Contacts of the strand formed by residues 156 - 159 (chain C) in PDB entry 1SMK
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 ILE 156 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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114C ASP 2.8 14.9 + - - +
115C LEU* 3.1 22.9 - - + +
116C ILE* 2.7 33.1 + - - +
154C ARG 4.4 1.8 - - - +
155C ALA* 1.3 73.6 - - - +
157C VAL* 1.3 57.2 + - - +
158C ASN* 4.1 3.4 - - - +
185C ARG* 3.7 27.6 - - + +
187C LEU* 3.6 24.7 - - + -
282C CYS* 4.3 11.2 - - + -
286C LEU* 3.9 26.0 - - + -
314C LEU* 6.4 0.2 - - + -
317C ASN* 4.0 2.5 - - - -
318C GLY* 3.7 32.1 - - - +
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Residues in contact with VAL 157 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116C ILE* 3.4 10.5 - - + +
118C VAL* 4.5 8.3 - - + -
145C CYS* 5.7 2.5 - - - -
148C ILE* 4.1 40.4 - - + -
155C ALA 3.9 10.5 - - - +
156C ILE* 1.3 76.3 - - - +
158C ASN* 1.3 72.1 + - - +
159C LEU* 3.8 13.9 - - + +
175C PHE* 4.4 14.8 - - + -
185C ARG 2.9 17.0 + - - +
186C LEU* 4.3 16.2 - - + -
187C LEU* 2.9 28.9 + - - +
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Residues in contact with ASN 158 (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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115C LEU* 3.8 17.7 - - - +
116C ILE 2.7 13.1 + - - +
117C ILE* 3.5 11.4 - - + +
118C VAL 2.8 24.7 + - - -
157C VAL* 1.3 78.7 - - - +
159C LEU* 1.3 62.4 + - - +
160C ILE* 3.6 4.0 + - - +
187C LEU* 3.4 8.9 - - - +
189C VAL* 3.7 12.6 - - + -
275C ALA 5.0 1.0 + - - -
278C PHE* 3.4 33.7 - - - -
279C ALA* 3.6 25.1 - - - +
282C CYS* 3.5 15.3 - - - -
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Residues in contact with LEU 159 (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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118C VAL* 3.8 18.8 - - + -
141C VAL* 4.0 14.1 - - + -
145C CYS* 5.0 3.6 - - - -
157C VAL* 3.8 9.8 - - + -
158C ASN* 1.3 71.9 - - - +
160C ILE* 1.3 61.3 - - - +
161C SER* 3.4 30.3 - - - +
164C VAL* 4.4 3.3 - - - +
167C THR* 3.5 43.1 - - - +
168C VAL* 3.9 13.2 - - + -
171C ALA* 3.8 18.6 - - + -
186C LEU* 4.6 4.0 - - + -
187C LEU 2.8 13.4 + - - +
188C GLY* 3.4 3.6 - - - -
189C VAL 2.9 24.8 + - - -
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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