Contacts of the helix formed by residues 38 - 48 (chain A) in PDB entry 1MUK
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 THR 38 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A MET 3.2 8.9 + - - +
37A PHE* 1.3 75.7 - - - +
39A ARG* 1.3 65.7 + - - +
40A SER* 3.8 5.8 + - - -
41A ASP* 2.6 50.5 + - - +
42A VAL* 3.5 6.8 + - - +
44A LYS* 4.8 0.9 + - - -
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Residues in contact with ARG 39 (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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37A PHE 3.7 1.6 + - - -
38A THR* 1.3 71.8 - - - +
40A SER* 1.3 65.7 + - - +
42A VAL* 3.0 26.4 + - - +
43A TYR* 3.4 9.0 - - + -
150A PRO* 3.5 27.7 - - - +
152A GLU* 2.8 52.5 + - + +
153A LYS* 5.9 1.0 - - - +
205A ALA* 3.7 15.0 - - + -
207A TYR 5.2 0.4 - - - -
208A LEU* 3.6 35.5 - - - +
209A TYR 5.2 6.4 + - - +
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Residues in contact with SER 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A THR* 3.4 6.0 + - - -
39A ARG* 1.3 78.6 - - - +
41A ASP* 1.3 62.6 + - - +
43A TYR* 3.2 15.0 + - - +
44A LYS* 3.0 30.1 + - - +
112A TYR* 5.6 0.2 + - - -
202A PRO 3.7 9.3 + - - -
203A ASP* 3.7 8.0 + - - -
204A ARG* 3.1 33.0 + - - +
205A ALA* 4.6 2.1 + - - +
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Residues in contact with ASP 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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4A MET* 3.9 11.2 - - - +
37A PHE* 3.8 21.5 - - + -
38A THR* 2.6 44.9 + - - +
40A SER* 1.3 75.0 - - - +
42A VAL* 1.3 61.0 + - - +
44A LYS* 2.5 39.6 + - - +
45A ALA* 2.8 29.1 + - - +
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Residues in contact with VAL 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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37A PHE* 3.9 19.3 - - + +
38A THR 3.8 9.4 - - - +
39A ARG* 3.3 15.0 - - - +
41A ASP* 1.3 78.4 - - - +
43A TYR* 1.3 59.8 + - + +
45A ALA* 3.0 8.0 + - - +
46A LEU* 2.9 27.4 + - + +
152A GLU* 4.1 36.8 - - + +
155A VAL* 3.9 28.9 - - + -
156A LEU* 4.2 15.9 - - + +
159A LEU* 4.5 4.0 - - + -
190A PHE* 6.3 0.9 - - + -
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Residues in contact with TYR 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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39A ARG 3.4 12.8 - - - -
40A SER* 3.2 4.6 + - - +
41A ASP 3.2 0.2 - - - -
42A VAL* 1.3 76.3 - - + +
44A LYS* 1.3 64.3 + - - +
46A LEU* 3.1 14.6 + - + +
47A ASP* 3.0 25.6 + - - +
152A GLU* 2.5 43.0 + - + -
190A PHE* 3.4 39.4 - + - -
191A ARG* 5.7 3.1 - - + -
194A CYS* 3.9 22.2 - - + -
204A ARG* 3.4 50.6 + - + +
205A ALA* 3.8 19.1 - - + -
206A PRO* 3.7 12.0 - - - +
230A LEU* 5.7 0.2 - - - +
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Residues in contact with LYS 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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4A MET* 4.1 20.0 - - + -
38A THR* 4.8 0.6 + - - -
40A SER* 3.0 15.4 + - - +
41A ASP* 2.5 50.3 + - - +
43A TYR* 1.3 76.5 - - - +
45A ALA* 1.3 62.1 + - - +
47A ASP* 3.1 26.0 + - - +
48A GLU* 3.4 12.1 + - - +
204A ARG* 4.2 13.7 - - + +
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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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2A SER* 5.9 1.6 - - - -
4A MET* 4.0 13.4 - - + -
5A ILE* 4.0 23.9 - - + +
37A PHE* 4.7 0.4 - - + -
41A ASP 2.8 12.5 + - - +
42A VAL* 3.0 15.2 + - - +
44A LYS* 1.3 79.1 - - - +
46A LEU* 1.3 61.1 + - - +
48A GLU* 3.2 22.5 + - - +
49A ILE* 3.8 8.8 + - - +
159A LEU* 3.7 20.9 - - + +
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Residues in contact with LEU 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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42A VAL* 2.9 17.6 + - + +
43A TYR* 3.1 19.0 + - + +
45A ALA* 1.3 78.3 - - - +
47A ASP* 1.3 61.3 + - - +
49A ILE* 3.2 18.5 + - + +
51A PHE* 4.1 2.0 - - + -
155A VAL* 3.9 13.7 - - + -
159A LEU* 3.8 19.3 - - + -
187A LEU* 3.6 37.0 - - + -
190A PHE* 3.6 35.2 - - + -
191A ARG* 3.1 37.7 + - + -
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Residues in contact with ASP 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 TYR 3.0 12.7 + - - +
44A LYS* 3.2 17.1 - - - +
46A LEU* 1.3 78.5 - - - +
48A GLU* 1.3 58.0 + - + +
49A ILE 3.3 3.1 + - - +
191A ARG* 3.4 16.7 + - - +
195A ARG* 2.5 31.3 + - - +
204A ARG* 2.7 38.5 + - - -
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Residues in contact with GLU 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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2A SER* 3.3 14.4 - - - +
3A SER* 3.9 10.4 - - - -
4A MET* 3.1 53.7 + - + +
5A ILE* 5.6 0.3 - - - +
44A LYS 3.5 14.1 - - - +
45A ALA* 3.2 11.7 + - - +
47A ASP* 1.3 76.3 - - + +
49A ILE* 1.3 62.5 + - + +
50A PRO* 3.4 9.0 - - - +
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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