Contacts of the strand formed by residues 164 - 169 (chain g) in PDB entry 5OA3
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 g).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156g PHE* 5.0 0.8 - - - -
157g SER* 3.0 41.0 + - - +
162g ASN* 3.5 17.2 + - - +
163g PRO* 1.3 80.7 - - - +
165g ILE* 1.3 66.2 + - - +
166g VAL* 3.9 17.2 + - + -
176g VAL* 3.5 33.7 - - + -
177g TRP 3.2 10.3 - - - +
178g ASN* 4.7 2.5 - - + +
179g LEU* 5.0 1.3 - - - +
185g LYS* 6.2 1.8 - - + -
221g LEU* 4.3 26.5 - - + +
222g ASN* 4.7 13.0 - - - +
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Residues in contact with ILE 165 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121g VAL* 3.7 30.5 - - + -
129g ILE* 5.2 4.9 - - + -
131g LEU* 4.9 5.4 - - + -
154g VAL* 5.3 2.7 - - + -
155g ARG 3.7 4.9 - - - +
156g PHE* 3.7 44.2 - - + +
164g ILE* 1.3 76.4 - - - +
166g VAL* 1.3 63.1 + - - +
176g VAL* 3.6 1.0 - - - -
177g TRP* 2.9 59.4 + - + +
178g ASN 5.6 0.4 - - - -
179g LEU* 3.7 24.0 - - + -
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Residues in contact with VAL 166 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154g VAL* 3.9 1.4 - - - -
155g ARG 3.1 28.6 + - - -
164g ILE* 3.9 5.2 - - + +
165g ILE* 1.3 78.1 - - - +
167g SER* 1.3 62.4 + - - +
174g VAL* 3.6 24.5 - - + -
175g LYS 3.5 5.4 - - - +
176g VAL* 3.8 13.2 - - + -
198g VAL* 3.4 30.1 - - + +
200g VAL* 3.8 11.2 - - + -
207g CYS* 4.2 9.0 - - - -
221g LEU* 3.6 35.7 - - + -
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Residues in contact with SER 167 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129g ILE* 4.2 16.0 - - - +
146g SER 5.1 0.2 + - - -
147g HIS* 3.9 11.1 + - - -
151g VAL* 4.1 15.3 - - - -
153g CYS 3.3 12.8 - - - -
154g VAL* 4.3 7.0 - - - -
165g ILE 4.2 1.0 + - - -
166g VAL* 1.3 73.6 - - - +
168g CYS* 1.3 61.2 + - - +
174g VAL* 3.4 1.7 - - - -
175g LYS* 2.9 32.8 + - - +
177g TRP* 3.6 21.7 + - - -
198g VAL* 4.5 3.4 - - - -
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Residues in contact with CYS 168 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147g HIS* 3.6 2.9 - - - -
151g VAL* 3.8 1.4 - - - -
152g SER* 2.8 56.2 + - - -
153g CYS* 3.3 10.1 + - - -
167g SER* 1.3 75.6 - - - +
169g GLY* 1.3 57.8 + - - +
173g LEU 3.6 3.4 - - - -
174g VAL* 3.8 1.8 - - + -
195g LEU* 3.6 26.2 - - + -
196g ASN 3.9 1.6 - - - -
197g THR* 3.7 7.9 - - - -
198g VAL* 3.5 44.0 - - + -
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Residues in contact with GLY 169 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147g HIS* 3.0 17.4 + - - -
150g TRP 3.2 12.1 - - - -
168g CYS* 1.3 74.7 - - - +
170g TRP* 1.3 64.9 + - - -
171g ASP* 3.1 12.8 + - - -
172g LYS 3.4 6.8 + - - -
173g LEU 3.0 11.5 + - - -
195g LEU* 3.2 22.2 + - - +
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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