Contacts of the helix formed by residues 46 - 57 (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 LYS 46 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43C LEU 5.2 6.3 + - - -
44C GLY 5.0 0.2 - - - -
45C ALA* 1.3 82.4 + - - +
47C ASP* 1.3 78.5 + - - +
49C THR* 3.3 10.0 + - - -
50C ARG* 3.3 15.6 + - - +
311C ASN* 3.1 26.9 + - - +
313C SER* 3.6 20.0 - - - +
314C GLY* 4.0 26.9 - - - +
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Residues in contact with ASP 47 (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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46C LYS* 1.3 79.5 - - - +
48C SER* 1.3 60.8 + - - +
50C ARG* 3.2 5.0 + - - +
51C THR* 2.9 32.3 + - - -
311C ASN* 3.4 19.6 - - + +
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Residues in contact with SER 48 (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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47C ASP* 1.3 77.7 - - - +
49C THR* 1.3 65.3 + - - +
51C THR* 3.5 9.1 - - - +
52C GLN* 3.0 32.1 + - - +
304C ASP* 2.6 24.3 + - - -
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Residues in contact with THR 49 (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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45C ALA* 3.8 11.2 - - + -
46C LYS 3.3 9.8 + - - -
48C SER* 1.3 79.6 - - - +
50C ARG* 1.3 63.2 + - - +
52C GLN* 3.6 3.8 + - - +
53C ILE* 3.4 23.8 + - + +
302C ILE* 5.6 0.3 - - - +
304C ASP* 3.5 21.3 + - - +
305C VAL* 3.8 35.3 - - + +
309C SER 4.2 1.6 + - - -
310C ALA* 3.6 0.9 - - - -
311C ASN* 2.8 39.9 + - - +
312C LEU* 4.2 1.6 - - + -
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Residues in contact with ARG 50 (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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42C TYR* 2.9 65.4 + - + +
43C LEU* 4.4 1.0 + - - +
45C ALA* 3.4 34.6 + - - +
46C LYS* 3.3 8.6 + - - +
47C ASP 3.2 10.4 + - - +
49C THR* 1.3 77.6 - - - +
51C THR* 1.3 66.3 + - - +
53C ILE* 3.3 2.2 + - - +
54C ASN* 3.0 22.1 + - + +
66C GLY* 5.1 8.7 - - - -
67C ASP 5.5 1.0 + - - -
70C GLU* 2.4 46.3 + - - +
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Residues in contact with THR 51 (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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47C ASP 2.9 19.1 + - - -
48C SER* 3.2 13.1 + - - +
50C ARG* 1.3 78.3 - - - +
52C GLN* 1.3 64.3 + - + +
54C ASN* 3.3 6.6 + - - +
55C LYS* 3.0 46.8 + - + +
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Residues in contact with GLN 52 (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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48C SER* 3.0 21.5 + - - +
49C THR 4.0 4.1 - - - +
51C THR* 1.3 78.8 - - + +
53C ILE* 1.3 57.7 + - - +
55C LYS* 3.5 3.5 + - - +
56C VAL* 3.0 37.2 + - - +
301C GLY 3.3 23.5 + - - +
302C ILE* 3.9 7.3 - - + +
303C THR* 3.0 23.7 + - - +
304C ASP* 2.8 43.9 + - - +
305C VAL 4.6 0.7 + - - -
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Residues in contact with ILE 53 (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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38C LEU* 4.1 19.7 - - + +
41C VAL* 4.0 25.8 - - + -
42C TYR* 4.0 16.4 - - + -
45C ALA* 4.5 8.7 - - + -
49C THR* 3.4 21.5 + - + +
50C ARG 3.3 6.3 + - - +
52C GLN* 1.3 75.9 - - - +
54C ASN* 1.3 58.6 + - - +
57C VAL* 2.8 41.6 + - + +
59C PHE* 3.7 23.6 - - + -
302C ILE* 4.1 25.6 - - + -
305C VAL* 4.7 6.7 - - + -
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Residues in contact with ASN 54 (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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42C TYR* 3.3 27.1 + - + +
50C ARG* 3.0 18.5 + - + +
51C THR* 3.5 7.2 - - - +
53C ILE* 1.3 76.7 - - - +
55C LYS* 1.3 71.2 + - - +
58C ARG 3.3 0.9 + - - -
59C PHE* 3.1 44.1 + - - +
60C ASP* 2.9 40.1 + - - +
65C PHE* 5.8 1.2 - - - +
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Residues in contact with LYS 55 (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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51C THR* 3.0 35.4 + - + +
52C GLN* 3.9 3.6 - - - +
54C ASN* 1.3 83.8 + - - +
56C VAL* 1.3 67.1 + - + +
58C ARG* 3.3 23.0 + - - -
60C ASP* 3.7 25.3 + - - +
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Residues in contact with VAL 56 (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* 3.5 12.4 - - + -
13C ASP* 4.9 3.9 - - - +
52C GLN* 3.0 18.8 + - - +
55C LYS* 1.3 79.7 - - + +
57C VAL* 1.3 60.0 + - - +
58C ARG* 3.2 11.5 - - - +
300C MET* 3.5 51.0 - - + +
301C GLY* 3.9 10.8 - - - +
302C ILE* 3.6 32.3 - - + -
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Residues in contact with VAL 57 (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* 3.9 16.7 - - + +
35C MET* 3.6 40.5 - - + +
38C LEU* 4.2 12.6 - - + -
53C ILE* 2.8 37.0 + - + +
56C VAL* 1.3 72.2 - - - +
58C ARG* 1.3 75.0 + - - +
59C PHE* 3.4 30.8 + - + -
302C ILE* 4.0 16.6 - - + -
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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