Contacts of the strand formed by residues 166 - 173 (chain L) in PDB entry 3IXS
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 VAL 166 (chain L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158J GLN* 3.7 24.2 - - + +
253K ASN* 4.2 24.0 - - - +
255K THR* 6.1 0.2 - - + -
258K HIS* 2.9 39.2 + - + +
162L THR* 4.3 0.2 - - - -
163L VAL 3.0 23.3 + - - +
164L GLY 3.4 0.8 - - - -
165L ASN* 1.3 95.3 - - - +
167L THR* 1.3 67.6 + - - +
168L VAL* 4.6 0.9 - - + -
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Residues in contact with THR 167 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265I VAL* 4.9 0.2 - - + -
266I ARG* 3.9 17.4 + - - -
269I LEU* 4.4 9.4 - - + -
157J GLN* 5.6 0.9 + - - -
158J GLN 2.8 16.7 + - - +
159J LEU* 3.4 21.0 - - + -
160J ALA* 3.1 24.6 + - - +
160L ALA* 4.3 11.4 - - + -
161L VAL 3.4 11.9 - - - +
162L THR* 2.7 32.7 + - - +
165L ASN 5.2 0.9 + - - -
166L VAL* 1.3 76.1 - - - +
168L VAL* 1.3 74.7 + - - +
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Residues in contact with VAL 168 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160J ALA* 4.4 5.8 - - + -
250K THR* 4.0 7.2 - - - +
251K SER* 3.7 17.7 - - - +
253K ASN* 4.0 13.0 - - - +
254K ALA* 3.7 22.0 - - + -
258K HIS* 3.5 37.5 - - + +
160L ALA* 3.4 4.3 - - - -
161L VAL* 2.9 35.5 + - + +
166L VAL* 4.2 2.2 + - + -
167L THR* 1.3 79.9 - - - +
169L ILE* 1.3 65.6 + - - +
170L ILE* 4.1 20.0 - - + -
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Residues in contact with ILE 169 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261I LYS* 5.2 11.9 - - - +
265I VAL* 4.1 26.2 - - + -
159J LEU* 4.2 6.7 - - + -
160J ALA 3.8 19.2 + - - +
161J VAL* 5.3 4.5 - - + -
162J THR 6.0 0.9 - - - +
249K LYS 4.0 0.2 - - - +
250K THR* 2.7 28.0 + - - -
251K SER* 4.5 2.2 + - - -
158L GLN* 4.0 37.0 - - + +
159L LEU 3.3 7.0 - - - +
160L ALA* 3.9 21.8 - - + +
168L VAL* 1.3 82.1 - - - +
170L ILE* 1.3 59.7 + - - +
171L THR* 3.9 4.2 + - - +
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Residues in contact with ILE 170 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248K ILE* 4.0 23.8 - - + -
249K LYS 3.7 2.2 - - - +
250K THR* 3.2 32.3 - - + +
254K ALA* 4.8 0.2 - - + -
258K HIS* 5.2 2.0 - - + +
259K LEU* 4.1 17.7 - - + -
262K TYR* 3.6 37.6 - - + -
157L GLN 3.6 1.0 - - - +
158L GLN* 3.4 2.5 - - - -
159L LEU* 2.7 41.2 + - + +
161L VAL* 3.9 23.8 - - + -
168L VAL* 4.1 13.7 - - + -
169L ILE* 1.3 73.2 - - - +
171L THR* 1.3 65.2 + - - +
172L ASP* 3.8 0.9 + - - +
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Residues in contact with THR 171 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225K GLU* 5.1 0.7 + - - -
248K ILE* 3.1 9.0 - - - +
249K LYS* 2.8 63.7 + - - -
156L ALA* 3.6 21.8 - - + -
157L GLN 3.3 6.7 - - - +
158L GLN* 3.6 24.4 + - + +
169L ILE* 4.8 4.9 + - - +
170L ILE* 1.3 75.0 - - - +
172L ASP* 1.3 62.9 + - - +
173L PHE* 3.6 23.4 - - + -
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Residues in contact with ASP 172 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246K ARG* 4.2 5.7 + - - +
247K TYR 3.3 16.0 + - - +
248K ILE* 3.3 3.1 - - - +
262K TYR* 2.4 34.5 + - + -
266K ARG* 2.8 41.3 + - - +
155L THR 3.9 0.6 - - - +
156L ALA* 3.2 8.0 - - - -
157L GLN* 2.6 44.7 + - + +
170L ILE 3.8 0.9 + - - +
171L THR* 1.3 69.8 - - - +
173L PHE* 1.3 69.0 + - - +
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Residues in contact with PHE 173 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227K GLU* 4.7 0.2 - - - -
246K ARG* 5.6 0.3 - - - -
247K TYR* 3.1 46.3 + - + +
248K ILE* 4.3 1.8 - - - -
249K LYS* 3.7 33.4 - - + -
148L LEU* 4.6 4.3 - - + -
151L VAL* 3.3 34.3 - - + -
152L ASP 4.4 0.7 - - - -
153L ARG* 3.6 37.2 - - - -
155L THR* 3.9 3.4 - - - +
156L ALA* 3.4 31.2 - - + -
171L THR* 3.6 20.6 - - + -
172L ASP* 1.3 80.8 + - - +
174L LYS* 1.3 66.5 + - - +
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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
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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