Contacts of the strand formed by residues 151 - 155 (chain C) in PDB entry 1JIQ
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 ASP 151 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149C ILE* 3.6 5.9 - - - +
150C THR* 1.3 95.2 + - - +
152C VAL* 1.3 63.7 + - - +
153C ILE* 4.0 1.6 - - + -
180C ARG* 2.8 46.8 + - - +
182C TRP* 2.9 22.1 + - + +
198C GLN 5.7 0.2 - - - +
199C LEU* 3.6 28.4 - - + +
200C ASN 5.7 1.0 + - - -
203C SER* 3.3 3.3 + - - +
204C SER* 3.5 11.1 + - - +
205C LEU 2.9 26.0 + - - -
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Residues in contact with VAL 152 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136C VAL* 4.9 1.3 - - + -
149C ILE* 4.6 3.4 - - + -
151C ASP* 1.3 75.2 - - - +
153C ILE* 1.3 60.6 + - - +
154C ASN 4.8 0.2 - - - +
179C PRO* 3.5 27.6 - - + -
180C ARG 2.8 10.8 + - - +
181C VAL* 3.2 18.2 - - + +
182C TRP* 2.8 33.3 + - - +
205C LEU* 3.3 18.6 - - + +
207C ILE* 3.4 34.1 - - + -
283C SER* 4.6 5.2 - - - -
286C LEU* 4.0 17.9 - - + -
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Residues in contact with ILE 153 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151C ASP* 3.9 14.6 - - + +
152C VAL* 1.3 80.3 - - - +
154C ASN* 1.3 59.8 + - - +
155C ILE* 3.7 4.5 + - + +
182C TRP* 3.5 19.5 - - + +
184C VAL* 3.9 28.5 - - + -
192C ILE* 5.2 0.7 - - + -
195C THR* 4.4 3.4 - - + -
199C LEU* 3.7 31.0 - - + -
204C SER* 3.9 15.9 - - - +
205C LEU 2.8 18.6 + - - +
206C PHE* 3.4 30.2 - - + +
207C ILE* 2.8 32.1 + - - +
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Residues in contact with ASN 154 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152C VAL* 4.1 2.2 - - - +
153C ILE* 1.3 73.1 - - - +
155C ILE* 1.3 70.9 + - - +
156C GLY 4.1 1.2 - - - +
160C SER 2.9 27.4 + - - +
161C ASP* 4.4 2.5 + - - +
164C PRO* 5.0 1.1 - - - +
182C TRP 2.9 6.2 + - - +
183C TYR* 3.5 36.8 - - + -
184C VAL* 2.9 27.9 + - - +
207C ILE* 3.6 27.5 - - + +
209C ALA* 4.4 1.9 - - - +
246C LEU* 4.4 8.3 - - - +
280C ILE 4.7 2.6 - - - +
283C SER* 3.9 17.9 + - - -
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Residues in contact with ILE 155 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153C ILE* 4.2 9.9 - - + +
154C ASN* 1.3 79.0 - - - +
156C GLY* 1.3 59.8 - - - +
184C VAL* 3.4 17.7 - - + +
192C ILE* 4.4 7.6 - - + -
206C PHE* 4.0 18.8 - - + -
207C ILE 2.8 12.5 + - - +
208C ILE* 3.7 24.7 - - + -
209C ALA* 2.9 27.2 + - - +
218C THR* 3.6 21.5 - - + +
221C ASN* 3.5 33.9 - - + +
222C ALA* 3.9 14.4 - - - +
225C ALA* 4.0 5.6 - - + -
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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