Contacts of the helix formed by residues 41 - 56 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28A HIS* 4.4 6.5 - - - -
39A GLN 3.6 1.4 + - - -
40A LEU* 1.3 76.0 - - - +
42A THR* 1.3 61.2 + - - -
43A VAL 3.3 2.5 - - - -
44A GLU* 3.1 20.1 + - - -
45A GLY 2.9 22.5 + - - -
69A PHE* 3.6 7.6 - - - -
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Residues in contact with THR 42 (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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14A ASN* 3.0 25.0 + - - -
18A ALA* 3.6 8.1 - - - +
19A VAL* 3.0 47.0 + - + +
25A LEU* 3.6 23.3 - - + -
28A HIS* 5.6 3.8 - - + -
41A GLY* 1.3 70.2 - - - -
43A VAL* 1.3 62.9 + - - +
45A GLY 3.4 0.4 + - - +
46A GLN 3.2 12.5 + - - -
69A PHE* 4.1 19.1 - - + -
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Residues in contact with VAL 43 (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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13A LEU* 3.6 51.1 - - + +
14A ASN* 3.7 24.0 + - - +
17A PHE* 3.8 13.8 - - + +
18A ALA* 3.9 3.8 - - + +
41A GLY 3.3 0.6 - - - -
42A THR* 1.3 78.3 + - - +
44A GLU* 1.3 72.1 + - - +
46A GLN* 3.3 5.2 + - - +
47A MET* 3.1 20.1 + - - +
304A IOD 4.3 17.7 - - + -
203F THR* 5.0 6.4 + - + -
204F ILE 5.9 0.9 - - - +
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Residues in contact with GLU 44 (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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40A LEU* 4.1 25.6 - - + -
41A GLY* 3.1 29.1 + - - +
43A VAL* 1.3 84.7 + - - +
45A GLY* 1.3 65.7 + - - +
47A MET* 3.2 12.7 + - + +
48A LEU* 3.1 25.5 + - - +
162A ASP* 5.7 0.7 - - - +
207A THR* 4.4 24.5 - - + +
209A GLU* 4.5 13.6 - - - +
211A MET* 4.6 7.2 - - + -
304A IOD 4.4 3.8 - - + -
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Residues in contact with GLY 45 (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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19A VAL* 3.7 6.7 - - - -
40A LEU* 4.2 11.8 - - - +
41A GLY 2.9 16.5 + - - -
42A THR 3.8 3.1 - - - -
43A VAL 3.2 0.2 - - - -
44A GLU* 1.3 78.4 - - - +
46A GLN* 1.3 59.5 + - - +
48A LEU* 3.4 5.6 + - - +
49A GLN* 3.2 24.4 + - - +
73A CYS* 4.1 23.5 - - - +
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Residues in contact with GLN 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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16A LEU 4.7 0.4 + - - -
17A PHE* 3.4 36.2 - - - +
18A ALA 3.2 9.2 - - - +
19A VAL* 3.5 7.7 + - + +
42A THR 3.2 11.4 + - - +
43A VAL 3.3 2.4 + - - +
44A GLU 3.2 0.2 - - - -
45A GLY* 1.3 75.2 - - - +
47A MET* 1.3 59.5 + - - +
49A GLN* 3.2 14.8 + - - +
50A LEU* 2.9 26.3 + - - +
197F LYS* 3.1 31.1 + - - +
200F TYR 5.9 0.2 + - - -
201F LEU* 3.9 19.4 - - + +
202F SER 2.8 35.0 + - - +
203F THR* 4.4 0.7 - - - +
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Residues in contact with MET 47 (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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43A VAL 3.1 7.9 + - - +
44A GLU* 3.2 11.0 + - - +
46A GLN* 1.3 76.1 - - - +
48A LEU* 1.3 64.3 + - + +
50A LEU* 3.2 7.3 + - + +
51A LEU* 3.0 27.4 + - + +
205A ILE* 3.4 40.8 - - + -
207A THR* 4.4 2.5 - - + -
211A MET* 3.8 36.1 - - + -
304A IOD 2.7 43.5 - - + -
203F THR* 3.5 20.3 + - + +
205F ILE* 4.1 8.5 - - + -
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Residues in contact with LEU 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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40A LEU* 3.4 26.7 - - + -
44A GLU 3.1 15.5 + - - +
45A GLY* 3.7 8.7 - - - +
47A MET* 1.3 77.0 - - + +
49A GLN* 1.3 58.1 + - - +
51A LEU* 3.2 13.6 + - + +
52A ILE* 2.9 36.1 + - + +
70A SER* 4.7 3.6 - - - +
73A CYS* 6.0 0.2 - - + -
74A MET* 3.8 35.7 - - + -
132A MET* 4.8 6.9 - - + +
134A PHE* 4.1 17.7 - - + -
160A VAL* 3.9 27.4 - - + -
211A MET* 4.5 11.4 - - + -
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Residues in contact with GLN 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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19A VAL* 3.7 25.2 - - - +
21A THR* 6.3 1.0 - - - +
45A GLY 3.2 9.3 + - - +
46A GLN* 3.2 25.1 + - - +
48A LEU* 1.3 77.4 - - - +
50A LEU* 1.3 63.6 + - - +
52A ILE* 3.3 3.6 + - - +
53A ARG* 2.9 28.6 + - - +
73A CYS* 2.9 36.7 + - - +
76A HIS* 3.9 17.6 + - - +
77A ALA* 3.7 17.0 - - + +
305A IOD 3.8 15.4 - - + +
201F LEU* 3.8 12.2 - - + +
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Residues in contact with LEU 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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46A GLN 2.9 12.5 + - - +
47A MET* 3.3 13.2 - - + +
48A LEU 3.2 0.2 - - - -
49A GLN* 1.3 76.9 - - - +
51A LEU* 1.3 60.6 + - + +
53A ARG* 3.3 1.7 + - - +
54A MET* 2.8 45.2 + - + +
51F LEU* 6.1 0.2 - - + -
201F LEU* 3.4 37.6 - - + +
202F SER 5.6 0.2 - - - -
203F THR* 3.8 22.9 - - - +
205F ILE* 5.6 3.4 - - + -
213F VAL* 3.6 36.6 - - + +
215F ILE* 3.6 28.0 - - + +
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Residues in contact with LEU 51 (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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47A MET* 3.0 24.3 + - + +
48A LEU* 3.2 25.1 + - + +
50A LEU* 1.3 79.3 - - + +
52A ILE* 1.3 63.2 + - + +
54A MET* 3.3 8.2 + - - -
55A ALA* 3.0 28.6 + - - +
132A MET* 5.7 1.8 - - + -
158A LEU* 4.5 8.5 - - + -
160A VAL* 4.4 10.5 - - + -
205A ILE* 5.0 10.1 - - + -
213A VAL* 3.7 35.2 - - + -
50F LEU* 6.2 0.2 - - + -
51F LEU* 5.3 5.6 - - + -
54F MET* 3.6 32.4 - - + +
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Residues in contact with ILE 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 LEU 2.9 22.8 + - - +
49A GLN* 3.6 4.7 - - - +
50A LEU 3.3 0.2 - - - -
51A LEU* 1.3 74.4 - - - +
53A ARG* 1.3 63.3 + - - +
56A GLY* 3.2 3.6 + - - -
57A ILE* 3.1 39.3 + - + +
60A ILE* 3.6 13.0 - - + -
74A MET* 3.5 48.0 - - + +
77A ALA* 3.8 20.6 - - + +
78A LEU* 3.8 23.6 - - + -
79A PRO* 5.6 0.4 - - + -
132A MET* 3.9 21.8 - - + -
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Residues in contact with ARG 53 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49A GLN 2.9 20.5 + - - +
52A ILE* 1.3 74.4 - - - +
54A MET* 1.3 66.8 + - - +
56A GLY* 3.4 10.5 + - - -
76A HIS 3.9 17.2 + - - -
77A ALA* 3.2 26.9 + - + +
78A LEU 5.3 2.2 + - - -
305A IOD 3.9 14.2 - - - +
201F LEU* 3.5 15.6 - - + +
215F ILE* 3.3 20.9 - - + +
217F LEU* 4.7 19.2 - - + +
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Residues in contact with MET 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 LEU* 2.8 41.5 + - + +
51A LEU* 3.7 7.0 - - - +
53A ARG* 1.3 74.3 - - - +
55A ALA* 1.3 61.5 - - - +
56A GLY 3.5 0.5 + - - -
51F LEU* 3.6 54.5 - - + +
54F MET* 3.5 17.3 - - + +
55F ALA* 3.4 23.8 - - + +
158F LEU* 3.9 20.4 - - + -
213F VAL* 4.1 10.5 - - - -
215F ILE* 3.6 21.5 - - + -
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Residues in contact with ALA 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 LEU 3.0 16.2 + - - +
54A MET* 1.3 76.2 - - - +
56A GLY* 1.3 63.4 + - - +
57A ILE* 3.3 23.1 + - + +
154A ARG* 4.4 9.4 + - - +
158A LEU* 3.9 16.6 - - + -
54F MET* 3.4 25.0 - - + +
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Residues in contact with GLY 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 ILE 3.2 6.5 + - - -
53A ARG* 3.4 7.0 + - - -
54A MET 3.3 4.8 + - - -
55A ALA* 1.3 77.3 - - - +
57A ILE* 1.3 65.6 + - - +
58A HIS* 3.1 21.9 + - - -
79A PRO* 6.0 0.7 - - - -
131A ASP* 4.8 1.2 - - - +
154A 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