Contacts of the helix formed by residues 42 - 54 (chain A) in PDB entry 1CCW
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 PRO 42 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11A ILE* 4.9 0.2 - - + -
12A GLY* 4.7 5.6 - - - +
40A LEU 3.7 7.6 - - - +
41A SER* 1.3 89.4 - - - +
43A GLN* 1.3 67.3 + - - +
44A GLU* 3.8 14.6 - - + +
45A LEU* 2.9 46.7 + - + +
46A PHE* 3.4 8.3 - - - -
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Residues in contact with GLN 43 (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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11A ILE* 4.0 17.7 - - + +
42A PRO* 1.3 72.9 - - - +
44A GLU* 1.3 70.1 + - - +
46A PHE* 3.0 23.9 + - - +
47A ILE* 3.1 15.6 + - - +
69A ILE 5.2 0.2 + - - -
70A ASP 2.8 20.9 + - - +
71A CYS* 3.7 5.1 + - - +
72A LYS 2.8 28.5 + - - -
73A GLY 3.7 0.3 - - - -
74A LEU* 3.6 28.8 + - + +
77A LYS* 2.5 45.1 + - + +
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Residues in contact with GLU 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 PRO* 3.1 12.2 + - + +
43A GLN* 1.3 87.5 + - - +
45A LEU* 1.3 64.5 + - + +
47A ILE* 3.3 9.3 + - + +
48A LYS* 2.9 29.5 + - - +
77A LYS* 3.6 28.3 + - + +
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Residues in contact with LEU 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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37A ILE* 3.8 21.9 - - + +
40A LEU 5.4 0.4 - - - +
41A SER* 4.5 7.9 - - - +
42A PRO* 2.9 39.1 + - + +
44A GLU* 1.3 82.3 - - + +
46A PHE* 1.3 67.5 - - - +
48A LYS* 4.0 18.2 - - + +
49A ALA* 3.1 23.6 + - - +
183B LYS* 6.2 1.1 - - - +
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Residues in contact with PHE 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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7A VAL* 4.0 11.8 - - + +
9A GLY* 3.7 45.5 - - - -
10A VAL 4.0 3.6 - - - -
11A ILE* 3.9 24.0 - - + -
37A ILE* 3.6 12.3 - - + -
41A SER* 3.5 26.9 - - - -
42A PRO 3.4 18.2 - - - -
43A GLN* 3.0 13.8 + - - +
45A LEU* 1.3 80.1 - - - +
47A ILE* 1.3 59.7 + - + +
49A ALA* 3.7 2.6 - - - +
50A ALA* 3.0 28.2 + - - +
58A ILE* 3.6 33.8 - - + +
59A LEU 4.0 6.7 - - - -
60A VAL* 4.3 13.5 - - + -
74A LEU* 5.0 5.4 - - + -
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Residues in contact with ILE 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 GLN 3.1 14.3 + - - +
44A GLU* 3.8 8.5 - - + +
46A PHE* 1.3 75.2 - - + +
48A LYS* 1.3 66.1 + - - +
50A ALA* 3.1 6.7 + - - +
51A ILE* 3.0 30.9 + - + +
58A ILE* 4.9 0.9 - - + -
74A LEU* 3.7 18.6 - - + -
77A LYS* 3.4 40.6 - - + -
78A CYS* 3.8 19.5 - - - +
81A ALA* 3.6 28.7 - - + -
83A LEU* 4.0 6.3 - - + -
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Residues in contact with LYS 48 (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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44A GLU 2.9 16.6 + - - +
45A LEU* 4.0 18.2 - - + +
47A ILE* 1.3 78.3 - - - +
49A ALA* 1.3 58.5 + - - +
51A ILE* 3.3 8.4 + - - +
52A GLU* 2.9 63.9 + - + +
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Residues in contact with ALA 49 (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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7A VAL* 3.7 16.4 - - + -
35A VAL* 4.1 11.2 - - + -
37A ILE* 3.7 21.5 - - + -
45A LEU 3.1 18.7 + - - +
46A PHE 3.7 2.0 - - - +
48A LYS* 1.3 75.6 - - - +
50A ALA* 1.3 57.3 + - - +
52A GLU* 3.4 9.8 + - - -
53A THR* 2.7 38.1 + - - +
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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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7A VAL* 3.5 16.1 - - + +
46A PHE 3.0 18.3 + - - +
47A ILE 3.1 4.0 + - - +
49A ALA* 1.3 76.4 - - - +
51A ILE* 1.3 59.3 + - - +
54A LYS* 2.9 24.8 + - - -
55A ALA* 3.1 19.8 + - + -
58A ILE* 4.0 13.0 - - + -
83A LEU* 3.9 24.2 - - + +
86A ILE* 4.2 4.5 - - + -
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Residues in contact with ILE 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 ILE* 3.0 34.9 + - + +
48A LYS* 3.8 6.7 - - - +
50A ALA* 1.3 81.5 - - - +
52A GLU* 1.3 66.4 + - + +
53A THR 3.2 0.9 + - - -
54A LYS* 3.4 18.6 + - - +
81A ALA* 4.2 19.5 - - + +
83A LEU* 4.2 22.0 - - + -
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Residues in contact with GLU 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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48A LYS* 2.9 56.6 + - + +
49A ALA* 4.0 7.9 - - - +
51A ILE* 1.3 81.4 - - + +
53A THR* 1.3 65.1 + - + +
54A LYS* 3.6 6.3 + - - +
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Residues in contact with THR 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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5A THR* 3.8 23.8 + - - +
7A VAL* 4.3 0.7 - - - +
33A ASN* 5.3 2.6 + - - +
35A VAL* 3.8 33.2 - - + +
49A ALA* 2.7 23.5 + - - +
52A GLU* 1.3 86.0 - - + +
54A LYS* 1.3 73.4 + - - +
55A ALA* 3.3 6.6 + - - +
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Residues in contact with LYS 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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5A THR* 4.4 1.9 - - - -
50A ALA 2.9 9.2 + - - -
51A ILE* 3.4 13.7 + - - +
52A GLU 4.5 5.9 + - - +
53A THR* 1.3 82.6 - - - +
55A ALA* 1.3 65.7 + - - +
56A ASP* 3.6 10.7 + - - +
83A LEU* 6.5 0.2 - - - -
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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