA* 3.8 21.5 - - + -
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Residues in contact with LYS 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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166A ASN* 3.0 28.7 + - - +
167A ASP* 3.1 43.0 + - - +
168A LEU 3.3 0.4 - - - -
169A LEU* 1.3 77.3 - - - +
171A ARG* 1.3 64.9 + - + +
172A MET 3.2 5.5 + - - +
202A THR* 3.9 10.1 - - - +
206A LEU* 3.5 22.4 - - + +
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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