Contacts of the helix formed by residues 46 - 55 (chain A) in PDB entry 4U2M
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 SER 46 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42A LEU 2.9 12.3 + - - +
43A ALA 3.4 10.2 + - - +
44A ALA 3.7 0.2 - - - -
45A CYS* 1.3 79.2 - - - +
47A GLU* 1.3 63.5 + - - +
48A TYR 3.3 0.9 + - - -
49A PHE* 3.3 28.1 + - - -
50A LYS 3.0 18.4 + - - -
77A MET* 4.3 1.1 - - - -
99A LEU* 2.9 31.0 + - - +
100A GLN 5.6 0.4 - - - -
101A MET* 4.3 12.8 - - - -
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Residues in contact with GLU 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 5.4 1.4 - - - +
46A SER* 1.3 72.4 + - - +
48A TYR* 1.3 63.4 + - - +
50A LYS* 3.3 33.1 + - - +
51A MET* 3.1 24.3 + - - +
99A LEU 4.2 2.2 + - - -
100A GLN* 5.0 15.0 + - + +
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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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46A SER* 3.1 8.2 + - - +
47A GLU* 1.3 80.5 - - - +
49A PHE* 1.3 63.8 + + - +
51A MET* 3.5 5.4 + - + +
52A LEU* 2.9 53.9 + - + +
98A PHE* 3.4 50.7 - + - +
99A LEU* 3.7 31.9 + - + +
100A GLN* 5.2 3.0 - - + +
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Residues in contact with PHE 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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28A PHE* 3.9 34.5 - + - -
42A LEU* 3.8 35.9 - - + +
43A ALA* 4.4 0.2 - - - -
46A SER* 3.1 26.8 + - - +
48A TYR* 1.3 84.5 - + - +
50A LYS* 1.3 58.5 + - - +
52A LEU* 3.6 16.3 - - + +
53A PHE* 2.9 58.5 + + + -
70A LEU* 4.8 10.1 - - + -
74A LEU* 5.5 1.3 - - + -
77A MET* 4.2 8.1 - - + -
99A LEU* 3.6 35.9 - - + -
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Residues in contact with LYS 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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43A ALA* 3.7 27.8 - - + +
46A SER 3.0 12.2 + - - +
47A GLU* 3.5 35.9 + - - +
48A TYR 3.2 0.2 - - - -
49A PHE* 1.3 77.9 - - - +
51A MET* 1.3 62.0 + - - +
53A PHE* 4.0 1.5 - - - +
54A VAL* 3.1 34.8 + - + +
147A ARG* 6.3 1.2 - - - +
148A LEU* 4.0 22.9 - - + +
153A ILE* 4.5 6.5 - - + +
154A LEU* 5.2 0.6 - - - +
-1B LEU* 3.2 34.7 - - + +
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Residues in contact with MET 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 GLU 3.1 13.2 + - - +
48A TYR* 3.8 5.8 - - + +
50A LYS* 1.3 80.3 - - - +
52A LEU* 1.3 65.6 + - - +
54A VAL* 3.5 3.9 + - - +
55A ASP* 2.9 56.0 + - - +
-1B LEU* 6.1 7.0 - - - -
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Residues in contact with LEU 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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28A PHE* 6.4 0.7 - - + -
48A TYR* 2.9 43.6 + - + +
49A PHE* 3.3 27.8 + - + +
51A MET* 1.3 79.1 - - - +
53A PHE* 1.3 71.7 + - + +
55A ASP* 3.8 3.0 - - + +
56A GLN* 2.9 41.1 + - - +
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Residues in contact with PHE 53 (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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26A CYS* 4.4 10.1 - - + -
28A PHE* 4.9 4.0 - + - -
39A LYS* 3.8 58.2 + - + -
42A LEU* 3.9 22.7 - - + -
49A PHE* 2.9 55.7 + + + +
50A LYS 4.3 0.2 - - - +
52A LEU* 1.3 89.9 - - + +
54A VAL* 1.3 67.6 + - - +
55A ASP 3.3 0.2 - - - -
56A GLN* 3.5 18.2 + - - +
154A LEU* 3.9 31.0 - - + +
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Residues in contact with VAL 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 LYS 3.1 22.9 + - - +
51A MET* 3.9 4.9 - - - +
53A PHE* 1.3 80.0 - - - +
55A ASP* 1.3 69.7 + - - +
56A GLN* 3.5 5.0 + - - +
153A ILE* 3.6 32.3 - - + -
154A LEU* 4.8 3.1 - - + +
-1B LEU* 3.7 35.0 - - + -
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Residues in contact with ASP 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 MET* 2.9 50.7 + - - +
52A LEU* 4.3 3.1 - - + +
54A VAL* 1.3 86.4 - - - +
56A GLN* 1.3 71.9 + - - +
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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