Contacts of the strand formed by residues 241 - 247 (chain C) in PDB entry 5HMG
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 ASP 241 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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169C PRO* 3.6 2.4 - - - +
170C ASN 2.8 23.7 + - - -
206C THR* 3.5 13.4 + - - +
207C ARG* 2.9 48.8 + - - +
208C ARG* 3.7 23.7 + - - +
237C VAL* 3.7 10.8 - - + -
238C LYS* 3.1 27.4 + - + +
239C PRO 3.3 1.4 + - - +
240C GLY* 1.4 80.7 - - - +
242C VAL* 1.3 76.7 + - - +
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Residues in contact with VAL 242 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221A PRO* 4.2 12.9 - - + +
167C THR* 3.1 28.0 - - + +
168C MET 3.9 1.8 - - - -
169C PRO* 4.0 21.1 - - + -
206C THR* 3.2 28.6 - - - +
207C ARG* 3.6 29.4 - - - +
237C VAL* 4.1 4.3 - - - -
240C GLY 4.7 0.7 - - - +
241C ASP* 1.3 86.7 + - - +
243C LEU* 1.3 62.5 + - - +
244C VAL* 4.1 1.3 + - + -
2H NAG 3.8 23.1 - - + -
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Residues in contact with LEU 243 (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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125C PHE* 4.4 5.8 - - + -
167C THR* 3.1 8.3 + - - -
168C MET* 2.9 42.7 + - + +
178C TYR* 3.7 40.6 - - + -
180C TRP* 6.3 0.2 - - + -
204C VAL* 3.5 30.3 - - + -
205C SER 3.5 7.0 - - - +
206C THR* 4.3 0.7 - - - -
235C THR* 3.9 19.5 - - + -
237C VAL* 4.0 13.8 - - + +
242C VAL* 1.3 72.9 - - - +
244C VAL* 1.3 59.4 + - - +
245C ILE* 3.8 29.6 - - + -
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Residues in contact with VAL 244 (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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219A SER* 3.2 29.4 - - - +
221A PRO* 3.5 35.2 - - + -
165C ASN* 4.3 13.0 - - - +
166C VAL 3.3 9.0 - - - +
167C THR* 3.4 23.6 - - - +
203C THR 3.8 0.5 - - - +
204C VAL* 3.5 3.1 - - - +
205C SER* 2.9 34.6 + - - +
242C VAL* 4.5 1.6 - - + -
243C LEU* 1.3 72.3 - - - +
245C ILE* 1.3 66.2 + - - +
246C ASN 4.8 0.2 - - - +
1H NAG 4.2 15.5 - - - +
2H NAG 4.8 0.4 - - + -
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Residues in contact with ILE 245 (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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125C PHE* 4.1 14.8 - - + -
127C TRP* 4.3 7.4 - - + -
164C LEU* 3.9 2.5 - - + +
165C ASN* 3.5 1.9 + - - -
166C VAL* 2.9 41.0 + - + +
180C TRP* 5.9 1.3 - - + -
202C VAL* 4.9 0.7 - - + -
203C THR 3.7 2.7 - - - +
204C VAL* 4.1 24.2 - - + +
243C LEU* 3.8 25.1 - - + -
244C VAL* 1.3 74.9 - - - +
246C ASN* 1.3 63.4 + - - +
251C LEU* 3.9 34.1 - - + -
254C PRO* 3.5 36.1 - - + -
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Residues in contact with ASN 246 (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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218A GLY* 4.1 7.7 - - - -
219A SER* 3.6 31.5 + - - +
163C VAL* 3.9 11.2 - - - +
164C LEU 3.1 11.4 + - - +
165C ASN* 2.9 28.8 + - - +
201C ARG* 4.0 23.0 + - - +
202C VAL* 3.7 0.5 - - - +
203C THR* 2.9 43.3 + - - +
244C VAL* 4.0 0.6 - - + -
245C ILE* 1.3 75.4 - - - +
247C SER* 1.3 65.8 + - - +
1H NAG 6.0 0.4 - - - +
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Residues in contact with SER 247 (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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161C TYR* 3.9 2.3 + - - -
162C PRO 3.7 0.7 - - - +
163C VAL* 3.4 2.6 - - - -
164C LEU* 2.7 44.9 + - - +
201C ARG* 2.9 20.8 + - - +
202C VAL* 3.7 3.9 - - - +
246C ASN* 1.3 81.5 + - - +
248C ASN* 1.3 57.0 + - - +
249C GLY 2.9 22.3 + - - -
251C LEU* 3.7 33.2 - - - +
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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