Contacts of the strand formed by residues 164 - 170 (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 LEU 164 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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127C TRP* 3.7 24.7 - - + -
128C THR 4.1 13.0 - - - +
130C VAL* 3.9 14.1 - - + -
154C LEU* 3.7 22.7 - - + -
161C TYR* 3.2 34.8 - - + +
162C PRO* 3.0 31.6 + - + +
163C VAL* 1.3 73.1 - - - +
165C ASN* 1.3 59.3 + - - +
166C VAL* 4.1 2.0 - - + -
245C ILE 4.2 1.3 - - - +
246C ASN* 3.1 8.7 - - - -
247C SER* 2.7 38.4 + - - +
251C LEU* 4.3 7.4 - - + -
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Residues in contact with ASN 165 (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* 3.3 9.9 - - - -
163C VAL* 3.6 8.8 + - + +
164C LEU* 1.3 75.8 - - - +
166C VAL* 1.3 65.6 + - - +
244C VAL* 4.3 3.4 - - - +
245C ILE 3.5 4.5 - - - -
246C ASN* 2.9 26.8 + - - +
1H NAG 1.5 69.8 + - - +
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Residues in contact with VAL 166 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125C PHE* 4.2 15.7 - - + -
126C THR* 3.9 24.5 - - - +
127C TRP* 3.5 45.8 - - + -
128C THR* 5.9 0.7 - - - +
164C LEU* 5.2 1.1 - - + -
165C ASN* 1.3 81.7 - - - +
167C THR* 1.3 62.0 + - - +
244C VAL* 3.3 8.0 - - - +
245C ILE* 2.9 46.9 + - + +
1H NAG 4.8 1.8 - - - -
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Residues in contact with THR 167 (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* 4.8 2.4 - - - -
166C VAL* 1.3 79.3 - - - +
168C MET* 1.3 69.4 + - - +
169C PRO* 4.3 7.5 - - + +
242C VAL* 3.1 27.3 - - + +
243C LEU 3.1 8.3 + - - -
244C VAL* 3.4 6.6 - - - +
1H NAG 3.3 32.4 - - - +
2H NAG 4.1 2.4 - - + +
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Residues in contact with MET 168 (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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123C GLU* 3.4 43.5 - - + +
124C GLY 3.9 20.6 - - - +
125C PHE* 3.5 43.5 - - + -
167C THR* 1.3 82.2 + - - +
169C PRO* 1.3 72.6 - - - +
178C TYR* 3.5 11.8 + - - +
237C VAL* 5.1 1.4 - - - +
242C VAL* 4.1 0.7 - - - -
243C LEU* 2.9 37.7 + - + +
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Residues in contact with PRO 169 (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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167C THR* 4.2 8.1 - - + +
168C MET* 1.3 95.3 - - - +
170C ASN* 1.3 61.5 + - - +
171C ASN* 3.4 29.6 + - + +
176C LYS* 3.2 20.0 + - - -
241C ASP 3.6 8.7 - - - +
242C VAL* 4.0 14.3 - - + -
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Residues in contact with ASN 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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168C MET 3.9 0.2 + - - -
169C PRO* 1.3 74.1 - - - +
171C ASN* 1.3 57.8 + - - +
172C ASP* 3.1 24.3 - - - +
174C PHE 2.8 24.1 + - - -
176C LYS* 3.3 20.5 - - + +
237C VAL* 2.9 31.3 + - + -
238C LYS 3.1 22.0 + - - +
239C PRO* 3.5 4.2 - - - -
240C GLY* 2.7 27.5 + - - -
241C ASP 2.8 14.6 + - - +
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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