Contacts of the helix formed by residues 46 - 55 (chain A) in PDB entry 3Q0U
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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44A ASP 4.1 0.6 + - - -
45A ILE* 1.3 76.5 - - - +
47A VAL* 1.3 64.6 + - - +
48A ASP* 3.4 13.5 - - - +
49A ASP* 2.8 46.5 + - - +
50A LEU* 3.2 14.9 + - - +
68A LYS* 4.7 3.8 - - - +
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Residues in contact with VAL 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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45A ILE 4.2 0.2 + - - -
46A SER* 1.3 71.8 - - - +
48A ASP* 1.3 56.2 + - - +
50A LEU* 3.3 9.9 + - - +
51A ALA* 3.0 27.4 + - - +
58A ARG* 3.7 21.7 - - + +
61A PHE* 3.5 39.0 - - + -
62A TYR* 3.4 37.9 - - + +
67A SER* 5.0 1.1 - - - -
68A LYS* 4.4 22.7 - - + +
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Residues in contact with ASP 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* 3.0 13.1 + - - +
47A VAL* 1.3 79.5 - - - +
49A ASP* 1.3 57.4 + - - +
51A ALA* 3.4 5.1 + - - +
52A LYS* 2.9 38.5 + - - +
58A ARG* 4.6 21.8 + - - +
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Residues in contact with ASP 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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32A THR* 3.9 3.1 - - - +
36A LEU* 3.7 21.8 - - + +
40A ARG* 3.1 29.6 + - - +
44A ASP 4.1 0.3 - - - +
45A ILE* 4.2 0.9 - - + -
46A SER* 2.8 39.8 + - - +
48A ASP* 1.3 75.8 - - - +
50A LEU* 1.3 57.2 + - - +
52A LYS* 3.8 5.0 - - - +
53A GLY* 2.9 27.2 + - - -
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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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29A ILE* 4.6 6.0 - - + +
32A THR* 3.9 7.1 - - + +
33A ALA* 3.6 38.8 - - + +
36A LEU* 4.2 5.6 - - + -
42A LEU* 5.8 2.2 - - + -
45A ILE* 3.9 18.4 - - + -
46A SER 3.2 12.4 + - - +
47A VAL* 3.6 7.6 - - - +
48A ASP 3.2 0.2 - - - -
49A ASP* 1.3 78.0 - - - +
51A ALA* 1.3 65.0 + - - +
53A GLY* 3.5 0.9 + - - -
54A ALA* 3.0 25.9 + - - +
61A PHE* 3.8 31.4 - - + -
68A LYS* 3.8 27.4 - - + -
71A VAL* 4.2 12.6 - - + -
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Residues in contact with ALA 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 VAL 3.0 17.4 + - - +
48A ASP* 3.8 6.1 - - - +
50A LEU* 1.3 73.7 - - - +
52A LYS* 1.3 65.2 + - - +
54A ALA 3.1 2.6 + - - -
55A GLY 2.9 18.9 + - - -
56A ILE* 3.0 36.7 + - + +
57A SER 3.7 21.3 - - - +
58A ARG* 3.9 8.1 - - + +
61A PHE* 4.3 6.0 - - + -
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Residues in contact with LYS 52 (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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48A ASP* 2.9 27.1 + - - +
49A ASP* 3.8 6.1 - - - +
51A ALA* 1.3 75.9 - - - +
53A GLY* 1.3 63.2 + - - +
55A GLY* 3.1 14.7 + - - -
56A ILE 4.5 3.1 - - - +
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Residues in contact with GLY 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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28A ALA* 5.4 0.7 - - - +
32A THR* 3.2 29.7 + - - -
49A ASP 2.9 12.2 + - - -
52A LYS* 1.3 78.0 - - - +
54A ALA* 1.3 58.3 + - - +
55A GLY 3.3 0.7 + - - -
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Residues in contact with ALA 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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25A ARG* 4.5 3.6 - - - +
28A ALA* 3.8 20.2 - - + +
29A ILE* 3.7 38.4 - - + +
32A THR* 3.5 2.7 + - - -
50A LEU 3.0 18.2 + - - +
51A ALA 3.1 3.8 + - - +
53A GLY* 1.3 74.5 - - - +
55A GLY* 1.3 63.2 + - - +
56A ILE* 3.3 14.4 + - + +
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Residues in contact with GLY 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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25A ARG* 4.9 3.1 + - - -
51A ALA 2.9 3.4 + - - -
52A LYS* 3.1 14.0 + - - -
53A GLY 3.3 1.6 + - - -
54A ALA* 1.3 79.0 - - - +
56A ILE* 1.3 62.2 + - - +
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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