Contacts of the strand formed by residues 168 - 173 (chain C) in PDB entry 4UM8
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 ARG 168 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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163C PHE* 3.7 6.6 - - - -
164C THR* 3.1 44.1 + - + +
166C ALA* 4.4 6.5 - - + +
167C ASP* 1.3 78.2 - - - +
169C VAL* 1.3 62.6 + - - +
185C SER* 3.1 28.8 + - - +
186C ASP 3.2 17.0 - - - +
187C GLN* 3.7 29.6 - - + +
188C VAL* 4.3 1.3 - - - +
206C ASN* 2.5 33.7 + - - +
208C LEU* 3.3 37.2 - - - +
239C PHE* 4.9 5.6 - - - -
258C GLY 4.4 9.0 + - - -
259C LYS* 5.0 2.8 + - - +
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Residues in contact with VAL 169 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106C LEU* 3.7 26.7 - - + -
130C LEU* 5.1 3.6 - - + -
139C TYR* 4.4 19.3 - - + +
161C ILE* 5.3 0.7 - - + -
162C ASP 4.1 4.0 - - - +
163C PHE* 3.6 26.9 - - + -
164C THR* 5.6 0.2 - - - -
168C ARG* 1.3 72.9 - - - +
170C LEU* 1.3 70.8 + - - +
171C LEU* 4.5 3.8 - - + +
184C ILE 3.8 0.7 - - - +
185C SER* 3.2 28.5 + - - -
186C ASP 2.8 18.5 + - - +
188C VAL* 3.7 13.7 - - + -
191C ILE* 3.7 18.2 - - + -
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Residues in contact with LEU 170 (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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160C SER 3.8 0.3 - - - +
161C ILE* 3.2 8.1 - - - +
162C ASP* 2.9 40.6 + - + +
164C THR* 5.0 1.6 - - + -
168C ARG 3.8 0.6 + - - -
169C VAL* 1.3 73.6 - - - +
171C LEU* 1.3 68.5 + - - +
183C LEU* 4.8 14.8 - - + -
184C ILE 3.8 6.3 - - - +
185C SER* 4.7 0.9 - - - -
226C VAL* 3.9 25.7 - - + +
227C ALA 3.9 21.3 - - - +
228C VAL* 3.9 11.2 - - + -
239C PHE* 3.6 54.7 - - + -
240C VAL 4.7 1.6 - - - +
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Residues in contact with LEU 171 (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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106C LEU* 6.1 0.2 - - + -
128C CYS* 3.8 14.6 - - - -
139C TYR* 3.6 31.4 - - + -
141C PRO* 4.1 17.9 - - + -
142C CYS* 4.9 0.2 - - - -
157C GLY* 3.7 13.2 - - - -
158C GLY* 3.4 37.5 - - - +
160C SER 3.6 3.4 - - - -
161C ILE* 4.2 8.3 - - + -
169C VAL* 4.0 3.3 - - + -
170C LEU* 1.3 77.3 - - - +
172C GLY* 1.3 64.0 + - - +
173C GLY 4.5 1.1 - - - +
183C LEU* 3.6 7.4 - - - +
184C ILE* 2.8 56.0 + - + +
226C VAL* 4.9 1.3 - - - -
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Residues in contact with GLY 172 (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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158C GLY 3.5 2.9 + - - -
159C PHE* 3.4 29.1 + - - +
160C SER* 2.9 18.0 + - - -
171C LEU* 1.3 80.4 - - - +
173C GLY* 1.3 58.3 + - - -
182C GLN 3.6 5.2 - - - -
183C LEU* 4.2 3.4 - - - -
223C GLY* 3.6 24.2 - - - -
226C VAL* 4.5 0.8 - - - +
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Residues in contact with GLY 173 (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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155C CYS* 3.2 26.7 - - - -
156C GLN 4.1 2.2 - - - -
157C GLY* 4.3 0.7 - - - -
171C LEU* 4.5 1.6 - - - +
172C GLY* 1.3 74.6 - - - -
174C PRO* 1.3 67.6 - - - +
175C GLY 3.3 3.8 + - - -
176C SER* 3.7 6.4 + - - -
181C GLY* 3.3 1.2 - - - -
182C GLN 2.9 34.9 + - - -
184C ILE* 6.1 0.4 - - - +
222C LEU 3.5 2.7 - - - -
223C GLY* 4.1 0.6 + - - -
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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