Contacts of the helix formed by residues 45 - 56 (chain D) in PDB entry 3CJC
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 LEU 45 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A MET* 5.0 2.9 - - - -
60A SER 5.2 0.2 - - - +
61A LYS* 4.2 22.7 - - + -
63A GLY* 3.3 12.0 - - - -
64A ILE* 3.4 37.2 + - + +
42D ASP* 3.1 16.5 + - - +
44D HIS* 1.3 80.3 - - - +
46D VAL* 1.3 59.8 + - - +
48D VAL* 3.9 19.7 - - + -
49D GLY 3.1 18.2 + - - -
67D VAL* 4.4 17.7 - - + -
79D ARG* 3.5 50.5 - - - +
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Residues in contact with VAL 46 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A ARG* 5.4 3.4 - - + +
63A GLY* 3.7 16.0 - - - +
203A THR* 4.1 13.9 - - - +
13D GLU* 3.3 35.4 - - + +
42D ASP* 2.9 3.2 + - - -
44D HIS* 3.9 12.6 - - + +
45D LEU* 1.3 74.7 - - - +
47D ALA* 1.3 56.2 + - - +
49D GLY* 3.2 1.7 + - - -
50D LYS* 2.7 57.9 + - + +
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Residues in contact with ALA 47 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D PHE* 4.3 11.4 - - + -
12D GLY 3.3 32.8 - - - +
13D GLU* 4.1 5.1 - - - +
16D MET* 3.5 22.5 - - + +
42D ASP* 2.7 17.1 + - - +
46D VAL* 1.3 72.3 - - - +
48D VAL* 1.3 59.2 + - - +
50D LYS* 3.2 7.3 + - - +
51D LEU* 2.8 31.0 + - - +
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Residues in contact with VAL 48 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A ILE* 4.4 7.2 - - + -
11D PHE* 4.3 5.6 - - + -
40D VAL* 4.0 23.6 - - + -
42D ASP* 3.1 11.4 + - - +
45D LEU* 3.9 29.8 - - + +
47D ALA* 1.3 75.8 - - - +
49D GLY* 1.3 63.4 + - - +
51D LEU* 3.6 6.2 + - - +
52D LEU* 3.1 42.7 + - + +
65D TYR* 5.7 2.5 - - + -
67D VAL* 5.4 4.0 - - + -
81D LEU* 3.7 36.8 - - + -
83D LEU* 5.9 0.2 - - + -
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Residues in contact with GLY 49 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A ARG* 3.7 17.2 + - - -
40A HIS* 4.0 1.3 + - - -
63A GLY 4.1 1.1 - - - -
64A ILE* 3.8 15.4 - - - +
45D LEU 3.1 17.4 + - - -
46D VAL 3.5 4.3 - - - -
47D ALA 3.2 0.2 - - - -
48D VAL* 1.3 76.6 - - - +
50D LYS* 1.3 60.0 + - - +
52D LEU* 3.4 6.6 + - - +
53D ASP* 2.9 28.9 + - - +
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Residues in contact with LYS 50 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A ARG* 6.1 0.4 - - - +
13D GLU 5.9 0.4 - - - +
16D MET* 4.5 26.7 - - + +
17D SER* 5.1 11.7 - - - +
46D VAL* 2.7 41.4 + - + +
47D ALA* 3.2 8.0 + - - +
49D GLY* 1.3 71.0 - - - +
51D LEU* 1.3 63.8 + - - +
53D ASP* 3.1 22.9 + - - +
54D TYR* 3.1 33.3 - - + +
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Residues in contact with LEU 51 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D PHE* 4.2 15.3 - - + -
16D MET* 3.7 16.9 - - + +
25D ILE* 4.6 6.7 - - + -
26D VAL* 3.4 37.2 - - + +
29D VAL* 4.6 4.3 - - + -
37D ILE* 4.0 18.4 - - + -
47D ALA 2.8 20.3 + - - +
48D VAL 3.9 5.8 - - - +
50D LYS* 1.3 72.9 - - - +
52D LEU* 1.3 62.3 + - + +
53D ASP 3.4 0.2 + - - -
54D TYR* 3.5 3.6 + - - +
55D LEU* 3.3 34.6 + - + +
81D LEU* 4.9 6.3 - - + -
83D LEU* 3.6 26.2 - - + -
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Residues in contact with LEU 52 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A HIS* 3.3 33.0 - - + +
64A ILE* 4.4 5.4 - - + -
48D VAL* 3.1 33.1 + - + +
49D GLY* 3.7 4.9 - - - +
50D LYS 3.2 0.4 - - - -
51D LEU* 1.3 75.1 - - + +
53D ASP* 1.3 60.5 + - - +
55D LEU* 4.5 6.3 - - + -
56D ASN* 2.9 36.2 + - - +
63D TYR* 4.5 18.6 - - + +
65D TYR* 3.9 31.6 - - + -
83D LEU* 3.6 30.5 - - + -
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Residues in contact with ASP 53 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A ARG* 3.3 25.8 + - - -
40A HIS* 2.8 27.8 + - - -
49D GLY 2.9 12.8 - - - +
50D LYS* 3.1 17.7 + - - +
52D LEU* 1.3 74.7 - - - +
54D TYR* 1.3 68.2 + - + +
56D ASN 3.7 0.3 - - - -
57D GLN* 3.1 28.3 + - - +
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Residues in contact with TYR 54 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16D MET* 4.5 15.2 + - + -
19D ALA* 6.1 1.4 - - - -
22D ALA* 4.9 12.7 - - + +
26D VAL* 4.0 31.6 - - + -
30D ARG* 4.2 9.6 + - - +
50D LYS* 3.1 42.7 + - + +
51D LEU* 4.0 2.5 - - - +
53D ASP* 1.3 77.6 - - + +
55D LEU* 1.3 62.0 + - - +
57D GLN* 3.4 35.6 + - - +
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Residues in contact with LEU 55 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26D VAL* 3.4 29.4 - - + +
29D VAL* 3.7 22.2 - - + -
30D ARG* 3.5 27.5 + - + +
51D LEU* 3.3 34.3 + - + +
52D LEU* 4.0 5.4 - - + +
53D ASP 3.3 0.2 - - - -
54D TYR* 1.3 79.5 - - - +
56D ASN* 1.3 68.4 + - - +
57D GLN* 3.4 2.0 + - - +
58D ASP* 5.0 2.1 + - - +
59D ASP 5.2 0.2 + - - -
62D THR* 3.3 20.1 + - - +
63D TYR* 3.7 25.1 - - + -
83D LEU* 4.0 9.6 - - + -
273D SO4 4.3 4.7 + - - +
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Residues in contact with ASN 56 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A HIS* 3.6 25.9 + - + +
41A GLN 5.7 0.4 - - - +
52D LEU* 2.9 19.4 + - - +
53D ASP* 3.7 2.7 - - - -
55D LEU* 1.3 88.7 - - - +
57D GLN* 1.3 62.1 - - - +
58D ASP 3.5 0.4 - - - -
59D ASP 3.1 21.5 - - - +
60D PRO* 2.6 35.7 + - + +
62D THR* 3.6 0.2 - - - -
63D TYR* 2.9 44.0 + - - +
64D HIS* 5.4 0.4 - - - -
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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