Contacts of the strand formed by residues 181 - 188 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27A ASP 5.5 0.4 - - - -
29A ASP* 4.9 0.4 - - - -
146B SER 3.6 0.3 - - - -
147B ASP* 2.9 26.0 + - - -
148B PHE* 2.9 42.5 + - + -
149B TYR* 3.9 19.5 - + - -
150B PRO 3.9 2.0 - - - -
151B GLY* 3.3 33.0 - - - -
173B LEU* 3.5 31.0 - - + -
174B VAL 3.2 18.6 - - - +
175B ARG* 3.6 53.2 - - + -
176B ASN* 3.8 4.1 + - - +
180B THR* 1.3 75.5 - - - +
182B GLN* 1.3 62.6 + - - +
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Residues in contact with GLN 182 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A LEU* 3.8 16.4 - - - +
93A SER* 3.1 21.2 + - - +
94A ARG* 2.9 21.4 + - - +
95A SER* 4.7 4.5 - - - -
96A PRO* 5.4 1.0 - - - +
106A ILE* 4.5 0.2 - - - +
145B VAL 3.3 12.3 - - - +
146B SER* 3.9 12.9 - - - -
148B PHE* 3.8 3.1 - - - -
173B LEU* 4.2 0.9 - - - +
174B VAL* 2.9 41.2 + - + +
176B ASN* 2.7 27.4 + - - +
181B PHE* 1.3 77.6 - - - +
183B THR* 1.3 64.0 + - - +
184B LEU* 6.0 3.1 - - - +
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Residues in contact with THR 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143B CYS 4.0 0.5 - - - +
145B VAL* 2.8 54.3 + - + +
148B PHE* 4.3 11.7 - - + -
153B ILE* 4.5 12.3 - - + -
155B VAL* 4.8 1.1 - - + -
170B SER* 3.7 10.0 + - - -
171B THR* 3.6 6.9 + - - -
172B GLY 2.7 25.5 + - - -
173B LEU* 4.6 3.6 - - - -
174B VAL* 5.3 0.7 - - - -
182B GLN* 1.3 80.5 - - - +
184B LEU* 1.3 70.8 + - - +
185B VAL* 4.4 10.9 - - + +
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Residues in contact with LEU 184 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96A PRO* 5.9 1.6 - - + -
128B TYR* 4.5 7.6 - - - +
142B VAL* 4.1 18.6 - - + -
143B CYS 3.5 2.7 - - - +
144B SER* 3.7 32.5 - - - +
170B SER* 3.3 6.9 + - - -
171B THR* 3.2 49.0 + - + +
182B GLN* 6.0 3.6 - - - +
183B THR* 1.3 78.1 + - - +
185B VAL* 1.3 62.6 + - - +
186B MET* 4.1 11.8 + - + +
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Residues in contact with VAL 185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143B CYS* 2.7 44.3 + - + +
145B VAL* 5.6 0.2 - - + -
155B VAL* 3.6 45.5 - - + +
157B TRP* 3.3 20.2 + - + +
168B ILE* 3.8 24.7 - - + -
169B VAL 3.7 3.8 - - - +
170B SER* 4.2 13.7 - - - +
183B THR* 4.4 9.0 - - + +
184B LEU* 1.3 77.9 - - - +
186B MET* 1.3 59.7 + - - +
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Residues in contact with MET 186 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130B THR* 4.8 2.5 - - + +
140B LEU* 3.5 45.3 - - + -
141B LEU 3.4 6.3 - - - +
142B VAL* 3.9 33.2 - - + -
157B TRP* 3.8 3.1 - - - -
167B GLY 3.6 0.9 - - - +
168B ILE* 3.5 6.2 - - - +
169B VAL* 2.7 50.5 + - + +
170B SER* 5.4 0.2 - - - -
171B THR* 5.4 2.0 - - - -
184B LEU* 4.7 18.2 - - + +
185B VAL* 1.3 80.1 - - - +
187B LEU* 1.3 61.5 + - - +
188B GLU* 4.8 0.2 - - - +
20D VAL* 5.3 12.1 - - - -
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Residues in contact with LEU 187 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140B LEU* 3.4 7.6 - - - -
141B LEU* 3.0 36.8 + - + +
157B TRP* 3.7 43.0 - - + +
164B GLU* 4.0 18.2 - - + +
166B THR 3.9 12.3 - - - +
167B GLY 3.9 4.0 - - - +
168B ILE* 3.5 22.4 - - + -
186B MET* 1.3 73.6 - - - +
188B GLU* 1.3 68.0 + - - +
189B THR* 3.4 32.0 + - + +
197B TYR* 4.2 16.2 - - + -
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Residues in contact with GLU 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139B ASN 4.7 1.6 - - - -
140B LEU* 3.6 23.3 - - + +
166B THR 4.9 1.2 - - - +
167B GLY* 2.8 52.0 + - - +
169B VAL* 3.3 25.7 - - + +
186B MET 4.8 0.7 - - - +
187B LEU* 1.3 72.8 - - - +
189B THR* 1.3 66.5 + - - +
305C NAG 5.9 1.7 - - - +
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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