Contacts of the strand formed by residues 174 - 179 (chain K) in PDB entry 1S9C
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 ALA 174 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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175J VAL 3.4 8.7 - - - -
176J LEU* 3.5 21.5 - - + -
172K PRO* 3.2 2.1 - - - +
173K ASP* 1.3 83.0 - - - +
175K VAL* 1.3 61.4 + - - +
176K LEU* 4.4 0.4 - - + -
230K GLN* 3.7 16.6 - - + +
231K PHE* 4.3 17.9 - - + -
259K GLU* 3.8 0.2 - - - -
260K MET* 2.8 36.1 + - + +
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Residues in contact with VAL 175 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173J ASP 4.8 0.2 - - - -
174J ALA* 3.5 1.6 - - - -
175J VAL* 3.2 59.1 + - + +
177J THR* 6.3 1.3 - - + -
172K PRO* 4.7 12.3 - - + +
174K ALA* 1.3 78.6 - - - +
176K LEU* 1.3 67.7 + - - +
177K THR* 4.3 4.2 + - + +
257K GLN* 4.1 26.0 - - + -
258K THR 3.2 16.4 - - - +
259K GLU* 4.0 14.6 - - + +
260K MET* 4.8 0.2 - - - -
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Residues in contact with LEU 176 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173J ASP 3.6 4.0 - - - +
174J ALA* 3.2 30.5 - - + -
175J VAL 4.9 0.2 - - - +
230J GLN* 3.8 2.9 - - - +
174K ALA* 5.3 0.4 - - + -
175K VAL* 1.3 78.5 - - - +
177K THR* 1.3 63.2 + - - +
178K ASP* 4.3 2.4 - - - +
226K ARG* 3.2 46.7 - - + +
229K GLN* 4.3 3.8 - - + +
230K GLN* 3.5 34.8 - - + +
256K LEU 4.3 0.3 - - - +
257K GLN* 3.9 0.2 - - - -
258K THR* 3.0 31.2 + - - +
260K MET* 3.5 27.6 - - + -
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Residues in contact with THR 177 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170J ARG* 5.6 0.2 + - - -
171J PRO* 4.2 15.5 + - + +
172J PRO* 2.5 32.9 + - + +
173J ASP* 3.4 14.4 + - - +
175K VAL* 5.0 5.4 - - + +
176K LEU* 1.3 74.1 - - - +
178K ASP* 1.3 64.2 + - - +
226K ARG* 3.0 20.1 + - - -
255K THR* 4.4 10.1 - - + -
256K LEU 3.3 7.4 - - - +
257K GLN* 4.0 30.3 - - + +
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Residues in contact with ASP 178 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35K GLY 5.0 0.5 - - - +
176K LEU 4.3 2.6 - - - +
177K THR* 1.3 82.9 - - - +
179K THR* 1.3 62.7 + - - +
180K THR 3.6 0.3 + - - -
222K PHE* 3.7 29.0 - - + -
225K ARG* 3.2 25.8 + - - -
226K ARG* 2.5 38.2 + - - +
255K THR* 3.3 4.4 - - - +
256K LEU* 2.7 48.0 + - + +
258K THR* 5.1 2.4 + - - -
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Residues in contact with THR 179 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171J PRO* 6.0 1.4 - - - +
178K ASP* 1.3 74.6 - - - +
180K THR* 1.3 73.0 + - - +
181K SER* 3.8 0.9 + - - -
184K GLN* 4.7 1.7 - - - +
222K PHE* 4.9 6.3 - - - -
253K GLY 4.5 4.5 - - - +
255K THR* 4.0 20.3 + - - +
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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