Contacts of the helix formed by residues 41 - 56 (chain D) in PDB entry 4OA5
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 41 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14D ASN* 5.9 0.2 - - - -
28D HIS* 4.4 6.1 - - - -
39D GLN 3.6 1.6 + - - -
40D LEU* 1.3 76.5 - - - +
42D THR* 1.3 60.5 + - - -
43D VAL 3.2 2.9 - - - -
44D GLU* 3.1 20.2 + - - -
45D GLY 2.9 24.6 + - - -
69D PHE* 3.6 7.4 - - - -
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Residues in contact with THR 42 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14D ASN* 3.0 24.8 + - - -
18D ALA* 3.6 8.3 - - - +
19D VAL* 3.0 49.6 + - + +
25D LEU* 3.6 22.9 - - + -
28D HIS* 5.5 4.3 - - + -
41D GLY* 1.3 72.9 - - - -
43D VAL* 1.3 59.7 + - - +
45D GLY 3.4 0.2 + - - -
46D GLN 3.2 12.0 + - - -
69D PHE* 4.1 18.8 - - + -
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Residues in contact with VAL 43 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13D LEU* 3.5 51.8 - - + +
14D ASN* 3.7 24.1 + - - +
17D PHE* 3.8 14.3 - - + +
18D ALA* 3.9 3.8 - - + -
41D GLY 3.2 0.6 - - - -
42D THR* 1.3 75.3 + - - +
44D GLU* 1.3 77.8 + - - +
46D GLN* 3.2 5.2 + - - +
47D MET* 3.1 29.8 + - + +
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Residues in contact with GLU 44 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40D LEU* 4.1 24.9 - - + -
41D GLY* 3.1 30.5 + - - +
43D VAL* 1.3 86.0 + - - +
45D GLY* 1.3 62.5 + - - +
47D MET* 3.2 14.5 + - + +
48D LEU* 3.1 25.6 + - - +
162D ASP* 5.6 0.9 - - - +
207D THR* 4.4 24.0 - - + +
209D GLU* 4.5 14.1 - - - +
211D MET* 4.6 10.3 - - + +
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Residues in contact with GLY 45 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19D VAL* 3.7 6.7 - - - -
40D LEU* 4.2 11.6 - - - +
41D GLY 2.9 16.9 + - - -
42D THR 3.4 3.1 + - - -
43D VAL 3.2 0.2 - - - -
44D GLU* 1.3 77.4 - - - +
46D GLN* 1.3 60.0 + - - +
48D LEU* 3.4 6.1 + - - +
49D GLN* 3.2 24.8 + - - +
69D PHE* 4.9 0.4 - - - -
73D CYS* 4.1 23.4 - - - +
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Residues in contact with GLN 46 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16D LEU 4.7 1.2 + - - -
17D PHE* 3.4 48.8 - - - +
18D ALA 3.2 20.8 + - - +
19D VAL* 3.5 8.8 + - + +
42D THR 3.2 10.4 + - - +
43D VAL 3.7 2.0 - - - +
44D GLU 3.2 0.2 - - - -
45D GLY* 1.3 74.1 - - - +
47D MET* 1.3 66.6 + - - +
49D GLN* 3.2 20.3 + - + +
50D LEU* 3.0 23.0 + - + +
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Residues in contact with MET 47 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43D VAL* 3.1 20.1 + - + +
44D GLU* 3.2 22.0 + - + +
46D GLN* 1.3 77.2 - - - +
48D LEU* 1.3 61.7 + - + +
50D LEU* 3.2 17.1 + - + +
51D LEU* 3.1 28.8 + - + +
205D ILE* 3.3 43.3 - - + -
207D THR* 4.1 23.8 - - + -
211D MET* 5.2 9.2 - - + -
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Residues in contact with LEU 48 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40D LEU* 3.4 25.4 - - + -
44D GLU 3.1 15.7 + - - +
45D GLY* 3.6 7.6 - - - +
46D GLN 3.3 0.2 - - - -
47D MET* 1.3 73.9 - - + +
49D GLN* 1.3 67.5 + - - +
51D LEU* 3.2 13.1 + - + +
52D ILE* 2.9 29.5 + - + +
70D SER* 4.7 3.8 - - - +
73D CYS* 6.0 0.7 - - + -
74D MET* 3.9 35.0 - - + -
132D MET* 4.8 6.9 - - + +
134D PHE* 4.1 18.8 - - + -
160D VAL* 3.9 28.0 - - + -
211D MET* 4.5 9.9 - - + -
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Residues in contact with GLN 49 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19D VAL* 3.7 26.1 - - - +
21D THR* 6.1 1.6 - - - +
45D GLY 3.2 8.5 + - - +
46D GLN* 3.2 25.5 + - + +
48D LEU* 1.3 79.2 - - - +
50D LEU* 1.3 56.4 + - - +
52D ILE* 3.3 3.6 + - - +
53D ARG* 2.9 35.8 + - - +
73D CYS* 2.9 37.1 + - - +
74D MET 4.7 0.2 - - - +
76D HIS* 3.9 16.8 - - - +
77D ALA* 3.7 15.9 - - + -
308D IOD 3.7 21.7 - - + +
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Residues in contact with LEU 50 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46D GLN* 3.0 13.4 + - + +
47D MET* 3.4 20.2 - - + +
49D GLN* 1.3 76.5 - - - +
51D LEU* 1.3 61.9 + - + +
53D ARG* 3.3 6.7 + - + +
54D MET* 2.8 59.2 + - + +
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Residues in contact with LEU 51 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47D MET* 3.1 21.8 + - + +
48D LEU* 3.2 25.3 + - + +
50D LEU* 1.3 80.2 - - + +
52D ILE* 1.3 64.5 + - + +
54D MET* 3.3 15.9 + - + +
55D ALA* 3.0 28.6 + - - +
132D MET* 5.6 1.8 - - + -
158D LEU* 4.2 12.9 - - + +
160D VAL* 4.4 10.5 - - + -
205D ILE* 5.0 6.3 - - + -
211D MET* 5.7 0.9 - - + -
213D VAL* 3.7 43.3 - - + -
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Residues in contact with ILE 52 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48D LEU 2.9 21.8 + - - +
49D GLN* 3.6 4.7 - - - +
50D LEU 3.3 0.2 - - - -
51D LEU* 1.3 76.0 - - - +
53D ARG* 1.3 65.0 + - - +
56D GLY* 3.1 3.6 + - - -
57D ILE* 3.1 38.7 + - + +
60D ILE* 3.6 11.4 - - + -
74D MET* 3.5 48.2 - - + +
77D ALA* 3.8 20.9 - - + +
78D LEU* 3.8 24.2 - - + -
79D PRO* 5.6 0.2 - - + -
132D MET* 3.9 22.2 - - + -
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Residues in contact with ARG 53 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49D GLN* 2.9 21.9 + - + +
50D LEU* 3.7 7.0 - - + +
52D ILE* 1.3 74.0 - - - +
54D MET* 1.3 66.7 + - + +
56D GLY* 3.4 10.5 + - - -
76D HIS 5.7 1.2 + - - -
77D ALA* 3.4 32.6 + - + +
78D LEU 5.5 3.4 + - - -
79D PRO* 5.7 2.0 - - - +
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Residues in contact with MET 54 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50D LEU* 2.8 50.8 + - + +
51D LEU* 3.3 15.7 + - + +
53D ARG* 1.3 76.1 - - + +
55D ALA* 1.3 60.0 + - + +
56D GLY 3.5 0.5 + - - -
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Residues in contact with ALA 55 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51D LEU 3.0 16.9 + - - +
54D MET* 1.3 75.4 - - + +
56D GLY* 1.3 64.1 + - - +
57D ILE* 3.2 23.2 + - + +
154D ARG* 4.5 9.2 + - - +
158D LEU* 3.9 18.4 - - + -
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Residues in contact with GLY 56 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52D ILE 3.1 6.8 + - - -
53D ARG* 3.4 7.2 + - - -
54D MET 3.3 4.4 + - - -
55D ALA* 1.3 78.0 - - - +
57D ILE* 1.3 65.8 - - - +
58D HIS* 3.1 21.3 + - - -
79D PRO* 5.9 0.7 - - - -
131D ASP* 4.8 0.9 - - - +
154D ARG* 5.2 3.3 + - - -
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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