Contacts of the strand formed by residues 157 - 163 (chain C) in PDB entry 1SBB
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 VAL 157 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113C ARG* 4.0 8.2 + - - +
125C PRO* 4.9 0.9 - - + -
149C ALA* 6.0 0.2 - - + -
152C PHE* 3.6 37.5 - - + -
155C ASP 3.3 7.1 + - - +
156C HIS* 1.3 80.2 - - - +
158C GLU* 1.3 69.2 + - - +
178C ALA* 5.2 2.5 - - + -
192C LEU* 3.6 27.3 - - + +
214C VAL* 4.3 17.3 - - + -
215C GLN 3.0 10.8 - - - +
216C PHE* 3.7 25.6 - - + -
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Residues in contact with GLU 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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113C ARG* 3.0 29.0 + - - +
157C VAL* 1.3 80.9 - - - +
159C LEU* 1.3 61.9 + - - +
160C SER* 5.3 0.6 + - - -
192C LEU* 5.6 0.4 - - - -
213C GLN 3.5 1.2 - - - +
214C VAL* 3.2 5.6 - - - -
215C GLN* 2.8 48.8 + - + +
217C HIS* 2.7 38.6 + - - -
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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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147C CYS* 4.3 6.3 - - + -
149C ALA* 5.0 2.2 - - + -
158C GLU* 1.3 76.0 - - - +
160C SER* 1.3 87.5 + - - +
161C TRP* 4.3 3.1 - - + +
174C THR* 4.7 16.3 + - + +
192C LEU* 4.4 30.6 - - + +
193C SER 4.4 11.4 - - - +
194C SER* 3.5 37.2 - - - +
212C CYS* 3.7 26.2 - - - -
213C GLN 3.1 8.7 - - - +
214C VAL* 4.0 10.3 - - + -
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Residues in contact with SER 160 (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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158C GLU 5.3 0.7 + - - -
159C LEU* 1.3 82.1 - - - +
161C TRP* 1.3 65.6 + - - +
162C TRP* 3.1 23.7 + - - -
167C GLU* 4.4 16.6 - - - -
172C VAL* 6.2 1.1 - - - -
212C CYS* 3.4 6.1 - - - -
213C GLN* 2.9 41.3 + - - +
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Residues in contact with TRP 161 (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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129C LEU* 3.5 33.9 - - + -
145C LEU* 3.9 24.0 - - + -
147C CYS* 3.7 28.9 - - + -
159C LEU* 4.5 3.4 - - + -
160C SER* 1.3 77.9 - - - +
162C TRP* 1.3 63.5 + - - +
163C VAL* 5.8 0.4 - - + -
167C GLU* 3.2 6.8 - - - +
168C VAL* 2.8 48.3 + - + +
172C VAL* 3.6 28.6 - - + +
194C SER* 2.7 29.7 + - - -
195C ARG 4.0 3.4 - - - -
196C LEU* 3.7 37.5 - - + +
211C ARG 3.2 31.0 - - - -
212C CYS* 3.8 7.9 - - + -
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Residues in contact with TRP 162 (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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160C SER* 3.1 27.2 + - - -
161C TRP* 1.3 83.2 - - - +
163C VAL* 1.3 64.3 - - - +
164C ASN 3.6 2.6 + - - -
165C GLY* 3.7 22.5 + - - -
166C LYS* 3.0 12.3 - - - +
167C GLU* 3.3 44.6 - - + +
209C HIS* 3.8 2.6 + - - +
211C ARG* 2.9 45.9 + - + +
213C GLN* 2.8 36.9 - - + +
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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
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162C TRP* 1.3 72.5 - - - +
164C ASN* 1.3 72.5 + - + +
166C LYS* 2.9 19.3 + - + +
168C VAL* 3.3 30.2 - - + +
196C LEU* 3.8 29.8 - - + -
198C VAL* 5.3 2.5 - - + -
202C PHE* 4.4 24.7 - - + -
209C HIS 3.2 8.5 - - - +
210C PHE* 3.9 15.3 - - + -
211C ARG 5.6 0.2 - - - +
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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