Contacts of the helix formed by residues 45 - 57 (chain C) in PDB entry 1S89
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 THR 45 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16C LEU 3.6 1.4 + - - -
17C VAL* 3.7 21.7 - - + +
44C ALA* 1.3 76.1 - - - +
46C GLY* 1.3 67.3 + - - +
47C THR 3.2 1.0 + - - -
48C THR* 3.3 9.2 + - - -
49C GLY* 2.8 20.1 + - - -
62C ALA* 4.5 0.2 - - - +
63C MET* 4.2 2.7 - - - +
64C LEU 3.6 13.2 - - - +
66C GLY 4.0 0.9 - - - +
70C GLY* 3.9 16.8 - - - +
71C ASP* 3.8 21.8 - - - +
74C VAL* 4.6 3.8 - - + -
203C PGA 2.6 36.5 + - - +
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Residues in contact with GLY 46 (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 THR* 1.3 70.5 - - - +
47C THR* 1.3 61.6 + - - +
49C GLY* 4.2 0.3 - - - -
50C ASN* 3.0 33.5 + - - -
62C ALA* 4.3 4.7 - - - +
63C MET 2.9 20.0 + - - -
64C LEU 2.9 21.7 + - - -
65C SER 3.7 3.3 - - - +
143D TYR* 3.9 6.5 - - - -
147D LEU* 4.2 4.7 - - - -
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Residues in contact with THR 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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23C LYS* 3.6 17.7 - - + -
46C GLY* 1.3 68.7 - - - -
48C THR* 1.3 66.9 + - - +
50C ASN* 3.3 3.8 + - - +
51C LEU* 3.2 33.7 + - + +
65C SER* 3.9 3.3 + - - -
203C PGA 2.8 27.5 + - - -
147D LEU* 4.1 13.6 - - - +
150D ARG* 3.1 36.3 + - + +
151D LEU* 4.0 19.0 - - + +
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Residues in contact with THR 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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16C LEU 3.7 17.5 - - - +
18C ALA* 3.4 22.9 + - + +
23C LYS* 3.7 11.6 - - + +
26C LEU* 3.8 26.7 - - + -
27C MET* 5.0 2.4 - - - +
44C ALA* 4.4 0.4 - - + -
45C THR* 3.6 9.2 - - - -
47C THR* 1.3 73.4 - - - +
49C GLY* 1.3 64.0 + - - +
51C LEU* 3.5 5.8 + - - +
52C ILE* 3.2 38.5 + - + +
203C PGA 2.6 28.7 + - - -
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Residues in contact with GLY 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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44C ALA* 3.5 21.7 - - - +
45C THR 2.8 18.0 + - - -
46C GLY 4.2 0.4 - - - -
48C THR* 1.3 74.5 - - - +
50C ASN* 1.3 60.7 + - - +
52C ILE* 3.4 5.3 + - - +
53C SER* 3.1 24.1 + - - -
60C VAL* 3.8 16.4 - - - +
62C ALA* 4.4 7.9 - - - -
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Residues in contact with ASN 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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46C GLY* 3.0 23.7 + - - +
47C THR 3.3 4.5 + - - +
49C GLY* 1.3 71.5 - - - +
51C LEU* 1.3 62.0 + - - +
53C SER* 3.1 9.8 + - - -
54C ARG* 2.8 34.3 + - + +
62C ALA* 4.6 11.4 - - - +
147D LEU* 3.9 24.0 - - - +
151D LEU* 4.0 26.4 - - + +
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Residues in contact with LEU 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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23C LYS* 3.6 34.8 - - + -
27C MET* 3.4 24.9 - - + +
47C THR* 3.2 25.2 + - + +
48C THR* 3.8 4.5 - - - +
50C ASN* 1.3 76.9 - - - +
52C ILE* 1.3 63.7 + - - +
54C ARG* 3.3 6.6 + - + +
55C ALA* 3.2 25.6 + - - +
150D ARG 5.5 1.8 - - - +
151D LEU* 4.2 19.7 - - + -
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Residues in contact with ILE 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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16C LEU* 3.8 30.5 - - + -
26C LEU* 4.8 4.0 - - + -
27C MET* 3.9 21.5 - - - -
30C VAL* 4.1 29.6 - - + -
42C LEU* 5.3 0.2 - - + -
44C ALA* 5.2 0.7 - - + -
48C THR* 3.2 31.0 + - + +
49C GLY* 3.6 10.5 - - - +
51C LEU* 1.3 77.5 - - - +
53C SER* 1.3 55.4 + - - +
55C ALA* 3.2 1.3 + - - -
56C THR* 2.7 50.9 + - + +
58C MET* 4.5 3.6 - - + -
60C VAL* 3.9 17.9 - - + -
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Residues in contact with SER 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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49C GLY 3.1 10.9 + - - -
50C ASN* 3.1 16.3 + - - -
52C ILE* 1.3 80.3 - - - +
54C ARG* 1.3 60.5 + - - +
55C ALA 3.0 0.7 + - - -
56C THR* 4.1 1.8 - - - -
57C GLY* 2.8 28.1 + - - -
58C MET 3.3 25.8 - - - -
60C VAL* 4.4 10.8 - - - -
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Residues in contact with ARG 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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50C ASN* 2.8 21.4 + - + +
51C LEU* 3.5 6.3 - - + +
52C ILE 3.2 0.2 - - - -
53C SER* 1.3 75.8 + - - +
55C ALA* 1.3 59.3 + - - +
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Residues in contact with ALA 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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27C MET* 4.1 15.5 - - + -
31C GLU* 4.5 14.8 - - - +
51C LEU 3.2 15.5 + - - +
52C ILE 3.2 2.6 + - - +
53C SER 3.0 0.4 + - - -
54C ARG* 1.3 80.2 - - - +
56C THR* 1.3 67.3 + - + +
57C GLY 3.6 0.9 - - - -
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Residues in contact with THR 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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27C MET* 5.5 0.7 - - + +
30C VAL* 4.2 18.6 - - + -
31C GLU* 4.1 21.3 - - + -
34C GLN* 3.0 45.9 + - - +
52C ILE* 2.7 26.3 + - + +
55C ALA* 1.3 82.3 - - + +
57C GLY* 1.3 58.6 + - - +
58C MET* 3.0 25.9 + - - +
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Residues in contact with GLY 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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53C SER* 2.8 17.4 + - - -
54C ARG 5.0 0.2 - - - -
55C ALA 3.6 1.0 - - - -
56C THR* 1.3 77.7 - - - +
58C MET* 1.3 63.7 + - - +
59C ASN 3.9 0.3 + - - -
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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