Contacts of the strand formed by residues 181 - 188 (chain C) in PDB entry 5X1V
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 181 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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134C LEU* 3.9 23.6 - - + -
174C ILE 4.0 0.2 - - - +
175C TYR* 3.4 5.0 - - - +
176C VAL* 2.8 51.0 + - + +
177C ASP* 5.2 7.2 - - + -
179C GLY 4.2 1.9 - - - -
180C LEU* 1.3 82.6 - - + +
182C SER* 1.3 61.2 + - - +
183C LEU* 4.1 15.0 - - + -
199C ASN 3.5 14.4 - - - +
200C GLY 4.2 12.6 - - - +
201C GLY* 4.3 5.4 - - - +
202C SER 3.7 26.0 - - - +
203C LEU* 3.9 26.9 - - + -
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Residues in contact with SER 182 (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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173C LYS* 5.4 0.2 - - - -
174C ILE 3.6 3.4 - - - -
175C TYR* 3.7 29.6 - - - -
179C GLY 5.3 1.1 - - - -
180C LEU 4.0 1.6 + - - -
181C ILE* 1.3 73.9 - - - +
183C LEU* 1.3 69.8 + - - +
197C VAL* 3.9 0.2 - - - -
198C GLU* 2.9 45.6 + - - +
199C ASN* 3.1 36.8 + - - +
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Residues in contact with LEU 183 (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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140C LEU* 4.0 20.0 - - + -
142C ILE* 3.9 24.2 - - + -
157C LEU* 4.6 1.6 - - + -
173C LYS* 3.4 11.6 - - - +
174C ILE* 2.8 47.4 + - + +
176C VAL* 4.3 16.8 - - + -
181C ILE* 4.1 14.4 - - + -
182C SER* 1.3 82.8 - - - +
184C GLN* 1.3 61.2 + - - +
185C VAL 4.3 0.2 - - - -
195C THR* 3.8 25.8 - - + +
196C GLU 3.4 3.1 - - - -
197C VAL* 3.9 26.2 - - + -
198C GLU* 4.8 2.5 - - - -
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Residues in contact with GLN 184 (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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171C GLY* 3.5 31.7 + - - +
172C SER 3.4 4.0 - - - +
173C LYS* 3.8 26.2 - - + +
183C LEU* 1.3 75.8 - - - +
185C VAL* 1.3 65.1 + - - +
186C LYS* 3.4 26.5 + - - +
195C THR* 3.9 2.2 - - - -
196C GLU* 2.6 48.4 + - + +
198C GLU* 4.9 8.5 - - + +
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Residues in contact with VAL 185 (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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168C VAL* 3.8 23.8 - - + -
169C GLU 3.7 16.4 - - - +
170C VAL* 4.8 2.2 - - - -
171C GLY* 2.9 29.0 + - - +
172C SER* 3.2 16.1 + - - +
174C ILE* 4.0 17.9 - - + -
184C GLN* 1.3 72.1 - - - +
186C LYS* 1.3 63.0 + - - +
187C GLN* 3.5 28.5 - - - +
188C LYS* 4.5 3.8 - - + -
193C LEU* 4.3 18.4 - - + -
194C VAL 3.7 8.1 - - - +
195C THR* 4.1 6.2 - - + +
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Residues in contact with LYS 186 (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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170C VAL* 3.6 13.4 - - - +
171C GLY* 6.2 0.4 - - - -
184C GLN* 3.4 30.2 + - - +
185C VAL* 1.3 77.0 - - - +
187C GLN* 1.3 68.4 + - + +
194C VAL* 3.0 13.7 + - + +
195C THR 4.9 0.4 - - - -
196C GLU* 3.3 55.7 + - + +
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Residues in contact with GLN 187 (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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170C VAL* 3.8 7.2 - - + -
185C VAL* 3.5 8.0 - - - +
186C LYS* 1.3 81.8 - - + +
188C LYS* 1.3 63.1 + - - +
192C PHE* 6.0 3.0 - - + -
194C VAL* 3.0 59.3 + - + +
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Residues in contact with LYS 188 (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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165C CYS* 2.8 29.3 + - - +
166C LYS* 5.1 1.2 - - - +
168C VAL 3.0 21.9 + - - +
169C GLU* 4.3 15.5 - - - +
170C VAL* 4.1 19.6 - - + +
185C VAL* 4.5 2.2 - - + -
187C GLN* 1.3 78.5 - - - +
189C GLY* 1.3 66.6 + - - +
192C PHE* 3.9 3.6 - - - -
193C LEU* 3.8 20.4 - - + -
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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