Contacts of the helix formed by residues 40 - 50 (chain D) in PDB entry 6P7B
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 40 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38D THR 3.9 2.4 + - - -
39D LYS* 1.3 95.2 + - - +
41D TRP* 1.3 54.7 + - - +
42D GLU* 3.3 5.6 - - + -
43D ARG* 3.1 29.2 + - + +
44D SER* 2.6 43.0 + - - -
47D ARG* 3.8 12.3 + - - -
15F T 4.2 13.5 - - + +
16F T 4.4 13.9 + - - +
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Residues in contact with TRP 41 (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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73B TYR* 3.9 27.1 - + - -
76B LYS* 5.6 1.3 - - - -
37D TRP* 3.9 30.7 - - + +
38D THR* 4.5 4.7 - - - +
39D LYS 3.3 4.4 + - - -
40D ASN* 1.3 75.2 - - - +
42D GLU* 1.3 96.5 + - + +
44D SER* 3.7 5.3 - - - -
45D VAL* 2.7 39.7 + - + +
70D LYS* 3.6 25.1 - - + -
71D ILE* 4.2 28.0 - - + -
74D PHE* 4.3 22.2 - + + -
16F T 3.6 24.9 + - - -
17F C 3.2 33.4 + - - -
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Residues in contact with GLU 42 (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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76B LYS* 3.3 38.3 + - - +
80B TYR* 4.4 18.2 - - + -
85B LYS* 6.0 0.3 + - - -
40D ASN* 5.0 2.7 - - + -
41D TRP* 1.3 105.9 - - + +
43D ARG* 1.3 69.3 + - + +
45D VAL* 3.3 3.6 + - - +
46D ALA* 3.0 24.3 + - - +
74D PHE* 3.6 34.2 - - + -
16F T 5.3 6.2 + - - +
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Residues in contact with ARG 43 (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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80B TYR* 3.3 24.7 + - - +
40D ASN* 3.1 28.0 + - + +
42D GLU* 1.3 83.3 - - + +
44D SER* 1.3 58.2 + - - +
46D ALA* 3.4 2.3 + - - +
47D ARG* 2.9 58.9 + - + +
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Residues in contact with SER 44 (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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35D SER* 4.5 0.3 + - - -
36D ASP 3.4 8.9 + - - -
37D TRP* 3.2 21.6 - - - -
39D LYS* 3.8 12.1 - - - +
40D ASN* 2.6 23.5 + - - -
41D TRP* 3.7 5.6 - - - -
43D ARG* 1.3 72.9 - - - +
45D VAL* 1.3 57.0 + - - +
47D ARG* 2.7 32.7 + - - +
48D ASP* 2.9 39.2 + - - +
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Residues in contact with VAL 45 (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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37D TRP* 3.5 43.1 - - + +
41D TRP* 2.7 35.4 + - + +
42D GLU* 3.7 5.6 - - - +
44D SER* 1.3 74.1 - - - +
46D ALA* 1.3 58.6 + - - +
48D ASP* 3.2 1.6 + - - +
49D LEU* 2.9 56.1 + - + +
71D ILE* 4.0 11.0 - - + -
74D PHE* 4.2 15.0 - - + -
75D ILE* 4.0 16.6 - - + -
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Residues in contact with ALA 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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80B TYR* 3.8 28.5 - - + -
81B ASN* 4.4 2.2 - - - +
42D GLU 3.0 16.9 + - - +
43D ARG 3.8 3.4 - - - +
45D VAL* 1.3 79.2 - - - +
47D ARG* 1.3 57.2 + - - +
49D LEU* 3.3 5.5 + - - -
50D THR* 2.8 37.7 + - + +
74D PHE* 4.9 3.8 - - + -
78D PHE* 4.3 20.6 - - + -
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Residues in contact with ARG 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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35D SER* 5.6 0.8 + - - -
36D ASP 5.2 0.2 + - - -
39D LYS* 5.5 2.2 + - - +
40D ASN* 3.8 6.5 + - - -
43D ARG* 2.9 49.9 + - + +
44D SER* 2.7 47.0 + - - +
46D ALA* 1.3 77.4 - - - +
48D ASP* 1.3 68.1 + - - +
50D THR* 3.4 14.1 + - - -
51D ARG* 3.1 32.3 + - - +
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Residues in contact with ASP 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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15D TYR* 4.0 32.9 + - + -
17D ILE* 5.3 2.8 - - - +
35D SER* 2.9 17.1 + - - -
37D TRP* 2.6 37.8 + - + +
44D SER* 2.9 20.1 + - - +
45D VAL 3.8 3.1 - - - +
47D ARG* 1.3 85.9 + - - +
49D LEU* 1.3 64.4 + - + +
51D ARG* 3.3 37.9 + - - +
52D TYR 5.1 0.2 + - - -
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Residues in contact with LEU 49 (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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4D CYS* 4.4 23.7 - - - -
6D VAL* 4.5 12.8 - - + -
15D TYR* 5.6 4.3 - - + -
37D TRP* 5.2 8.1 - - + -
45D VAL* 2.9 30.1 + - + +
46D ALA* 3.9 5.4 - - - +
48D ASP* 1.3 83.1 - - + +
50D THR* 1.3 61.7 + - + +
51D ARG 3.3 0.7 + - - -
52D TYR 4.4 2.4 + - - +
53D ASN* 4.4 0.5 - - - -
54D PRO* 3.4 26.6 - - + +
57D VAL* 5.2 4.5 - - + -
75D ILE* 3.7 35.4 - - + -
78D PHE* 5.3 2.5 - - + -
79D PHE* 3.4 34.8 - - + -
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Residues in contact with THR 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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81B ASN* 5.6 1.3 - - - +
46D ALA* 2.8 24.3 + - + +
47D ARG* 3.4 10.6 + - - -
49D LEU* 1.3 76.7 - - - +
51D ARG* 1.3 66.7 + - - +
52D TYR 3.5 0.6 + - - -
53D ASN* 4.0 13.6 + - - +
78D PHE* 4.0 27.8 - - + -
79D PHE* 4.9 5.2 - - + -
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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