Contacts of the helix formed by residues 40 - 51 (chain A) in PDB entry 1ESD
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 ASN 40 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16A THR 2.8 26.7 + - - +
17A ALA* 3.5 15.9 - - - +
18A ASN* 3.2 15.5 - - + +
36A GLN* 4.0 5.7 - - - +
37A ALA* 3.4 15.3 + - - +
38A LYS 3.8 5.0 - - - +
39A GLU* 1.3 78.4 - - - +
41A TYR* 1.3 69.0 + - - +
42A PRO* 3.2 7.2 - - - +
43A ALA* 2.9 22.2 + - - +
44A VAL* 3.2 7.8 + - - +
61A ASP* 2.8 28.8 + - - +
63A SER* 3.8 5.5 + - - -
289A ARG* 3.9 1.8 - - - -
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Residues in contact with TYR 41 (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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10A PHE* 5.1 0.7 - + - -
15A TYR 3.3 20.4 - - - -
16A THR* 2.8 31.3 + - + +
18A ASN* 3.1 8.0 + - - -
40A ASN* 1.3 69.9 - - - +
42A PRO* 1.3 82.1 - - + +
44A VAL 3.2 0.2 + - - -
45A ALA* 2.7 25.3 + - + +
100A VAL* 4.4 5.6 - - + -
101A GLY* 3.9 5.4 - - - -
102A SER* 4.4 0.8 + - - -
184A VAL* 3.2 35.3 - - + +
289A ARG* 3.8 11.7 - - - +
292A GLN* 3.5 48.0 - - + +
293A ALA* 3.7 11.0 - - - +
296A VAL* 3.8 37.0 - - + -
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Residues in contact with PRO 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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10A PHE* 3.4 49.6 - - + -
16A THR* 3.5 27.4 - - + +
40A ASN* 3.4 13.0 - - - +
41A TYR* 1.3 104.8 - - + +
43A ALA* 1.3 58.8 + - - +
45A ALA* 4.0 1.6 - - + +
46A THR* 2.7 29.0 + - - -
61A ASP* 3.7 13.0 - - - +
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Residues in contact with ALA 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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38A LYS 3.3 26.2 - - - +
39A GLU* 4.1 3.1 - - - -
40A ASN* 2.9 19.3 + - - +
42A PRO* 1.3 75.1 - - - +
44A VAL* 1.3 62.0 + - - +
46A THR* 3.3 7.1 + - - -
47A ARG* 3.3 42.1 + - - +
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Residues in contact with VAL 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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39A GLU* 3.9 31.2 - - - +
40A ASN 3.2 13.2 + - - +
43A ALA* 1.3 73.0 - - - +
45A ALA* 1.3 62.9 + - - +
47A ARG* 3.3 12.1 + - - +
48A SER* 3.0 27.3 + - - +
289A ARG* 3.9 15.3 - - - +
290A ASP* 4.6 11.0 - - + +
293A ALA* 3.5 26.0 - - + -
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Residues in contact with ALA 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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10A PHE* 5.5 4.3 - - + -
41A TYR 2.7 23.5 + - - +
42A PRO* 4.0 4.7 - - + +
44A VAL* 1.3 71.3 - - - +
46A THR* 1.3 52.8 + - - +
48A SER* 3.2 4.0 + - - +
49A LEU* 2.7 44.9 + - + +
56A LEU* 6.0 0.4 - - + -
293A ALA* 3.7 25.7 - - - +
296A VAL* 4.5 12.3 - - + -
297A ALA* 4.2 15.7 - - + +
300A ILE* 5.5 1.3 - - + -
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Residues in contact with THR 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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10A PHE* 3.8 20.4 - - - -
42A PRO 2.7 17.4 + - - -
43A ALA* 3.3 13.2 - - - -
45A ALA* 1.3 77.1 - - - +
47A ARG* 1.3 51.6 - - - +
49A LEU* 3.3 2.6 + - - +
50A ALA* 2.8 34.2 + - + +
54A ILE 4.5 0.9 - - - +
56A LEU* 4.0 27.6 + - + +
58A VAL* 4.1 16.0 - - + +
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Residues in contact with ARG 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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39A GLU* 2.5 45.6 + - - -
43A ALA* 3.3 27.8 + - - +
44A VAL* 3.7 10.4 - - - +
45A ALA 3.3 0.4 - - - -
46A THR* 1.3 75.3 - - - +
48A SER* 1.3 70.3 + - - +
50A ALA* 2.8 18.4 + - - +
51A ASP* 3.1 19.8 + - - +
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Residues in contact with SER 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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44A VAL* 3.0 19.5 + - - +
45A ALA* 3.7 6.1 - - - -
47A ARG* 1.3 80.7 - - - +
49A LEU* 1.3 62.6 - - - +
51A ASP* 3.3 20.9 - - - +
52A LYS* 3.4 15.1 - - - +
293A ALA* 5.9 1.9 - - - +
294A LYS* 6.0 1.5 - - - -
297A ALA* 4.4 15.7 - - - -
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Residues in contact with LEU 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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45A ALA* 2.7 23.2 + - + +
46A THR* 3.7 4.3 - - - +
48A SER* 1.3 72.1 - - - +
50A ALA* 1.3 59.1 + - - +
52A LYS* 2.7 30.8 + - + +
54A ILE* 2.8 51.7 + - + +
56A LEU* 4.1 16.6 - - + -
297A ALA* 3.7 28.9 - - + +
300A ILE* 3.3 42.8 - - + -
301A GLU* 4.5 13.5 - - + +
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Residues in contact with ALA 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 THR* 2.8 19.2 + - + +
47A ARG* 2.8 12.6 + - - +
49A LEU* 1.3 71.3 - - - +
51A ASP* 1.3 55.5 + - + +
53A GLY* 2.5 30.5 + - - -
54A ILE 3.2 12.9 + - - +
55A THR* 5.0 8.3 + - - +
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Residues in contact with ASP 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 ARG* 3.1 17.4 + - - +
48A SER* 3.3 12.0 - - - +
50A ALA* 1.3 80.4 - - + +
52A LYS* 1.3 59.9 + - - +
53A GLY 3.0 2.2 + - - -
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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