Contacts of the helix formed by residues 42 - 59 (chain A) in PDB entry 2C56
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 ASN 42 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38A PRO 4.0 1.9 + - - +
39A GLU* 3.1 17.1 + - - +
40A LEU 4.0 2.8 - - - +
41A ALA* 1.3 78.4 - - - +
43A PRO* 1.4 63.4 - - - +
44A LEU* 2.9 33.4 + - - +
45A THR* 2.8 35.9 + - - +
46A ALA* 3.9 1.9 + - - +
167A ARG* 3.3 31.1 - - - +
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Residues in contact with PRO 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 ALA 3.2 10.2 - - - +
42A ASN* 1.4 90.8 - - - +
44A LEU* 1.3 63.6 + - + +
45A THR 3.3 0.5 + - - -
46A ALA* 3.3 12.6 + - + +
47A HIS* 3.3 27.7 + - + +
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Residues in contact with LEU 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 ASN* 2.9 15.5 + - - +
43A PRO* 1.3 77.3 - - + +
45A THR* 1.3 60.1 + - - +
46A ALA 3.3 0.2 - - - -
47A HIS* 3.4 25.2 + - + +
48A LEU* 3.0 25.6 + - - +
167A ARG* 3.7 33.9 + - - +
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Residues in contact with THR 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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39A GLU 2.6 27.5 + - - +
40A LEU* 3.9 27.4 - - + -
42A ASN* 2.8 13.7 + - - +
44A LEU* 1.3 76.1 - - - +
46A ALA* 1.3 61.6 + - - +
48A LEU* 3.3 5.9 + - + +
49A LEU* 2.9 39.3 + - + +
167A ARG* 3.1 20.8 + - - +
168A PHE* 3.9 20.1 - - + -
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Residues in contact with ALA 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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40A LEU 5.7 0.8 + - - +
42A ASN 3.9 1.4 + - - +
43A PRO* 3.3 13.6 + - + +
44A LEU 3.3 0.4 - - - -
45A THR* 1.3 80.1 - - - +
47A HIS* 1.3 61.5 + - + +
49A LEU* 3.5 7.0 + - - +
50A ALA* 2.9 30.0 + - - +
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Residues in contact with HIS 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 PRO* 3.3 23.9 + - + +
44A LEU* 3.4 26.8 + - + +
45A THR 3.2 0.2 - - - -
46A ALA* 1.3 81.2 - - + +
48A LEU* 1.3 65.1 + - - +
50A ALA* 3.4 4.8 + - - +
51A GLU* 3.0 24.4 + - - +
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Residues in contact with LEU 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 LEU 3.0 14.3 + - - +
45A THR* 3.4 9.2 - - + +
47A HIS* 1.3 76.9 - - - +
49A LEU* 1.3 62.4 + - + +
51A GLU* 3.1 4.0 + - - +
52A TYR* 2.8 28.9 + - - +
163A ILE* 3.5 32.5 - - + +
164A GLY* 3.7 11.4 - - - +
165A TRP* 3.6 53.4 - - + +
167A ARG* 4.5 4.3 - - - +
168A PHE* 3.6 37.9 - - + -
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Residues in contact with LEU 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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22A PHE* 3.7 29.4 - - + -
26A PHE* 3.9 30.1 - - + -
40A LEU* 4.6 3.8 - - + -
45A THR* 2.9 33.1 + - + +
46A ALA* 4.0 6.3 - - - +
48A LEU* 1.3 75.1 - - + +
50A ALA* 1.3 62.3 + - - +
52A TYR* 3.7 5.7 - - + +
53A ASN* 2.8 41.5 + - - +
165A TRP* 4.6 18.4 - - + -
168A PHE* 6.5 0.2 - - + -
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Residues in contact with ALA 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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46A ALA 2.9 19.2 + - - +
47A HIS* 3.9 5.4 - - - +
49A LEU* 1.3 76.8 - - - +
51A GLU* 1.3 59.5 + - - +
53A ASN* 3.3 6.6 + - - +
54A ARG* 2.8 29.3 + - - +
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Residues in contact with GLU 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 HIS 3.0 17.7 + - - +
48A LEU* 3.6 5.4 - - - +
50A ALA* 1.3 76.0 - - - +
52A TYR* 1.3 59.8 + - - +
54A ARG* 2.7 49.9 + - - +
55A ARG* 2.8 45.6 + - + +
163A ILE* 3.9 29.6 - - + +
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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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26A PHE* 3.5 33.0 - + - -
48A LEU 2.8 20.2 + - - +
49A LEU* 3.7 10.1 - - + +
51A GLU* 1.3 71.8 - - - +
53A ASN* 1.3 75.8 + - - +
55A ARG* 3.2 4.7 + - - +
56A CYS* 2.9 56.1 + - - -
61A VAL* 4.1 6.9 - - + +
63A PRO 5.3 0.7 + - - -
65A ARG* 3.5 39.5 + - - +
68A VAL* 4.1 5.0 - - + +
151A THR* 3.6 35.2 - - + -
160A HIS* 5.3 1.3 - + - -
163A ILE* 4.2 12.5 - - + +
165A TRP* 4.0 18.6 - + + -
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Residues in contact with ASN 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 PHE* 5.6 2.4 - - - -
49A LEU* 2.8 35.8 + - - +
50A ALA* 3.7 6.2 - - - +
52A TYR* 1.3 91.7 - - - +
54A ARG* 1.3 66.8 + - - +
56A CYS* 3.2 5.1 + - - +
57A GLN* 3.2 36.2 + - + +
65A ARG* 4.2 17.3 + - - -
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Residues in contact with ARG 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 ALA 2.8 17.6 + - - +
51A GLU* 2.7 42.8 + - - +
53A ASN* 1.3 76.8 - - - +
55A ARG* 1.3 83.8 + - - +
57A GLN* 3.1 17.4 + - - +
58A THR* 3.2 34.2 + - + +
59A GLU* 5.5 0.4 + - - -
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Residues in contact with ARG 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 GLU* 2.8 43.0 + - + +
52A TYR* 3.4 8.7 - - - +
54A ARG* 1.3 89.5 - - - +
56A CYS* 1.3 57.9 + - - +
58A THR* 3.0 6.1 + - - -
59A GLU* 2.8 62.0 + - - +
61A VAL* 3.7 3.1 - - + -
153A LYS* 5.3 1.0 - - - +
159A SER* 4.0 15.2 + - - -
160A HIS* 3.6 46.3 - - + +
162A ARG* 5.5 6.3 - - - +
163A ILE* 3.8 18.9 - - + +
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Residues in contact with CYS 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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52A TYR* 2.9 62.3 + - - +
53A ASN* 3.2 5.1 + - - +
55A ARG* 1.3 75.7 - - - +
57A GLN* 1.3 75.5 + - - +
58A THR 3.3 0.2 - - - -
59A GLU 3.4 11.4 - - - +
61A VAL* 3.6 21.1 - - + +
65A ARG* 6.0 1.1 - - - -
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Residues in contact with GLN 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 ASN* 3.2 23.8 + - + +
54A ARG* 3.1 11.5 + - + +
56A CYS* 1.3 90.5 + - - +
58A THR* 1.3 65.6 + - + +
59A GLU 3.8 0.2 - - - -
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Residues in contact with THR 58 (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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54A ARG* 3.2 34.8 + - + +
55A ARG* 3.0 7.6 + - - -
57A GLN* 1.3 89.2 - - + +
59A GLU* 1.3 69.0 + - - +
153A LYS* 5.6 0.5 - - - -
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Residues in contact with GLU 59 (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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54A ARG* 5.5 0.2 + - - -
55A ARG* 2.8 48.8 + - - +
56A CYS 3.4 17.5 - - - +
57A GLN 3.8 0.4 - - - -
58A THR* 1.3 89.5 + - - +
60A GLU* 1.3 59.5 + - - +
61A VAL* 3.2 8.7 + - + +
153A LYS* 3.6 43.2 + - + +
160A HIS* 2.9 28.6 + - - -
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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