Contacts of the helix formed by residues 42 - 54 (chain D) in PDB entry 6DKS
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 LYS 42 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D ASN* 5.7 2.2 + - - -
40D PRO 3.6 0.4 + - - -
41D ASP* 1.4 74.7 - - + +
43D LEU* 1.4 59.3 + - - +
44D GLU* 3.2 18.2 - - - +
45D GLU* 3.2 27.4 + - + +
46D LYS* 2.9 24.3 + - - +
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Residues in contact with LEU 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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10D TRP* 4.1 14.1 - - + -
11D ILE 3.4 31.9 - - - +
12D ASN* 3.7 12.0 + - - +
40D PRO* 3.4 41.1 - - + +
41D ASP 3.4 1.8 - - - -
42D LYS* 1.4 72.9 - - - +
44D GLU* 1.4 61.3 + - - +
45D GLU 3.2 0.2 - - - -
46D LYS* 3.7 9.2 - - - -
47D PHE* 2.9 33.1 + - - +
60D ILE* 3.9 17.0 - - + -
61D PHE 3.8 13.7 - - - +
62D TRP* 3.7 25.8 - - + -
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Residues in contact with GLU 44 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12D ASN* 5.4 0.5 - - - +
42D LYS* 3.4 12.9 - - - +
43D LEU* 1.4 89.7 + - - +
45D GLU* 1.3 77.8 + - + +
48D PRO* 3.2 13.3 - - - +
60D ILE* 5.7 0.7 - - - -
62D TRP* 3.2 50.6 - - + -
66D ARG* 4.0 34.2 + - - +
70D TYR* 2.7 27.9 + - - +
153D GLU* 5.4 3.5 - - - +
344D ARG* 5.1 7.1 + - - -
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Residues in contact with GLU 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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42D LYS* 3.2 20.1 + - + +
44D GLU* 1.3 99.9 - - + +
46D LYS* 1.4 63.0 + - - +
48D PRO* 3.4 14.4 - - - +
49D GLN* 3.3 26.4 + - - +
66D ARG* 5.0 7.3 + - - +
344D ARG* 5.1 11.4 + - - -
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Residues in contact with LYS 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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10D TRP* 4.1 14.1 - - + -
40D PRO* 5.8 3.4 - - + -
41D ASP 4.8 4.3 - - - +
42D LYS 2.9 16.8 + - - +
43D LEU* 3.8 10.1 - - + -
45D GLU* 1.4 73.4 - - - +
47D PHE* 1.4 65.0 + - - +
49D GLN* 2.9 26.1 + - - +
50D VAL* 3.2 17.6 + - + +
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Residues in contact with PHE 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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10D TRP* 3.7 11.9 - - + -
43D LEU 2.9 21.5 + - - +
46D LYS* 1.4 70.8 - - - +
48D PRO* 1.4 63.0 - - + +
49D GLN 3.1 0.3 + - - -
50D VAL* 3.3 1.3 + - - -
51D ALA* 2.8 51.1 + - + +
57D PRO* 3.7 27.4 - - + -
60D ILE* 3.5 37.9 - - + -
70D TYR* 3.8 48.5 - + + +
75D LEU* 4.3 22.2 - - + -
76D LEU* 4.4 4.3 - - + -
267D ASN* 4.0 18.6 - - + -
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Residues in contact with PRO 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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44D GLU 3.2 25.6 - - - +
45D GLU* 3.4 15.5 - - - +
47D PHE* 1.4 89.2 - - + +
49D GLN* 1.3 59.2 + - + +
51D ALA 4.2 0.4 - - - -
52D ALA* 3.3 22.9 + - - +
70D TYR* 3.7 17.7 - - + -
73D SER* 6.1 0.7 - - - +
75D LEU* 3.7 26.7 - - + +
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Residues in contact with GLN 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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45D GLU* 3.3 26.9 + - - +
46D LYS* 2.9 14.7 + - - +
48D PRO* 1.3 76.4 - - + +
50D VAL* 1.4 64.6 + - - +
52D ALA* 3.5 16.0 + - - +
53D THR* 3.8 7.8 + - - +
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Residues in contact with VAL 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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10D TRP* 3.6 31.6 - - + -
46D LYS* 3.2 19.1 - - + +
47D PHE* 3.7 6.1 - - - +
49D GLN* 1.4 71.9 - - - +
51D ALA* 1.3 58.6 + - - +
53D THR* 2.9 18.8 - - + +
55D ASP* 2.9 32.2 + - + -
56D GLY* 3.9 19.5 - - - +
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Residues in contact with ALA 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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47D PHE* 2.8 50.4 + - + +
50D VAL* 1.3 69.8 - - - +
52D ALA* 1.4 64.2 + - - +
54D GLY* 3.1 14.4 + - - -
55D ASP 3.4 12.5 + - - +
56D GLY* 5.0 0.2 - - - -
75D LEU* 3.6 27.5 - - + +
267D ASN* 4.1 9.7 - - - +
269D ALA* 4.9 1.6 - - - +
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Residues in contact with ALA 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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48D PRO 3.3 19.3 + - - +
49D GLN* 3.6 8.1 - - - +
50D VAL 3.3 0.4 - - - -
51D ALA* 1.4 79.8 - - - +
53D THR* 1.3 59.6 + - - +
54D GLY 3.4 0.5 + - - -
75D LEU* 3.6 12.3 - - + +
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Residues in contact with THR 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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49D GLN 3.8 5.0 + - - +
50D VAL* 2.9 33.9 - - + +
52D ALA* 1.3 78.3 - - - +
54D GLY* 1.3 56.1 + - - +
55D ASP* 4.0 12.6 - - + +
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Residues in contact with GLY 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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2D ILE* 3.6 12.0 + - - +
51D ALA 3.1 14.5 + - - -
52D ALA 3.2 1.0 - - - -
53D THR* 1.3 79.6 - - - +
55D ASP* 1.4 60.8 + - - +
269D ALA* 3.5 27.7 - - - +
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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