Contacts of the strand formed by residues 160 - 163 (chain C) in PDB entry 1I9R
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 GLN 160 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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140C TRP* 5.9 0.2 - - - -
155C LEU* 3.5 7.9 - - - +
156C GLU* 3.1 58.8 + - + +
157C ASN* 4.8 3.0 - - - +
158C GLY 4.0 0.2 - - - -
159C LYS* 1.3 94.7 - - - +
161C LEU* 1.3 62.2 + - - +
162C THR* 3.6 8.0 + - - +
236C SER* 3.2 23.3 + - - +
237C VAL 2.6 24.0 - - - +
238C PHE* 3.7 9.7 - - + +
256C PHE* 4.6 2.2 - - - -
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Residues in contact with LEU 161 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124C ALA* 4.1 21.3 - - + +
126C VAL* 4.2 10.8 - - + -
148C MET* 4.2 17.0 - - + -
153C VAL* 5.0 3.8 - - + -
154C THR 3.6 4.3 - - - +
155C LEU* 4.3 10.8 - - + -
160C GLN* 1.3 74.9 - - - +
162C THR* 1.3 59.9 + - - +
163C VAL* 4.4 0.5 + - - +
236C SER* 3.1 2.4 - - - -
237C VAL* 2.7 36.3 + - + +
256C PHE* 3.4 42.2 - - + +
257C GLY* 3.9 17.9 - - - -
258C LEU* 3.9 28.0 - - + +
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Residues in contact with THR 162 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153C VAL* 3.5 4.9 - - - +
154C THR* 2.9 37.9 + - - +
156C GLU* 2.8 33.3 + - - +
160C GLN* 3.6 2.4 + - - -
161C LEU* 1.3 73.4 - - - +
163C VAL* 1.3 75.0 + - - +
164C LYS* 5.1 11.4 - - + +
234C GLY* 4.0 10.3 - - - +
235C ALA 3.3 11.2 - - - +
236C SER* 2.9 17.7 + - - -
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Residues in contact with VAL 163 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152C LEU 3.9 3.4 - - - +
153C VAL* 3.4 26.5 - - + -
161C LEU 5.5 0.4 - - - +
162C THR* 1.3 75.4 - - - +
164C LYS* 1.3 61.1 + - - +
165C ARG 4.3 4.0 - - - +
169C TYR* 3.7 33.0 - - + +
231C LEU* 4.0 19.3 - - + -
232C GLN 4.5 0.9 - - - +
234C GLY* 2.9 29.6 + - - -
235C ALA* 2.8 33.5 + - + +
236C SER* 5.3 0.2 - - - -
258C LEU* 4.2 13.2 - - + -
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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