Contacts of the strand formed by residues 171 - 177 (chain F) in PDB entry 3SKU
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 THR 171 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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150F ILE* 3.7 2.1 - - - +
151F GLU* 3.2 52.8 + - - +
170F ALA* 1.3 77.5 + - - +
172F CYS* 1.3 59.9 + - - +
173F THR* 3.5 11.1 + - - +
185F TRP* 4.8 0.2 - - - -
208F ILE* 3.4 33.0 - - + -
209F SER 3.5 2.2 - - - -
210F ARG* 3.4 28.0 + - - +
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Residues in contact with CYS 172 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149F TRP 3.4 6.7 - - - -
150F ILE* 3.8 6.5 - - + -
171F THR* 1.3 70.9 - - - +
173F THR* 1.3 73.6 + - - +
183F VAL* 4.5 20.4 - - + +
185F TRP* 3.4 18.3 - - + -
208F ILE* 3.6 2.8 - - - +
209F SER 3.3 28.3 + - - -
226F CYS* 2.0 55.0 - - + -
227F ILE 4.8 0.4 - - - -
228F VAL* 5.0 2.5 - - - -
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Residues in contact with THR 173 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147F THR 4.7 0.2 - - - -
148F ASN* 3.3 7.8 + - - +
149F TRP* 2.5 64.6 + - + +
151F GLU* 5.1 0.9 + - - -
171F THR* 3.5 14.7 + - - +
172F CYS* 1.3 87.0 + - - +
174F SER* 1.3 68.1 - - - +
175F ALA* 4.2 7.4 - - + +
183F VAL* 4.9 1.6 - - - -
206F THR* 4.5 7.9 - - + -
207F VAL 3.4 4.0 - - - +
208F ILE* 3.1 34.0 - - + +
228F VAL* 5.2 0.2 - - - +
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Residues in contact with SER 174 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146F PRO* 4.2 7.4 - - - +
147F THR 3.7 0.2 - - - -
148F ASN* 3.3 24.1 + - - -
173F THR* 1.3 73.6 - - - +
175F ALA* 1.3 59.1 + - - +
181F SER* 2.7 28.1 + - - -
183F VAL* 4.1 19.3 - - - -
205F VAL 4.4 1.6 + - - +
206F THR* 3.1 5.5 - - - +
207F VAL* 2.7 42.6 + - - -
228F VAL* 4.3 0.8 - - - +
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Residues in contact with ALA 175 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146F PRO* 3.0 2.3 - - - +
147F THR* 2.5 53.7 + - - +
149F TRP* 4.7 17.7 - - + -
173F THR* 4.8 7.0 - - + -
174F SER* 1.3 71.9 + - - +
176F ASN* 1.3 78.9 + - + +
177F GLY 3.6 0.7 - - - -
206F THR* 3.2 12.3 - - + -
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Residues in contact with ASN 176 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144F ALA* 4.1 5.2 - - - +
145F LYS 4.2 2.1 - - - +
146F PRO* 3.4 11.1 - - - +
147F THR* 6.1 0.2 - - - +
175F ALA* 1.3 80.3 - - - +
177F GLY* 1.3 59.6 + - - +
200F ASN* 2.6 32.8 + - - -
204F THR* 4.0 16.6 + - + +
205F VAL 4.1 0.2 - - - -
206F THR* 2.5 22.9 + - - -
1M NAG 3.2 46.2 + - + +
2M NAG 4.3 12.7 + - - +
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Residues in contact with GLY 177 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144F ALA 3.7 4.3 - - - -
146F PRO* 3.5 20.8 - - - +
175F ALA 3.6 1.0 - - - -
176F ASN* 1.3 75.5 - - - +
178F LYS* 1.3 60.0 + - - -
179F PRO 3.6 6.5 - - - -
180F PRO* 5.5 0.2 - - - -
181F SER* 5.9 0.7 - - - -
204F THR* 2.9 12.2 - - - -
205F VAL 2.7 40.0 + - - -
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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