Contacts of the helix formed by residues 47 - 57 (chain A) in PDB entry 2CPW
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 47 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22A ALA* 5.1 1.6 - - - -
40A LEU* 4.8 4.2 - - - +
43A THR* 5.1 2.9 + - - +
45A GLY* 5.3 0.3 - - - -
46A ARG* 1.3 92.7 + - - +
48A VAL* 1.3 66.1 - - - +
49A GLN* 4.1 9.9 - - - -
50A THR* 4.0 19.9 + - - -
51A ALA* 3.7 17.2 + - - +
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Residues in contact with VAL 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A ALA* 3.0 52.5 - - + +
25A VAL* 4.3 21.1 - - + -
26A LEU* 4.6 12.6 - - + +
29A MET* 4.5 10.1 - - + -
40A LEU* 5.7 0.4 - - - -
47A SER* 1.3 72.7 - - - +
49A GLN* 1.3 73.0 + - + +
50A THR 3.4 0.4 - - - -
51A ALA* 3.5 8.2 + - - +
52A CYS* 3.1 27.1 + - - +
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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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47A SER* 3.3 6.0 - - - -
48A VAL* 1.3 85.1 - - + +
50A THR* 1.3 67.3 + - - +
52A CYS* 3.2 9.6 + - + +
53A ASP* 3.1 19.9 + - - +
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Residues in contact with THR 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A THR* 3.9 24.7 - - + -
47A SER* 4.0 20.2 + - - -
48A VAL 3.4 0.2 - - - -
49A GLN* 1.3 76.1 - - - +
51A ALA* 1.3 66.8 + - - +
53A ASP* 3.2 14.0 + - + +
54A TRP* 3.0 19.1 + - - +
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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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26A LEU* 4.4 14.1 - - + -
39A ALA* 3.8 20.1 - - + +
40A LEU* 4.3 8.3 - - + +
43A THR* 4.0 16.5 + - - +
47A SER 3.7 12.1 + - - +
48A VAL* 3.5 10.9 + - - +
49A GLN 3.2 0.4 - - - -
50A THR* 1.3 78.5 - - - +
52A CYS* 1.3 53.1 + - - +
54A TRP* 2.8 6.6 + - - +
55A LEU* 2.5 38.5 + - - +
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Residues in contact with CYS 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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26A LEU* 3.8 26.2 - - - -
29A MET* 4.6 15.9 - - - -
31A PHE* 4.7 4.5 - - - -
48A VAL 3.1 13.3 + - - +
49A GLN* 3.3 14.6 - - + +
51A ALA* 1.3 75.3 - - - +
53A ASP* 1.3 65.3 + - - +
55A LEU* 2.7 22.9 + - - +
56A PHE* 2.8 43.5 + - + -
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Residues in contact with ASP 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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49A GLN 3.1 8.3 + - - +
50A THR* 3.3 14.9 - - - +
52A CYS* 1.3 77.9 - - - +
54A TRP* 1.3 60.0 + - - +
56A PHE* 3.7 9.6 + - - +
57A SER* 2.9 37.6 + - - -
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Residues in contact with TRP 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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35A ARG* 4.3 2.9 - - - -
38A LYS* 3.4 30.3 - - + -
39A ALA* 3.1 38.6 - - + -
42A SER* 3.3 32.3 + - - -
43A THR* 4.1 17.5 - - + -
50A THR 3.0 11.6 + - - +
51A ALA* 2.8 9.5 + - - +
53A ASP* 1.3 77.5 - - - +
55A LEU* 1.3 87.4 + - + +
57A SER* 2.5 42.6 + - - +
59A SER* 3.5 35.3 + - - -
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Residues in contact with LEU 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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26A LEU* 3.9 30.5 - - + -
31A PHE* 4.4 17.5 - - + -
35A ARG* 3.2 47.1 - - + +
36A ALA* 4.6 2.0 - - - -
39A ALA* 3.7 19.5 - - + -
51A ALA 2.5 19.4 + - - +
52A CYS* 2.7 14.8 + - - +
54A TRP* 1.3 87.8 - - + +
56A PHE* 1.3 70.0 + - + +
57A SER 3.2 4.5 - - - +
58A HIS* 5.2 0.3 - - - -
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Residues in contact with PHE 56 (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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31A PHE* 4.4 22.0 - + - -
52A CYS* 2.8 56.9 + - + +
53A ASP* 3.9 7.4 - - - +
55A LEU* 1.3 76.7 - - + +
57A SER* 1.3 64.1 + - - +
58A HIS* 3.1 4.7 + - - +
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Residues in contact with SER 57 (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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53A ASP* 2.9 29.2 + - - -
54A TRP* 2.5 48.2 + - - +
55A LEU 3.2 4.7 - - - +
56A PHE* 1.3 71.9 - - - +
58A HIS* 1.3 68.1 + - - +
59A SER* 3.1 5.5 + - - -
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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