Contacts of the strand formed by residues 156 - 161 (chain C) in PDB entry 5H1C
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 LYS 156 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145C GLN* 5.3 0.2 - - - +
154C GLU 4.1 1.8 + - - +
155C GLY* 1.3 69.6 - - - -
157C ALA* 1.3 52.9 + - - +
188C ASN* 3.3 42.3 - - - +
214C SER* 3.2 32.3 + - - +
215C ARG 3.6 3.9 + - - +
216C TYR* 2.0 73.2 - - + +
217C ALA 2.7 17.3 + - - -
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Residues in contact with ALA 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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141C ALA* 3.9 30.3 - - + +
144C CYS* 5.0 4.0 - - + -
145C GLN* 5.3 2.8 - - + +
155C GLY 3.4 5.1 + - - +
156C LYS* 1.3 74.5 - - - +
158C MET* 1.3 56.7 + - - +
159C TYR* 5.5 1.1 - - + -
188C ASN* 4.3 1.4 - - - +
189C VAL* 2.9 23.9 + - + +
190C ALA 2.8 28.6 + - - -
216C TYR* 3.0 3.2 - - - -
218C LEU* 3.8 18.6 - - + +
220C ILE* 5.9 1.8 - - + -
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Residues in contact with MET 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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157C ALA* 1.3 73.0 - - - +
159C TYR* 1.3 61.1 + - - +
160C ILE* 4.0 2.7 - - + -
190C ALA* 3.7 17.3 - - + +
207C ALA* 4.8 12.8 - - - +
210C MET* 5.1 2.5 - - + -
211C MET* 3.2 27.8 - - + +
216C TYR* 2.0 80.8 - - + +
218C LEU 3.2 10.8 + - - +
219C LEU* 3.6 31.0 - - + +
220C ILE* 3.3 22.7 + - - +
261C VAL* 5.9 0.7 - - + -
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Residues in contact with TYR 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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134C THR* 4.9 2.3 - - - -
137C CYS* 4.2 17.6 - - + +
138C HIS* 4.3 10.9 + + - -
141C ALA* 5.0 6.7 - - + -
157C ALA* 5.3 1.1 - - + +
158C MET* 1.3 76.5 - - - +
160C ILE* 1.3 58.9 + - - +
161C ASP* 3.1 21.0 + - + -
165C THR* 4.8 1.9 + - - -
166C PHE* 3.2 51.7 + + + +
189C VAL* 4.8 13.2 - - + -
190C ALA 3.3 7.0 + - - -
191C TYR* 3.9 13.2 - + - -
192C ALA 3.1 22.4 + - - -
220C ILE* 3.8 40.6 - - + -
222C ASP* 4.3 21.4 + - + +
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Residues in contact with ILE 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 MET* 5.3 2.5 - - + -
159C TYR* 1.3 72.8 - - - +
161C ASP* 1.3 64.5 + - - +
162C THR* 3.8 11.4 + - + +
192C ALA* 3.6 14.6 - - + +
194C ALA* 4.6 1.1 - - + -
200C GLN* 5.4 5.8 - - + +
203C LEU* 4.2 38.6 - - + +
204C LEU* 4.6 19.3 - - + -
207C ALA* 5.4 2.0 - - + -
219C LEU* 4.1 24.9 - - + -
220C ILE 3.0 15.4 + - - +
221C VAL* 3.7 37.2 - - + +
222C ASP 4.0 1.8 + - - -
248C PHE* 6.4 0.4 - - + -
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Residues in contact with ASP 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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159C TYR* 3.1 28.5 + - + -
160C ILE* 1.3 72.9 - - - +
162C THR* 1.3 79.4 + - - +
163C GLU* 2.6 14.4 + - - +
164C GLY* 3.0 14.2 + - - -
165C THR* 2.7 30.8 + - - -
166C PHE* 2.9 15.6 + - - +
191C TYR* 3.5 17.7 - - + +
192C ALA 2.9 9.6 + - - +
193C ARG* 3.7 2.7 - - - -
194C ALA* 3.2 23.4 + - - +
222C ASP* 4.4 8.9 - - - +
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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