Contacts of the strand formed by residues 174 - 179 (chain C) in PDB entry 3N2N
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 174 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40C TYR* 5.4 7.9 - - + +
142C ALA* 5.7 5.6 - - + -
143C SER 2.8 17.8 + - - +
144C VAL* 3.4 16.1 - - + +
145C ILE 2.8 28.2 + - - +
172C GLY 4.6 5.4 - - - +
173C ALA* 1.3 75.7 - - - +
175C VAL* 1.3 61.5 + - - +
176C TYR* 3.7 26.5 - - + +
193C ASP* 3.6 16.2 - - - +
197C HIS* 3.9 14.1 - - + +
215C ILE* 6.0 2.9 - - + -
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Residues in contact with VAL 175 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124C PHE* 3.7 35.2 - - + -
145C ILE* 3.7 18.8 - - + -
147C ALA* 5.3 0.2 - - + -
165C ALA 4.3 6.3 - - - +
168C SER* 4.5 2.9 - - - -
169C ARG* 3.6 28.7 - - + +
173C ALA* 4.6 1.8 - - + -
174C ILE* 1.3 76.0 - - - +
176C TYR* 1.3 72.2 + - - +
191C ILE* 3.5 17.7 - - + +
192C ALA* 3.4 7.3 - - - +
193C ASP* 2.9 38.5 + - - +
197C HIS* 3.5 9.2 - - - +
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Residues in contact with TYR 176 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144C VAL* 3.6 29.2 - - + -
145C ILE 2.7 14.4 + - - +
146C ILE* 4.4 6.5 - - + -
147C ALA* 2.9 28.6 + - - +
174C ILE* 3.7 20.1 - - + +
175C VAL* 1.3 80.6 - - - +
177C ALA* 1.3 61.7 + - - +
192C ALA* 4.1 1.1 - - - -
196C ASP 4.9 1.1 - - - -
197C HIS* 3.4 42.4 + + - +
199C PHE* 3.7 19.7 - + + -
208C LEU* 4.0 22.7 - - + -
211C ILE* 3.6 40.9 - - + +
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Residues in contact with ALA 177 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147C ALA* 3.4 11.2 - - + +
149C THR* 5.5 1.1 - - + -
176C TYR* 1.3 74.8 - - - +
178C VAL* 1.3 63.7 + - - +
179C GLY 4.0 0.7 - - - -
188C LEU* 4.1 34.1 - - + +
191C ILE* 5.0 4.5 - - + -
192C ALA* 3.7 19.6 - - + +
197C HIS 2.9 8.4 + - - +
198C VAL* 3.3 6.7 - - + +
199C PHE* 3.0 24.8 + - - +
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Residues in contact with VAL 178 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65C PHE* 4.0 11.4 - - + -
146C ILE* 3.9 12.3 - - + -
147C ALA 2.7 11.7 + - - +
148C LEU* 3.3 29.2 - - + +
149C THR 3.2 23.8 + - - -
176C TYR* 5.3 0.4 - - + -
177C ALA* 1.3 76.1 - - - +
179C GLY* 1.3 61.4 + - - +
180C VAL 3.9 0.2 + - - -
188C LEU* 4.6 1.3 - - - -
199C PHE* 3.2 19.1 - - + +
200C PRO 3.8 12.8 - - - +
201C VAL* 3.9 16.8 - - + -
204C GLY* 4.9 0.4 - - - -
208C LEU* 3.7 29.4 - - + -
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Residues in contact with GLY 179 (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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149C THR 3.2 9.2 - - - -
177C ALA 4.0 1.2 - - - -
178C VAL* 1.3 73.9 - - - +
180C VAL* 1.3 63.2 + - - -
181C LYS 4.8 0.2 - - - +
183C PHE* 3.5 28.7 - - - -
188C LEU* 3.7 13.2 - - - +
199C PHE 2.8 12.7 + - - -
200C PRO* 3.8 0.2 - - - +
201C VAL* 3.7 20.1 + - - +
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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