Contacts of the strand formed by residues 152 - 159 (chain C) in PDB entry 3H3B
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 152 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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144C GLU* 3.4 46.4 - - + +
146C VAL* 5.1 2.7 - - + -
151C SER* 1.3 76.8 - - - +
153C LYS* 1.3 64.8 + - - +
154C ILE* 4.4 12.3 - - + -
215C MET 3.6 1.0 - - - +
216C GLN* 3.2 5.7 - - - +
217C LEU* 2.8 64.5 + - + +
220C LEU* 3.8 19.7 - - + -
250C VAL* 4.3 11.9 - - + -
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Residues in contact with LYS 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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141C SER* 4.4 3.3 + - - -
144C GLU* 5.3 3.7 + - - +
152C VAL* 1.3 77.8 - - - +
154C ILE* 1.3 61.9 + - - +
155C SER* 3.7 3.5 + - - -
205C THR* 4.4 7.7 + - - -
214C PHE* 3.7 46.5 - - + -
215C MET 3.5 7.2 - - - +
216C GLN* 4.2 20.6 - - + +
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Residues in contact with ILE 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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140C GLN* 4.2 2.0 - - - +
141C SER* 3.8 8.1 - - - +
144C GLU* 5.6 0.7 - - + -
152C VAL* 4.4 15.0 - - + -
153C LYS* 1.3 71.6 - - - +
155C SER* 1.3 70.1 + - - +
170C TRP* 3.7 19.7 - - + -
214C PHE* 3.3 5.9 - - - +
215C MET* 2.9 61.3 + - + +
217C LEU* 4.0 7.4 - - + -
228C TYR* 3.8 17.9 - - + -
248C THR* 3.6 34.3 - - + +
250C VAL* 3.9 19.1 - - + -
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Residues in contact with SER 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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139C GLN 4.9 1.7 + - - -
140C GLN* 3.3 8.4 - - - +
141C SER* 3.1 43.5 + - - -
153C LYS 3.7 2.5 + - - -
154C ILE* 1.3 77.5 - - - +
156C CYS* 1.3 61.6 + - - +
157C LYS* 5.1 1.4 + - - +
170C TRP* 4.3 0.4 - - - -
212C THR* 4.0 7.0 - - - -
213C ALA 3.5 4.5 - - - -
214C PHE* 3.5 26.7 - - - -
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Residues in contact with CYS 156 (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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138C LEU* 3.8 24.9 - - - -
139C GLN 3.7 3.4 - - - -
140C GLN* 4.5 0.4 - - - +
155C SER* 1.3 76.5 - - - +
157C LYS* 1.3 59.4 + - - +
158C ALA* 3.7 1.9 + - - +
163C PHE* 5.3 0.5 - - - -
168C ILE* 4.7 8.0 - - - +
170C TRP* 3.6 12.1 - - + -
211C SER 3.8 0.5 - - - +
212C THR* 3.2 5.3 - - - -
213C ALA* 2.7 38.4 + - + +
230C CYS* 2.0 53.4 - - + -
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Residues in contact with LYS 157 (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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137C GLN 3.6 0.9 - - - +
138C LEU* 3.3 5.3 - - - -
139C GLN* 2.8 55.5 + - + +
155C SER* 4.2 0.9 - - - +
156C CYS* 1.3 71.3 - - - +
158C ALA* 1.3 79.2 + - - +
159C SER* 5.0 9.3 + - - -
210C SER 3.3 27.1 - - - +
211C SER* 3.8 4.7 - - - -
212C THR* 3.6 11.6 - - + +
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Residues in contact with ALA 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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137C GLN 3.5 4.7 - - - -
138C LEU* 3.8 8.1 - - + -
156C CYS 3.7 1.5 + - - +
157C LYS* 1.3 91.4 - - - +
159C SER* 1.3 59.9 + - - +
161C TYR* 3.3 33.9 - - + +
163C PHE* 3.7 16.4 - - + -
168C ILE* 5.3 0.4 - - + -
211C SER* 2.8 30.4 + - - +
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Residues in contact with SER 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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135C GLU 3.1 2.0 + - - +
136C VAL* 3.6 1.7 - - - -
137C GLN* 3.0 57.3 + - - +
157C LYS* 5.0 11.3 + - - -
158C ALA* 1.3 76.4 - - - +
160C GLY* 1.3 63.0 + - - +
161C TYR* 3.4 10.2 - - - +
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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