Contacts of the strand formed by residues 206 - 211 (chain C) in PDB entry 3H0Z
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 206 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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163C VAL* 3.6 3.1 - - - -
164C LEU* 2.9 42.0 + - + +
166C LYS* 3.6 36.3 - - + +
169C LEU* 4.4 13.2 - - + -
178C LEU* 4.3 23.6 - - + -
179C ARG* 6.4 2.0 - - - -
199C TYR* 5.1 8.5 - - + -
200C PHE 3.8 9.0 - - - +
201C HIS* 4.2 8.3 - - + +
205C ARG* 1.3 76.7 - - - +
207C TYR* 1.3 71.1 + - - +
208C LEU* 4.9 6.0 - - + +
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Residues in contact with TYR 207 (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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130C LEU* 3.6 31.8 - - + +
161C LEU* 3.6 10.8 - - + -
162C LYS 3.3 5.6 - - - +
163C VAL* 3.5 38.4 - - + -
199C TYR* 3.3 8.8 - - - +
200C PHE* 2.8 82.9 + + + +
201C HIS* 4.1 0.7 - - - -
202C ASP* 2.3 39.8 + - + -
205C ARG* 3.4 35.1 + - + +
206C VAL* 1.3 74.9 - - - +
208C LEU* 1.3 63.9 + - - +
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Residues in contact with LEU 208 (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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161C LEU* 3.1 7.7 - - - +
162C LYS* 2.9 54.5 + - + -
164C LEU* 4.9 9.2 - - + +
178C LEU* 4.4 28.9 - - + -
182C VAL* 4.1 15.3 - - + -
196C LEU* 4.4 17.7 - - + -
198C GLY 3.8 4.9 - - - +
199C TYR* 3.6 18.4 - - + -
206C VAL* 4.9 5.8 - - + +
207C TYR* 1.3 83.8 - - - +
209C ILE* 1.3 63.7 + - - +
210C LEU* 3.6 15.9 + - + -
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Residues in contact with ILE 209 (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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128C TRP* 3.3 38.1 - - + +
133C PHE* 3.5 28.9 - - + -
159C LEU* 3.3 34.3 - - + -
160C ALA 3.8 3.6 - - - +
161C LEU* 4.1 9.4 - - + -
196C LEU* 3.7 1.5 - - - +
197C TYR* 2.8 36.5 + - + -
198C GLY 3.1 24.6 + - - +
200C PHE* 4.2 12.1 - - + -
208C LEU* 1.3 73.1 - - - +
210C LEU* 1.3 60.2 + - - +
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Residues in contact with LEU 210 (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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1C 45B 3.8 22.4 - - - -
159C LEU* 3.6 9.0 - - - +
160C ALA* 2.8 36.8 + - + +
162C LYS* 3.8 22.2 - - + +
185C GLN* 5.7 2.2 - - - +
194C LEU* 4.6 13.2 - - + +
195C ARG 3.4 14.4 - - - +
196C LEU* 3.7 26.0 - - + -
197C TYR* 4.1 4.0 - - - -
208C LEU* 3.6 34.3 - - + +
209C ILE* 1.3 75.6 - - - +
211C GLU* 1.3 67.2 + - - +
273C ALA* 6.1 0.4 - - + -
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Residues in contact with GLU 211 (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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1C 45B 3.4 18.9 - - - -
157C PHE* 6.2 2.9 - - + -
158C ILE 5.8 0.2 - - - -
159C LEU* 5.2 0.9 - - - +
160C ALA 4.4 0.2 - - - -
193C ILE 3.7 4.7 - - - +
194C LEU* 3.7 21.4 - - + +
195C ARG* 2.9 48.7 + - + +
197C TYR* 3.8 17.8 - - - +
210C LEU* 1.3 75.8 - - - +
212C TYR* 1.3 73.4 + - - +
271C LYS* 2.8 33.5 + - - -
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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