Contacts of the strand formed by residues 180 - 189 (chain H) in PDB entry 1VPO
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 TYR 180 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90H THR* 6.0 1.9 - - - +
115H THR* 5.2 8.0 + - - +
148H LYS* 3.5 1.6 - - - -
149H GLY 2.9 25.1 + - - -
150H TYR* 2.9 44.8 + + + +
151H PHE* 3.6 32.8 - + - -
152H PRO* 4.1 0.9 - - + -
153H GLU* 3.6 40.2 + - + +
173H ALA* 3.9 15.7 - - + -
174H VAL 3.2 7.9 - - - -
175H LEU* 3.5 44.7 - - + +
179H LEU* 1.3 73.4 - - - +
181H THR* 1.3 62.2 + - - +
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Residues in contact with THR 181 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146H LEU* 3.6 20.9 - - + -
147H VAL 3.3 4.5 - - - -
148H LYS* 3.1 32.6 - - + +
149H GLY 4.0 1.0 + - - -
172H PRO 4.5 0.5 - - - +
173H ALA* 3.3 2.5 - - - -
174H VAL* 2.9 32.0 + - - +
176H GLN* 2.8 27.0 + - - +
180H TYR* 1.3 75.1 + - - +
182H LEU* 1.3 65.2 + - - +
165L LEU* 3.6 20.3 - - + +
183L THR* 5.2 8.5 - - + +
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Residues in contact with LEU 182 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146H LEU* 3.7 2.4 - - - +
147H VAL* 2.7 45.7 + - + +
150H TYR* 3.9 22.7 - - + +
153H GLU* 4.9 2.2 - - - +
155H VAL* 4.8 18.4 - - + +
157H VAL* 4.1 19.5 - - + -
170H THR* 4.1 16.4 - - + -
171H PHE* 3.1 22.7 - - - +
172H PRO* 5.0 1.1 - - + -
173H ALA* 4.1 10.5 - - + +
181H THR* 1.3 79.9 - - - +
183H SER* 1.3 90.9 + - - +
184H SER 4.4 0.2 - - - +
165L LEU* 6.3 0.2 - - - -
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Residues in contact with SER 183 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129H LEU* 5.1 1.8 - - - -
145H CYS 3.2 11.9 - - - -
146H LEU* 4.4 12.6 - - - -
171H PHE* 2.9 38.5 + - - +
182H LEU* 1.3 84.9 - - - +
184H SER* 1.3 60.7 - - - +
138L VAL* 5.2 3.1 - - - -
140L PHE* 3.7 11.5 - - - -
181L SER* 2.9 27.7 + - - -
183L THR* 5.1 2.4 + - - -
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Residues in contact with SER 184 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144H GLY* 3.1 2.6 - - - -
145H CYS* 2.9 34.6 + - - -
147H VAL* 6.4 0.2 - - - -
157H VAL* 4.0 23.2 - - - +
159H TRP* 3.0 26.3 + - - -
168H VAL* 3.7 1.9 - - - +
169H HIS 3.2 7.0 + - - -
170H THR* 3.0 25.6 + - - -
171H PHE* 4.5 0.2 - - - -
182H LEU* 4.8 0.2 - - - -
183H SER* 1.3 77.7 - - - +
185H SER* 1.3 61.4 + - - +
140L PHE* 3.8 4.3 - - - -
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Residues in contact with SER 185 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142H THR* 4.3 6.0 - - - +
143H LEU 3.3 7.6 - - - -
159H TRP* 4.3 1.6 - - - -
167H GLY 4.3 0.9 + - - -
168H VAL* 3.3 8.1 - - - +
169H HIS* 2.8 49.8 + - - +
171H PHE* 4.3 0.2 - - - -
184H SER* 1.3 74.3 - - - +
186H VAL* 1.3 63.0 + - - +
187H THR* 5.4 0.9 + - - -
140L PHE* 3.5 37.4 - - - -
142L ASN* 3.6 13.9 + - - -
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Residues in contact with VAL 186 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141H VAL 3.9 0.5 - - - +
142H THR* 3.4 1.3 - - - -
143H LEU* 2.7 52.6 + - + +
159H TRP* 3.9 38.4 - - + +
164H LEU* 3.4 29.2 - - + -
166H SER 4.3 1.1 - - - +
167H GLY 3.1 12.6 - - - +
168H VAL* 3.7 14.6 - - + -
185H SER* 1.3 76.0 - - - +
187H THR* 1.3 66.1 + - - +
188H VAL* 4.2 6.7 - - + -
198H VAL* 4.3 8.7 - - + -
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Residues in contact with THR 187 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140H MET* 3.4 38.2 - - + +
141H VAL 3.2 11.9 - - - +
142H THR* 3.0 23.4 + - - +
164H LEU* 5.3 0.3 - - - +
166H SER 4.4 2.9 - - - +
167H GLY* 3.0 24.1 + - - +
185H SER* 5.4 0.9 + - - -
186H VAL* 1.3 75.0 - - - +
188H VAL* 1.3 70.0 + - - +
142L ASN* 5.1 4.9 + - - -
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Residues in contact with VAL 188 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140H MET* 3.4 8.2 - - - -
141H VAL* 2.8 50.5 + - + +
143H LEU* 4.7 5.4 - - + -
164H LEU* 3.7 36.3 - - + -
186H VAL* 4.2 6.1 - - + -
187H THR* 1.3 81.0 - - - +
189H PRO* 1.3 80.2 - - + +
192H THR* 3.9 7.9 - - - +
193H TRP* 4.1 13.5 - - + -
198H VAL* 4.5 13.2 - - + -
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Residues in contact with PRO 189 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139H SER 3.3 10.5 - - - +
140H MET* 3.8 14.6 - - + -
141H VAL* 4.3 0.2 - - - -
188H VAL* 1.3 90.5 - - + +
190H SER* 1.3 63.8 + - - +
191H SER* 2.9 11.4 - - - +
192H THR* 2.8 46.4 + - + +
193H TRP 3.6 2.9 + - - -
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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