Contacts of the helix formed by residues 45 - 58 (chain C) in PDB entry 2ODE
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 GLY 45 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43C GLU 3.3 1.2 - - - -
44C SER* 1.3 78.1 - - - +
46C LYS* 1.3 65.3 + - - +
48C THR* 3.1 4.9 + - - -
49C ILE* 3.1 25.9 + - - +
224C CYS* 4.4 5.6 - - - -
269C ASN* 3.7 11.4 - - - -
326C ALA* 4.2 0.7 - - - +
1002C GDP 3.0 31.6 + - - -
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Residues in contact with LYS 46 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C LEU* 3.5 22.6 - - + +
39C LEU* 3.4 33.9 - - - +
40C GLY 3.0 8.5 + - - +
41C ALA 2.9 18.2 + - - -
44C SER* 3.8 8.2 - - - +
45C GLY* 1.3 75.4 - - - +
47C SER* 1.3 63.1 + - - +
49C ILE* 3.2 8.1 + - - +
50C VAL* 3.1 22.9 + - - +
200C ASP* 3.4 12.6 - - - +
201C VAL* 3.0 29.2 - - + +
203C GLY 4.2 0.9 - - - +
224C CYS* 4.1 13.4 - - - -
1002C GDP 2.8 19.3 + - - +
2002C ALF 2.7 29.1 - - - -
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Residues in contact with SER 47 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C LYS* 1.3 75.3 - - - +
48C THR* 1.3 57.4 + - - +
50C VAL* 3.3 6.0 + - - +
51C LYS* 3.0 40.7 + - - +
179C VAL 5.3 2.7 - - - -
181C THR* 2.8 10.3 + - - -
200C ASP* 2.8 19.7 + - - -
1002C GDP 3.0 15.8 + - - -
3002C MG 2.2 29.8 - - - -
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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
----------------------------------------------------------
45C GLY 3.1 7.8 + - - -
47C SER* 1.3 76.1 - - - +
49C ILE* 1.3 64.6 + - - +
50C VAL 3.2 0.2 - - - -
51C LYS* 3.2 12.5 + - - +
52C GLN* 3.0 26.1 + - - +
175C LEU* 3.8 26.9 + - + +
177C THR 5.2 0.7 + - - -
326C ALA* 3.4 33.2 - - + +
327C THR* 3.8 10.8 - - + -
1002C GDP 2.6 39.3 + - - -
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Residues in contact with ILE 49 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C LEU* 4.4 20.6 - - + -
45C GLY 3.1 15.6 + - - +
46C LYS* 3.5 8.1 - - - +
48C THR* 1.3 74.8 - - - +
50C VAL* 1.3 55.8 + - - +
52C GLN* 3.2 6.1 + - - +
53C MET* 3.0 42.8 + - + +
198C MET* 5.4 0.2 - - - -
222C ILE* 5.0 7.0 - - + -
224C CYS* 4.5 7.4 - - - -
267C PHE* 3.7 38.6 - - + -
269C ASN* 5.2 0.9 - - - +
324C THR* 5.2 2.0 - - - +
326C ALA* 3.7 23.6 - - + -
332C VAL* 3.9 22.4 - - + -
336C PHE* 5.7 0.9 - - + -
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Residues in contact with VAL 50 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C LEU* 3.0 31.2 - - + -
46C LYS 3.1 7.9 + - - +
47C SER* 3.4 10.8 - - - +
48C THR 3.2 0.4 - - - -
49C ILE* 1.3 72.0 - - - +
51C LYS* 1.3 66.2 + - + +
53C MET* 3.2 12.8 + - - +
54C LYS* 3.2 12.8 + - - +
58C GLU* 5.1 0.9 - - - +
187C THR* 4.5 11.2 - - + -
198C MET* 3.9 23.3 - - + +
200C ASP* 3.8 24.2 - - + +
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Residues in contact with LYS 51 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C SER* 3.0 30.3 + - - +
48C THR* 3.5 10.5 + - - +
50C VAL* 1.3 76.5 - - + +
52C GLN* 1.3 57.7 + - - +
54C LYS* 3.3 8.1 + - - +
55C ILE* 3.0 29.9 + - - +
61C TYR* 3.2 24.4 - - + +
69C TYR* 3.8 22.6 + - - -
174C VAL* 3.5 31.9 - - + +
175C LEU* 3.8 24.1 + - + +
177C THR* 4.1 16.1 + - - -
179C VAL* 6.1 3.0 - - - +
1002C GDP 5.8 1.0 + - - -
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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 THR 3.0 15.3 + - - +
49C ILE* 3.5 7.4 - - - +
50C VAL 3.2 0.4 - - - -
51C LYS* 1.3 73.5 - - - +
53C MET* 1.3 59.2 + - - +
55C ILE* 3.2 10.9 - - - +
56C ILE* 2.8 39.8 + - + +
175C LEU* 3.5 12.7 - - + +
326C ALA 2.9 28.9 + - - +
327C THR 3.3 11.5 + - - -
328C ASP 3.4 1.6 - - - -
329C THR* 2.7 55.0 + - - +
332C VAL* 3.8 24.0 - - + -
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Residues in contact with MET 53 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49C ILE* 3.0 20.8 + - + +
50C VAL 3.2 7.6 + - - +
52C GLN* 1.3 75.9 - - - +
54C LYS* 1.3 55.8 + - - +
56C ILE* 4.2 7.2 - - + -
57C HIS* 2.7 42.6 + - + +
58C GLU* 3.1 9.4 + - - +
189C PHE* 3.7 37.0 - - + -
198C MET* 3.9 24.2 - - + -
332C VAL* 3.7 29.2 - - + -
336C PHE* 3.7 36.3 - - + -
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Residues in contact with LYS 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 VAL* 3.2 9.3 + - + +
51C LYS* 3.3 9.4 - - - +
52C GLN 3.2 0.4 - - - -
53C MET* 1.3 78.5 - - - +
55C ILE* 1.3 61.7 + - - +
58C GLU* 3.1 40.7 + - + +
59C ASP* 4.8 5.9 - - - +
60C GLY 2.6 45.4 + - - +
61C TYR* 3.6 35.9 - - + +
65C GLU* 2.6 30.2 + - - -
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Residues in contact with ILE 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 LYS 3.0 18.4 + - - +
52C GLN* 3.2 26.9 + - - +
54C LYS* 1.3 76.9 - - - +
56C ILE* 1.3 62.3 + - - +
58C GLU 4.4 4.5 - - - +
60C GLY* 3.9 11.9 - - - -
61C TYR* 3.8 15.3 - - + -
171C GLN* 3.5 49.8 - - + +
175C LEU* 3.8 19.1 - - + -
329C THR* 3.9 20.4 - - + +
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Residues in contact with ILE 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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52C GLN* 2.8 40.1 + - + +
53C MET* 4.2 4.7 - - + -
55C ILE* 1.3 74.9 - - - +
57C HIS* 1.3 88.7 + - + +
58C GLU 3.8 1.4 - - - +
329C THR* 3.8 26.2 - - + +
332C VAL* 4.1 5.6 - - + -
333C GLN* 3.7 55.4 - - + +
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Residues in contact with HIS 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 MET* 2.7 44.1 + - + +
56C ILE* 1.3 101.4 + - + +
58C GLU* 1.3 62.4 + - - +
189C PHE* 3.7 29.1 - + + +
190C THR 4.1 11.2 + - - +
191C PHE* 3.2 45.6 - + + +
333C GLN* 5.5 1.9 + - + -
336C PHE* 3.5 22.5 - + - +
337C ASP* 5.0 2.8 + - - -
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Residues in contact with GLU 58 (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 VAL* 5.1 1.0 - - - +
53C MET* 3.7 5.0 - - - +
54C LYS* 3.1 47.3 + - + +
55C ILE 4.4 4.7 - - - +
56C ILE 4.9 0.7 - - - +
57C HIS* 1.3 78.0 + - - +
59C ASP* 1.3 71.2 + - + +
60C GLY 3.6 0.3 + - - -
187C THR* 4.0 15.4 + - - +
188C HIS 3.5 18.7 - - - +
189C PHE* 3.4 36.2 - - + +
198C MET* 4.7 0.5 - - - +
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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