Contacts of the helix formed by residues 45 - 58 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43A GLU 3.2 1.2 + - - -
44A SER* 1.3 79.8 - - - +
46A LYS* 1.3 65.5 + - - +
48A THR* 3.2 4.0 + - - -
49A ILE* 3.1 25.2 + - - +
224A CYS* 4.3 5.8 - - - -
269A ASN* 3.7 11.7 - - - -
326A ALA* 4.3 0.9 - - - +
1001A GDP 3.1 31.0 + - - -
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Residues in contact with LYS 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A LEU* 3.3 41.2 - - + +
39A LEU* 3.5 27.6 - - - +
40A GLY 3.1 9.3 + - - -
41A ALA 2.9 18.4 + - - -
44A SER* 3.8 6.0 - - - +
45A GLY* 1.3 76.8 - - - +
47A SER* 1.3 62.7 + - - +
49A ILE* 3.2 4.0 + - - +
50A VAL 3.1 15.9 + - - -
200A ASP* 3.4 12.6 - - - +
201A VAL* 3.1 27.4 - - - +
203A GLY 4.1 2.0 - - - +
224A CYS* 4.1 12.6 - - - -
1001A GDP 2.7 26.8 + - - +
2001A ALF 2.8 23.1 - - - -
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Residues in contact with SER 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A LYS* 1.3 75.5 - - - +
48A THR* 1.3 57.7 + - - +
50A VAL* 3.2 6.7 + - - +
51A LYS* 2.9 41.6 + - - +
179A VAL 5.4 2.7 - - - -
181A THR* 2.9 5.7 + - - -
200A ASP* 2.7 23.6 + - - -
1001A GDP 3.0 14.3 + - - -
3001A MG 2.1 30.9 - - - -
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Residues in contact with THR 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A GLY 3.5 5.8 - - - -
46A LYS 3.1 0.2 - - - -
47A SER* 1.3 75.3 - - - +
49A ILE* 1.3 64.6 + - - +
51A LYS* 3.2 11.5 + - - +
52A GLN* 3.0 27.5 + - - +
175A LEU* 3.8 16.4 + - + +
177A THR 5.3 0.3 + - - -
326A ALA* 3.4 34.5 - - + +
327A THR* 3.8 18.4 - - + -
1001A GDP 2.6 43.7 + - + -
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Residues in contact with ILE 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A LEU* 4.2 17.0 - - + -
45A GLY 3.1 14.0 + - - +
46A LYS* 3.4 7.9 - - - +
48A THR* 1.3 74.5 - - - +
50A VAL* 1.3 62.3 + - - +
52A GLN* 3.1 14.5 + - - +
53A MET* 3.1 29.6 + - + +
222A ILE* 4.8 9.0 - - + -
224A CYS* 4.3 8.7 - - - -
267A PHE* 3.9 39.7 - - + -
269A ASN* 5.2 1.1 - - - +
324A THR* 5.1 3.4 - - - +
326A ALA* 3.7 22.2 - - + -
332A VAL* 3.9 21.3 - - + -
336A PHE* 5.5 0.7 - - + -
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Residues in contact with VAL 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A LEU* 3.1 32.1 - - + -
46A LYS 3.1 9.7 + - - +
47A SER* 3.2 11.4 + - - +
49A ILE* 1.3 76.1 - - - +
51A LYS* 1.3 61.0 + - + +
53A MET* 3.1 12.8 + - - +
54A LYS* 3.3 11.7 + - + +
187A THR* 4.7 13.2 - - + +
198A MET* 3.8 26.6 - - + +
200A ASP* 3.8 26.5 - - + +
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Residues in contact with LYS 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A SER* 2.9 33.8 + - - +
48A THR* 3.2 12.4 + - - +
50A VAL* 1.3 73.1 - - + +
52A GLN* 1.3 57.9 + - - +
54A LYS* 3.3 6.8 + - - +
55A ILE* 3.1 31.0 + - - +
61A TYR* 3.2 23.7 - - + +
69A TYR* 3.6 27.4 + - - -
174A VAL* 3.7 29.8 - - + +
175A LEU* 3.6 25.2 + - + +
177A THR* 4.0 16.1 + - - -
179A VAL* 6.0 5.5 - - - +
1001A GDP 5.7 1.6 + - - -
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Residues in contact with GLN 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A THR 3.0 14.9 + - - +
49A ILE* 3.1 8.5 + - - +
51A LYS* 1.3 74.6 - - - +
53A MET* 1.3 60.7 + - - +
55A ILE* 3.3 9.2 + - - +
56A ILE* 2.8 36.5 + - + +
175A LEU* 3.6 13.6 - - + +
326A ALA 2.8 30.1 + - - +
327A THR 3.4 9.1 + - - -
328A ASP 3.4 1.4 + - - -
329A THR* 2.7 57.1 + - - +
332A VAL* 3.6 26.0 - - + -
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Residues in contact with MET 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A ILE* 3.1 20.0 + - + +
50A VAL 3.1 6.9 + - - +
52A GLN* 1.3 81.5 - - - +
54A LYS* 1.3 54.9 + - - +
56A ILE* 4.1 4.5 - - + -
57A HIS* 2.7 53.3 + - + +
58A GLU* 3.0 8.3 + - - +
189A PHE* 3.7 17.6 - - + -
198A MET* 3.9 32.5 - - + -
332A VAL* 3.9 24.7 - - + -
336A PHE* 3.7 41.1 - - + -
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Residues in contact with LYS 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A VAL 3.3 8.0 + - - +
51A LYS* 3.3 10.0 + - - +
52A GLN 3.3 0.2 - - - -
53A MET* 1.3 79.0 - - - +
55A ILE* 1.3 56.8 + - - +
58A GLU* 3.2 27.3 + - + -
59A ASP* 4.7 8.7 - - - +
60A GLY 2.7 57.0 + - - +
61A TYR* 3.5 41.1 - - + +
65A GLU* 3.2 21.6 + - - -
164B ARG* 4.8 4.3 - - - +
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Residues in contact with ILE 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A LYS 3.1 16.6 + - - +
52A GLN* 3.3 23.5 + - - +
54A LYS* 1.3 78.5 - - - +
56A ILE* 1.3 61.2 + - + +
58A GLU 4.8 1.6 - - - +
59A ASP 5.5 0.2 - - - -
60A GLY* 3.9 11.3 + - - -
61A TYR* 3.8 20.6 - - + -
171A GLN* 3.6 43.1 - - + +
175A LEU* 3.8 21.8 - - + -
329A THR* 3.8 23.8 - - + +
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Residues in contact with ILE 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A GLN* 2.8 30.4 + - + +
53A MET* 4.1 12.1 - - + -
55A ILE* 1.3 77.9 - - - +
57A HIS* 1.3 86.5 + - + +
58A GLU 3.9 2.2 - - - +
329A THR* 4.0 23.8 - - + +
332A VAL* 4.1 5.4 - - + -
333A GLN* 3.7 58.6 - - + +
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Residues in contact with HIS 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A MET* 2.7 44.4 + - + +
56A ILE* 1.3 100.0 + - + +
58A GLU* 1.3 60.6 + - - +
189A PHE* 3.4 37.9 - + + +
190A THR 4.1 11.4 + - - +
191A PHE* 3.4 44.8 - + - +
333A GLN* 5.7 3.2 + - + -
336A PHE* 3.5 19.2 - - - +
337A ASP 5.8 0.2 + - - -
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Residues in contact with GLU 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A MET 3.0 5.5 + - - +
54A LYS* 3.2 28.8 + - + +
55A ILE 4.8 1.6 - - - +
56A ILE 4.7 2.6 - - - +
57A HIS* 1.3 82.2 + - - +
59A ASP* 1.3 62.0 + - + +
188A HIS 5.1 4.0 - - - +
189A PHE* 4.6 12.1 - - + -
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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