Contacts of the strand formed by residues 159 - 172 (chain A) in PDB entry 1PG6
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 ILE 159 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95A GLN* 2.8 41.0 + - + +
96A ILE 4.5 0.2 - - - -
97A VAL* 4.0 31.0 - - + +
154A ASN 5.1 0.9 - - - -
155A SER* 3.2 36.3 - - - +
158A SER* 1.3 74.9 - - - +
160A LYS* 1.3 66.9 + - - +
161A LYS* 4.3 0.7 - - + +
177A VAL* 4.9 5.8 - - + -
214A TYR* 4.0 31.0 - - + -
215A ILE 3.3 9.6 - - - +
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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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158A SER 4.1 0.8 + - - +
159A ILE* 1.3 78.7 - - - +
161A LYS* 1.3 68.4 + - - +
162A ILE* 3.3 28.3 - - + +
213A ILE 3.7 0.5 - - - +
214A TYR* 3.5 3.5 - - - -
215A ILE* 2.9 56.3 + - + +
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Residues in contact with LYS 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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159A ILE* 4.7 1.0 - - + +
160A LYS* 1.3 81.2 + - - +
162A ILE* 1.3 69.2 + - - +
163A THR* 4.3 9.7 + - - +
212A GLU* 3.5 28.7 - - + +
213A ILE 3.7 2.9 - - - -
214A TYR* 3.6 36.9 + - + +
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Residues in contact with ILE 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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160A LYS* 3.3 32.3 - - + +
161A LYS* 1.3 74.8 - - - +
163A THR* 1.3 72.4 + - - +
164A LEU* 4.1 1.7 + - + +
169A MSE 3.9 39.7 - - + -
171A ILE* 4.5 4.9 - - + -
212A GLU* 3.3 5.0 - - - +
213A ILE* 2.8 50.8 + - + +
215A ILE* 3.9 31.4 - - + -
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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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161A LYS* 4.3 10.9 + - - +
162A ILE* 1.3 81.3 + - - +
164A LEU* 1.3 73.5 + - - +
165A ASP* 4.0 5.7 + - + +
211A GLY 3.7 7.0 - - - +
212A GLU* 4.1 21.4 + - - +
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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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162A ILE* 4.1 1.7 + - + -
163A THR* 1.3 80.4 - - - +
165A ASP* 1.3 62.4 + - - +
166A GLY 3.5 0.2 - - - -
167A GLY* 3.9 32.5 - - - +
168A THR 4.2 9.9 - - - +
169A MSE 4.3 22.0 - - + -
183A LEU* 4.1 12.3 - - + -
207A PHE* 3.7 34.1 - - + +
209A GLY 3.4 9.4 - - - +
210A HIS* 3.4 3.3 - - - +
211A GLY 2.9 32.1 + - - +
213A ILE* 3.8 17.7 - - + +
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Residues in contact with ASP 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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163A THR* 4.0 6.2 + - + +
164A LEU* 1.3 74.4 - - - +
166A GLY* 1.3 56.4 + - - +
167A GLY 3.6 3.8 - - - +
210A HIS* 3.1 26.3 + - - -
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Residues in contact with GLY 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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165A ASP* 1.3 73.5 - - - +
167A GLY* 1.3 65.2 + - - +
208A ARG* 5.7 0.3 - - - +
209A GLY* 2.8 28.4 + - - -
210A HIS* 3.4 19.3 - - - -
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Residues in contact with GLY 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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164A LEU* 3.9 11.4 - - - +
165A ASP 3.6 5.9 - - - +
166A GLY* 1.3 77.3 - - - +
168A THR* 1.3 61.5 + - - -
208A ARG* 3.5 2.8 - - - -
209A GLY 3.1 26.2 + - - +
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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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164A LEU* 4.2 4.9 - - - +
167A GLY* 1.3 75.6 - - - -
169A MSE 1.3 69.0 + - - +
170A THR* 5.0 0.5 + - - -
206A THR* 3.7 12.3 - - - +
207A PHE 2.8 17.9 + - - -
208A ARG* 3.5 19.8 + - - +
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Residues in contact with MSE 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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162A ILE* 3.9 36.3 - - + -
164A LEU* 4.3 21.7 - - + +
168A THR* 1.3 81.2 + - - +
170A THR* 1.3 67.2 + - - +
171A ILE* 4.1 26.0 - - + -
206A THR* 3.5 0.2 - - - -
207A PHE* 2.8 35.1 + - - +
213A ILE* 4.8 6.5 - - + -
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Residues in contact with THR 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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168A THR* 5.0 0.9 + - - -
169A MSE 1.3 74.9 - - - +
171A ILE* 1.3 69.2 + - - +
188A HIS* 5.3 0.4 - - + -
190A GLU* 3.9 12.3 - - - +
204A VAL* 3.5 30.1 - - + -
205A ASN 3.3 4.3 - - - +
206A THR* 2.8 34.8 + - - +
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Residues in contact with ILE 171 (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 ILE* 4.5 4.7 - - + -
169A MSE 4.1 27.6 - - + -
170A THR* 1.3 81.2 - - - +
172A ASP* 1.3 74.8 + - + +
173A ASN 3.0 0.2 + - - -
175A HIS* 4.4 9.4 - - + -
176A VAL* 4.1 12.1 - - + -
204A VAL* 4.2 4.5 - - - -
205A ASN* 2.8 39.9 + - - +
207A PHE* 4.1 10.3 - - + -
213A ILE* 4.0 15.9 - - + -
215A ILE* 3.8 33.0 - - + -
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Residues in contact with ASP 172 (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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171A ILE* 1.3 82.4 - - + +
173A ASN* 1.3 64.3 + - - +
174A ALA* 3.0 18.5 + - - +
175A HIS* 3.0 34.2 + - + +
176A VAL* 3.7 1.9 - - - +
201A GLU* 3.2 26.9 - - - +
202A GLY* 4.9 8.7 + - - -
203A VAL 3.8 10.3 - - - +
204A VAL* 4.3 10.3 - - + +
219A ASN* 3.5 18.1 + - - -
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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