Contacts of the helix formed by residues 293 - 301 (chain C) in PDB entry 1UHG
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 293 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14C VAL* 6.4 0.7 - - + -
34C ILE* 4.3 32.3 - - + -
37C ALA* 6.0 0.4 - - + -
38C LEU* 5.0 6.5 - - + -
174C LEU* 5.1 5.8 - - + -
176C ASN* 4.8 8.5 - - + -
291C TYR* 3.2 8.1 + - + +
292C ASN* 1.3 69.0 - - - +
294C THR* 1.3 60.4 + - - +
296C VAL* 3.8 12.8 - - + -
297C LEU* 2.8 56.7 + - + +
326C ALA* 2.8 24.4 + - + +
327C VAL 4.1 13.7 - - - +
328C HIS* 3.7 34.5 - - + +
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Residues in contact with THR 294 (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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292C ASN* 3.0 11.8 + - - -
293C LEU* 1.3 78.5 - - - +
295C SER* 1.3 57.7 + - - +
298C MET* 2.9 58.8 + - + +
306C PHE* 3.6 38.5 - - + -
324C SER 4.8 1.4 + - - +
325C GLN* 4.2 6.8 + - - -
326C ALA* 3.6 19.6 + - - +
1G NAG 3.9 15.5 - - - -
2G NAG 4.1 11.4 - - - +
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Residues in contact with SER 295 (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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17C GLU* 4.4 4.2 + - - +
21C HIS* 6.0 1.2 - - - -
292C ASN* 3.3 16.4 + - - -
294C THR* 1.3 81.3 - - - +
296C VAL* 1.3 63.4 + - - +
298C MET* 4.1 4.3 - - - +
299C ALA* 3.3 23.4 + - - +
1G NAG 3.8 28.4 + - - -
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Residues in contact with VAL 296 (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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14C VAL* 4.3 20.2 - - + -
17C GLU* 3.9 23.9 - - + +
18C LEU* 3.6 23.8 - - + -
22C HIS* 5.9 0.4 - - - +
291C TYR* 4.5 9.6 - - + -
292C ASN 3.2 19.1 + - - +
293C LEU* 4.0 13.0 - - + +
295C SER* 1.3 78.0 - - - +
297C LEU* 1.3 66.1 + - + +
299C ALA* 3.3 5.4 + - - +
300C MET* 3.2 37.9 + - - +
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Residues in contact with LEU 297 (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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10C PHE* 4.4 19.5 - - + -
14C VAL* 5.6 0.9 - - + -
34C ILE* 5.1 1.3 - - + -
38C LEU* 4.2 33.4 - - + -
174C LEU* 6.1 0.7 - - + -
293C LEU* 2.8 51.3 + - + +
296C VAL* 1.3 71.4 - - + +
298C MET* 1.3 62.5 + - - +
300C MET* 3.0 29.9 + - + +
301C GLY 3.1 0.5 + - - -
302C ILE* 2.9 44.4 + - + +
306C PHE* 4.1 22.2 - - + -
326C ALA* 5.6 1.1 - - + -
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Residues in contact with MET 298 (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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294C THR* 2.9 37.2 + - + +
295C SER* 4.1 4.5 - - - +
297C LEU* 1.3 75.4 - - - +
299C ALA* 1.3 63.5 + - - +
301C GLY* 3.1 13.3 + - - -
302C ILE 3.1 19.5 - - - +
303C THR* 3.8 21.9 - - + +
306C PHE* 3.5 17.3 - - + -
1G NAG 3.2 35.2 - - - +
2G NAG 3.7 22.9 - - - +
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Residues in contact with ALA 299 (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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17C GLU* 3.2 42.4 - - - +
295C SER 3.3 11.5 + - - +
296C VAL 3.7 0.9 - - - +
297C LEU 3.3 0.2 - - - -
298C MET* 1.3 79.2 - - - +
300C MET* 1.3 59.5 + - - +
301C GLY 3.6 0.3 + - - -
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Residues in contact with MET 300 (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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10C PHE* 3.7 27.8 - - + -
13C ASP* 3.6 38.4 - - + +
14C VAL* 3.9 24.9 - - + -
17C GLU* 4.3 7.6 - - + -
56C VAL* 3.5 30.0 - - + +
296C VAL* 3.2 23.3 + - - +
297C LEU* 3.0 18.6 + - - +
299C ALA* 1.3 79.2 - - - +
301C GLY* 1.3 56.0 + - - +
302C ILE 3.8 0.2 - - - -
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Residues in contact with GLY 301 (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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52C GLN* 3.3 28.9 + - - +
56C VAL* 3.9 7.7 - - - +
297C LEU 3.1 0.6 + - - -
298C MET 3.1 10.5 + - - -
299C ALA 3.3 1.0 + - - -
300C MET* 1.3 80.8 - - - +
302C ILE* 1.3 63.4 + - - +
303C THR* 3.8 4.0 - - - -
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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