Contacts of the helix formed by residues 42 - 52 (chain A) in PDB entry 1ML3
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 ASP 42 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40A ASN* 3.2 21.4 + - - +
41A THR* 1.3 75.6 - - - +
43A ALA* 1.3 53.3 + - - +
44A GLU* 3.0 13.3 + - - +
45A TYR* 2.6 43.8 + - + +
46A PHE* 3.2 8.7 + - - +
74A LYS* 3.2 33.9 - - - +
75A ASP 4.5 2.2 - - - -
208D VAL* 6.0 4.5 - - + -
211D TRP* 4.3 6.6 - - - -
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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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41A THR 3.1 6.7 + - - -
42A ASP* 1.3 72.3 - - - +
44A GLU* 1.3 55.6 + - - +
46A PHE* 3.2 5.2 + - - -
47A ALA* 2.8 26.0 + - - +
65A THR* 3.4 20.4 - - + +
75A ASP 3.5 18.2 + - - +
76A ASP* 3.9 3.1 - - - -
77A THR 3.6 26.5 - - - +
78A LEU* 3.6 4.7 - - + +
87A CYS* 3.9 16.6 - - - -
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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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42A ASP* 2.9 11.6 + - - +
43A ALA* 1.3 76.8 - - - +
45A TYR* 1.3 59.8 + - - +
47A ALA* 3.6 3.9 + - - +
48A TYR* 3.2 19.9 + - - +
51A ARG* 5.4 0.9 + - - -
65A THR* 3.9 21.3 - - - +
74A LYS* 2.6 49.5 + - - +
75A ASP* 3.6 21.9 + - + +
211D TRP* 3.8 14.7 - - + -
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Residues in contact with TYR 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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40A ASN* 4.0 15.7 - - + +
42A ASP* 2.6 32.5 + - + +
44A GLU* 1.3 67.9 - - - +
46A PHE* 1.3 64.6 + - - +
47A ALA 3.1 1.6 - - - -
48A TYR* 3.0 21.5 + + - +
49A GLN* 2.9 54.5 + - + +
205D GLY 3.5 12.1 + - - -
206D VAL* 4.3 6.7 - - + -
207D SER* 2.9 39.2 + - - -
208D VAL* 4.1 20.2 - - + -
211D TRP* 3.2 53.0 + + + +
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Residues in contact with PHE 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* 3.5 44.0 - + + -
15A ARG* 4.7 1.3 - - - -
36A VAL* 4.7 4.0 - - + -
38A ASP* 3.7 26.0 - - + -
40A ASN* 3.4 42.0 - - + -
42A ASP 3.2 6.2 + - - -
43A ALA* 3.2 8.1 + - - +
45A TYR* 1.3 78.0 - + - +
47A ALA* 1.3 61.1 + - - +
49A GLN* 3.4 25.0 + - + +
50A MET* 3.1 30.5 + - - +
78A LEU* 3.9 15.9 - - + -
87A CYS* 3.7 29.4 - - + -
206D VAL* 6.6 0.2 - - + -
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Residues in contact with ALA 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 ALA 2.8 16.9 + - - +
44A GLU* 3.7 6.7 - - - +
46A PHE* 1.3 75.3 - - - +
48A TYR* 1.3 61.4 + - - +
50A MET* 3.4 11.6 + - - +
51A ARG* 2.9 52.1 + - - +
63A VAL* 4.1 9.9 - - + +
65A THR* 3.8 17.5 - - + -
78A LEU* 4.0 4.9 - - + -
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Residues in contact with TYR 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 GLU 3.2 4.0 + - - +
45A TYR* 3.0 28.6 + + - +
47A ALA* 1.3 79.9 - - - +
49A GLN* 1.3 69.0 + - + +
51A ARG* 3.9 12.5 - - - +
52A TYR* 3.2 47.0 + + + +
294C GLU* 5.0 4.7 - - + +
295C GLU* 2.7 44.0 + - + -
211D TRP* 3.6 47.8 + + + -
215D ARG* 3.0 39.4 + - - +
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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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10A PHE 5.1 0.2 + - - -
15A ARG* 3.2 51.0 + - - +
19A GLN* 4.5 1.7 - - - +
45A TYR* 2.9 59.5 + - + +
46A PHE* 3.6 29.0 - - - +
47A ALA 3.3 0.2 - - - -
48A TYR* 1.3 85.0 - - + +
50A MET* 1.3 54.4 + - - +
52A TYR 2.6 22.2 - - - +
53A ASP* 5.0 1.9 - - - +
204D ASP* 6.1 0.2 - - - +
205D GLY 3.7 19.4 - - - +
206D VAL* 4.7 7.5 - - - +
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Residues in contact with MET 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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10A PHE* 4.4 5.6 - - + -
15A ARG* 4.0 18.4 - - + +
18A PHE* 3.6 35.9 - - + -
19A GLN* 3.8 21.2 + - + +
46A PHE* 3.1 27.0 + - + +
47A ALA 3.8 2.0 - - - +
49A GLN* 1.3 76.1 - - - +
51A ARG* 1.3 68.0 + - - +
52A TYR 3.3 3.3 + - - +
53A ASP* 5.3 1.4 - - - +
59A PHE* 3.2 24.4 + - + +
63A VAL* 3.7 26.0 - - + -
78A LEU* 3.2 44.2 - - + -
80A VAL* 4.9 0.7 - - - -
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Residues in contact with ARG 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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44A GLU 5.4 0.8 + - - -
47A ALA* 2.9 37.9 + - - +
48A TYR* 3.8 16.5 - - - +
50A MET* 1.3 77.3 - - - +
52A TYR* 1.3 92.3 + - + +
58A LYS* 3.6 7.5 - - + +
59A PHE* 3.3 26.8 + - - -
62A GLU* 6.1 1.0 - - - +
63A VAL* 2.7 40.7 + - + +
64A THR* 5.0 0.2 - - - +
294C GLU* 3.4 18.1 + - - -
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Residues in contact with TYR 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 TYR* 3.2 30.5 + + + +
49A GLN* 2.6 28.1 - - - +
50A MET 3.8 1.9 - - - +
51A ARG* 1.3 104.0 - - + +
53A ASP* 1.3 64.1 + - - +
57A GLY 4.2 2.7 - - - -
58A LYS* 4.3 28.7 - - + -
294C GLU* 2.4 41.6 + - - -
296C LEU* 3.5 28.6 - - + +
300C ASP* 3.4 29.4 - - + +
215D ARG* 4.1 11.3 + - - +
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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