Contacts of the strand formed by residues 164 - 168 (chain C) in PDB entry 3Q41
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 164 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163C ILE* 1.3 79.7 - - - +
165C LEU* 1.3 67.1 + - - +
166C LEU* 5.3 4.3 - - + -
192C GLU* 4.8 3.1 - - + +
193C LYS 3.5 11.2 - - - +
195C LEU* 4.1 25.6 - - + -
211C ALA* 3.4 32.1 - - + +
214C LEU* 3.7 23.8 - - + -
216C ALA* 3.9 27.8 - - + +
218C VAL 3.0 10.1 + - - +
219C ILE* 3.6 19.5 - - + +
220C ILE* 3.0 27.4 + - - +
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Residues in contact with LEU 165 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151C TRP* 5.1 4.0 - - + -
163C ILE* 4.2 2.8 - - + +
164C ILE* 1.3 73.1 - - - +
166C LEU* 1.3 56.7 + - - +
167C VAL* 4.1 12.6 - - + -
176C ALA 5.6 0.4 - - - +
177C GLN* 3.8 33.2 - - + +
180C LEU* 3.6 33.0 - - + -
181C GLU* 4.7 6.3 - - + -
191C ALA* 4.6 9.8 - - + +
193C LYS 3.0 7.7 + - - +
194C VAL* 3.4 28.8 - - + -
195C LEU* 2.7 34.7 + - - +
220C ILE* 3.6 29.2 - - + +
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Residues in contact with LEU 166 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164C ILE* 5.1 3.8 - - + +
165C LEU* 1.3 74.6 - - - +
167C VAL* 1.3 61.5 + - - +
195C LEU* 3.3 26.2 - - + +
197C PHE* 4.2 10.8 - - + -
204C VAL* 5.5 2.2 - - + -
207C LEU* 3.7 26.0 - - + -
208C LEU* 4.4 22.7 - - + -
211C ALA* 6.1 1.6 - - + -
219C ILE* 4.2 20.9 - - + -
220C ILE 2.8 14.6 + - - +
221C LEU* 3.3 27.6 - - + +
222C SER 2.9 22.3 + - - -
231C VAL* 4.9 11.2 - - + -
247C TRP* 5.0 2.5 - - + -
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Residues in contact with VAL 167 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165C LEU* 4.3 15.9 - - + +
166C LEU* 1.3 76.2 - - - +
168C SER* 1.3 63.6 + - - +
173C GLY 3.5 25.6 - - - +
174C ARG* 4.7 2.2 - - + +
176C ALA* 5.1 0.4 - - + -
177C GLN* 3.6 41.3 - - + +
194C VAL* 6.0 0.9 - - + -
195C LEU 2.9 17.4 + - - +
196C GLN* 3.2 18.6 - - + +
197C PHE* 2.9 32.6 + - - -
222C SER* 3.5 14.1 - - - -
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Residues in contact with SER 168 (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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167C VAL* 1.3 74.5 - - - +
169C ASP* 1.3 59.2 + - - +
170C ASP* 2.8 39.8 + - - +
172C GLU* 5.3 1.4 - - - +
173C GLY* 3.3 20.1 + - - -
174C ARG* 3.6 3.5 + - - -
197C PHE* 3.4 25.7 - - - -
199C PRO* 5.0 2.9 - - - -
222C SER 2.8 21.3 + - - -
223C ALA* 4.2 6.7 - - - -
224C SER 5.2 0.6 + - - -
227C ASP* 4.8 5.6 - - - -
252C ARG* 5.4 3.5 + - - -
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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
------------------------------------------------------------
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