Contacts of the strand formed by residues 181 - 190 (chain H) in PDB entry 1SY6
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 181 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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150H GLY 2.8 23.0 + - - -
151H TYR* 2.6 51.2 + + + +
152H PHE* 3.9 22.0 - + - -
153H PRO* 5.3 0.2 - - + -
154H GLU* 3.8 36.4 - - + +
174H ALA* 3.8 17.9 - - + -
175H VAL 3.5 16.4 - - - -
176H LEU* 3.7 42.0 - - + +
180H LEU* 1.3 73.9 - - - +
182H THR* 1.3 61.2 + - - +
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Residues in contact with THR 182 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147H LEU* 3.9 21.8 - - + -
148H VAL 3.3 9.9 - - - +
149H LYS* 3.1 30.7 - - + +
150H GLY* 3.6 0.9 + - - -
151H TYR* 4.5 0.4 - - - -
173H PRO 4.6 0.5 - - - +
174H ALA* 3.3 2.5 - - - -
175H VAL* 3.0 34.6 + - - +
180H LEU* 5.1 1.6 + - - +
181H TYR* 1.3 76.1 + - - +
183H LEU* 1.3 64.7 + - - +
159L LEU* 4.9 19.6 - - + +
177L THR* 5.3 8.7 - - + +
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Residues in contact with LEU 183 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147H LEU* 3.8 4.2 - - - +
148H VAL* 2.7 59.8 + - + +
151H TYR* 3.9 14.4 - - + +
154H GLU* 5.3 1.6 - - - +
156H VAL* 4.0 23.6 - - + -
158H LEU* 4.0 16.6 - - + -
171H THR* 4.2 14.1 - - + -
172H PHE 3.4 20.0 - - - +
173H PRO* 5.0 2.0 - - + -
174H ALA* 3.9 15.3 - - + +
182H THR* 1.3 77.5 - - - +
184H SER* 1.3 70.8 + - - +
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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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130H LEU* 5.3 0.2 - - - -
146H CYS 3.3 13.0 - - - -
147H LEU* 4.3 12.8 - - - -
171H THR* 3.7 0.7 - - - -
172H PHE* 2.9 35.0 + - - +
183H LEU* 1.3 81.9 - - - +
185H SER* 1.3 63.0 + - - +
132L VAL* 5.2 2.5 - - - -
134L PHE* 4.0 11.7 - - - -
161L SER* 5.8 0.2 - - - -
175L SER* 2.7 34.9 + - - -
177L THR* 5.2 2.2 + - - -
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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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145H GLY* 3.1 4.7 - - - -
146H CYS 2.9 31.2 + - - -
158H LEU* 3.6 25.7 - - - +
160H TRP* 3.1 23.9 + - - -
169H VAL* 4.1 0.5 - - - +
170H HIS 3.2 9.0 + - - -
171H THR* 3.1 23.9 + - - -
172H PHE* 4.4 0.7 - - - -
184H SER* 1.3 76.6 - - - +
186H SER* 1.3 62.1 + - - +
134L PHE* 3.7 4.4 - - - -
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Residues in contact with SER 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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143H THR* 4.2 4.0 - - - +
144H LEU 3.3 6.3 - - - -
160H TRP* 4.6 0.4 - - - -
168H GLY 3.7 0.9 + - - +
169H VAL* 3.3 4.9 - - - +
170H HIS* 2.7 52.7 + - - +
172H PHE* 4.2 2.5 - - - -
185H SER* 1.3 75.0 - - - +
187H VAL* 1.3 61.6 + - - +
188H THR* 5.4 0.9 + - - -
134L PHE* 3.3 34.5 - - - -
136L ASN* 3.4 19.9 + - - -
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Residues in contact with VAL 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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142H VAL 3.8 0.9 - - - +
143H THR* 3.5 1.5 - - - -
144H LEU* 2.9 50.2 + - + +
160H TRP* 3.9 36.6 - - + -
165H LEU* 3.5 30.1 - - + -
167H SER 4.6 0.2 - - - +
168H GLY 3.2 5.2 - - - +
169H VAL* 3.6 20.9 - - + -
186H SER* 1.3 75.6 - - - +
188H THR* 1.3 66.6 + - - +
189H VAL* 4.2 9.0 + - + +
199H ILE* 4.4 6.7 - - + -
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Residues in contact with THR 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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141H SER* 4.2 19.5 - - - +
142H VAL 3.3 11.7 - - - +
143H THR* 3.0 23.9 + - - +
167H SER 4.5 2.3 - - - +
168H GLY* 2.9 27.7 + - - +
186H SER* 5.4 0.9 + - - -
187H VAL* 1.3 74.0 - - - +
189H VAL* 1.3 72.1 + - - +
136L ASN* 4.7 6.8 + - - +
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Residues in contact with VAL 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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141H SER* 3.1 7.0 - - - -
142H VAL* 2.8 45.0 + - + +
144H LEU* 5.3 4.3 - - + -
165H LEU* 4.0 35.9 - - + -
187H VAL* 4.2 7.2 - - + +
188H THR* 1.3 79.1 - - - +
190H THR* 1.3 70.6 + - - +
193H THR* 4.1 17.9 - - + +
194H TRP* 4.2 11.2 - - + -
199H ILE* 4.6 9.6 - - + -
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Residues in contact with THR 190 (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 SER 3.5 11.2 - - - +
141H SER* 3.9 3.4 - - - +
142H VAL* 4.3 0.7 - - - +
189H VAL* 1.3 84.0 - - - +
191H SER* 1.3 65.3 + - - +
192H SER* 3.2 17.1 + - - -
193H THR* 2.6 42.0 + - - +
194H TRP 3.7 2.1 + - - -
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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