Contacts of the strand formed by residues 181 - 189 (chain H) in PDB entry 1I3R
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 PHE 181 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27G ASP 5.4 0.4 - - - -
29G ASP* 4.5 1.3 - - - -
147H ASP* 3.0 24.8 + - - -
148H PHE* 2.8 41.7 + - + -
149H TYR* 3.9 20.9 - + - -
150H PRO 3.9 0.7 - - - -
151H GLY* 3.4 32.1 - - - -
173H LEU* 3.3 34.8 - - + -
174H VAL 3.2 15.0 - - - -
175H ARG* 3.4 55.0 - - + -
176H ASN* 3.8 3.0 + - - -
180H THR* 1.3 77.4 - - - +
182H GLN* 1.3 61.7 + - - +
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Residues in contact with GLN 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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92G LEU* 4.1 14.2 - - - +
93G SER* 2.9 29.4 + - - +
94G ARG* 3.4 9.8 + - - +
95G SER* 4.7 5.4 - - - -
96G PRO* 5.4 1.0 - - - +
145H VAL 3.4 6.7 - - - -
146H SER* 4.0 18.0 - - - -
147H ASP 4.6 0.2 - - - +
148H PHE* 3.8 2.9 - - - -
173H LEU* 4.2 0.2 - - - -
174H VAL* 2.9 47.3 + - + +
176H ASN* 2.8 27.3 + - - +
181H PHE* 1.3 77.2 - - - +
183H THR* 1.3 63.6 + - - +
184H LEU* 5.8 5.2 - - - +
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Residues in contact with THR 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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143H CYS 4.0 0.5 - - - +
144H SER* 4.6 0.2 + - - -
145H VAL* 2.8 54.6 + - + +
148H PHE* 4.4 11.0 - - + -
153H ILE* 4.6 12.3 - - + -
155H VAL* 4.9 1.3 - - + -
170H SER* 3.6 11.3 + - - -
171H THR* 4.0 3.1 - - - -
172H GLY 2.8 28.1 + - - -
173H LEU* 4.5 4.0 - - - -
182H GLN* 1.3 79.6 + - - +
184H LEU* 1.3 67.5 + - - +
185H VAL* 4.5 12.0 - - + +
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Residues in contact with LEU 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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96G PRO* 6.0 0.7 - - + -
128H TYR* 4.3 9.2 - - - +
142H VAL* 4.1 18.2 - - + -
143H CYS 3.7 2.0 - - - -
144H SER* 3.6 34.1 - - - +
170H SER* 3.3 6.6 + - - -
171H THR* 3.2 46.5 + - + +
182H GLN* 5.8 4.5 - - - +
183H THR* 1.3 77.9 + - - +
185H VAL* 1.3 62.1 + - - +
186H MET* 4.0 12.2 + - + +
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Residues in contact with VAL 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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143H CYS* 2.9 34.6 + - + +
145H VAL* 5.6 0.2 - - + -
155H VAL* 3.8 45.8 - - + +
157H TRP* 3.2 25.8 + - + +
168H ILE* 3.9 22.7 - - + -
169H VAL 3.7 3.1 - - - +
170H SER* 4.1 12.8 - - - +
183H THR* 4.5 11.0 - - + -
184H LEU* 1.3 75.9 - - - +
186H MET* 1.3 61.9 + - - +
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Residues in contact with MET 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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309E NAG 5.7 4.7 - - + -
20F VAL* 5.3 10.5 - - + -
130H THR* 5.5 0.9 - - - +
140H LEU* 3.3 40.6 - - + -
141H LEU 3.3 2.7 - - - +
142H VAL* 3.3 33.2 - - + -
157H TRP* 3.9 2.2 - - - -
168H ILE* 3.3 11.3 - - - +
169H VAL* 2.7 50.2 + - + +
170H SER* 5.1 0.7 - - - -
171H THR* 5.1 6.7 - - + -
184H LEU* 4.3 25.8 - - + +
185H VAL* 1.3 75.4 - - - +
187H LEU* 1.3 60.8 + - - +
188H GLU 4.2 0.4 - - - -
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Residues in contact with LEU 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 LEU* 3.6 3.2 - - - +
141H LEU* 2.9 39.2 + - + +
157H TRP* 3.8 47.1 - - + +
158H PHE 5.3 0.4 - - - +
164H GLU* 3.9 20.6 - - + +
166H THR 3.9 15.5 - - - +
167H GLY 3.7 1.1 - - - +
168H ILE* 3.5 18.6 - - + -
186H MET* 1.3 74.0 - - - +
188H GLU* 1.3 62.5 + - - +
189H THR* 3.3 33.4 + - + +
197H TYR* 4.1 16.2 - - + -
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Residues in contact with GLU 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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309E NAG 5.3 5.0 - - - +
138H HIS* 5.1 13.0 - - + +
139H ASN 3.7 3.8 - - - +
140H LEU* 3.2 25.3 - - + +
166H THR 5.3 0.2 - - - +
167H GLY* 2.8 41.3 + - - +
169H VAL* 3.5 24.8 - - + +
187H LEU* 1.3 70.5 - - - +
189H THR* 1.3 64.7 + - - +
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Residues in contact with THR 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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138H HIS* 4.2 2.2 - - - +
139H ASN* 2.6 37.8 + - - +
141H LEU* 4.9 4.9 - - - +
159H ARG* 4.2 16.6 - - - +
164H GLU* 4.7 8.3 - - - +
187H LEU* 3.3 36.2 + - + +
188H GLU* 1.3 80.1 - - - +
190H VAL* 1.3 67.2 + - - +
191H PRO* 3.7 8.7 - - - +
197H TYR* 3.7 25.8 + - + -
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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