Contacts of the helix formed by residues 38 - 48 (chain D) in PDB entry 6WNX
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 CYS 38 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5D ASP* 5.1 0.2 - - - -
8D THR* 4.8 2.7 - - - -
35D GLU 3.7 0.9 - - - +
36D LEU 3.4 1.0 - - - -
37D VAL* 1.3 81.3 - - - +
39D LYS* 1.3 67.4 + - - +
40D GLU* 3.9 10.1 - - - -
41D TRP* 3.2 40.2 + - - +
42D GLN 3.1 17.7 + - - -
123E ILE* 4.2 13.2 - - + -
124E LYS 3.9 14.4 - - - +
126E ASP* 3.7 14.4 - - - +
127E PHE* 3.4 17.6 - - - -
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Residues in contact with LYS 39 (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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38D CYS* 1.3 73.3 - - - +
40D GLU* 1.3 51.8 + - - +
42D GLN* 3.3 22.5 + - - +
43D ARG* 2.7 35.8 + - - +
126E ASP* 3.1 34.8 + - - +
127E PHE* 3.5 28.0 - - + -
131E GLU* 4.8 8.5 - - - +
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Residues in contact with GLU 40 (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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7D ILE 4.8 0.4 - - - +
8D THR* 3.4 40.4 - - + +
11D PRO* 4.1 11.4 - - - +
12D GLU* 5.8 1.2 - - - +
38D CYS* 3.2 8.1 - - - -
39D LYS* 1.3 75.4 - - - +
41D TRP* 1.3 59.4 + - - +
43D ARG* 2.9 45.7 + - - +
44D VAL* 2.9 36.2 + - + +
126E ASP* 5.0 1.2 + - - -
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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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5D ASP* 3.3 33.2 + - - -
7D ILE* 3.4 48.0 - - + +
8D THR* 3.9 7.4 - - - -
23D LEU* 4.8 3.1 - - + -
34D ALA* 3.4 42.4 - - + +
37D VAL* 3.8 13.9 - - + -
38D CYS* 3.2 27.1 + - - +
40D GLU* 1.3 72.4 - - - +
42D GLN* 1.3 65.6 + - - +
44D VAL* 3.2 3.3 + - - +
45D ILE* 3.0 30.6 + - + +
109E ILE* 4.2 22.7 - - + -
117E ILE* 3.7 27.6 - - + -
121E PHE* 4.4 5.4 - + - -
123E ILE* 3.9 17.2 - - + +
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Residues in contact with GLN 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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35D GLU* 3.4 35.0 + - + +
38D CYS 3.1 9.1 + - - +
39D LYS* 3.4 39.0 + - - +
41D TRP* 1.3 75.1 - - - +
43D ARG* 1.3 61.7 + - - +
45D ILE* 3.4 4.4 + - - +
46D SER* 2.8 47.5 + - - -
127E PHE* 4.3 9.3 - - + -
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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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11D PRO* 3.9 6.9 - - - +
16D ASP* 3.7 20.6 + - - -
39D LYS 2.7 17.8 + - - +
40D GLU* 2.9 44.9 + - - +
42D GLN* 1.3 83.5 - - - +
44D VAL* 1.3 70.9 + - - +
46D SER* 3.3 2.2 + - - -
47D GLU* 2.8 76.6 + - + +
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Residues in contact with VAL 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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7D ILE* 3.9 28.0 - - + +
11D PRO* 3.9 7.2 - - + -
16D ASP* 5.1 3.8 - - + +
19D ALA* 4.5 9.0 - - + -
20D GLU* 4.4 15.9 - - + +
23D LEU* 3.7 23.1 - - + -
40D GLU* 2.9 23.0 + - - +
41D TRP 3.6 3.6 - - - +
43D ARG* 1.3 98.7 - - - +
45D ILE* 1.3 58.9 + - - +
47D GLU* 5.2 0.2 - - - -
48D GLY* 2.7 36.0 + - - +
50D LEU* 3.8 0.2 - - - +
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Residues in contact with ILE 45 (chain D).
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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23D LEU* 3.8 19.3 - - + -
31D LEU* 3.9 25.1 - - + +
34D ALA* 3.7 18.4 - - + -
35D GLU* 3.5 54.3 - - + +
41D TRP* 3.0 21.5 + - + +
42D GLN 3.7 3.4 - - - +
44D VAL* 1.3 74.2 - - - +
46D SER* 1.3 64.9 - - - +
49D MET 3.3 2.9 + - - -
50D LEU* 3.2 37.7 + - + -
51D TRP* 4.4 9.6 - - + +
89D ASN* 4.1 3.0 - - - +
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Residues in contact with SER 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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42D GLN* 2.8 32.3 + - - -
43D ARG* 3.6 4.5 - - - -
44D VAL 3.2 0.2 - - - -
45D ILE* 1.3 80.9 - - - +
47D GLU* 1.3 65.1 + - - +
49D MET* 3.3 10.4 + - - +
89D ASN* 3.4 37.4 + - - +
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Residues in contact with GLU 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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43D ARG* 2.8 58.0 + - + +
44D VAL 4.6 0.4 - - - +
46D SER* 1.3 73.6 - - - +
48D GLY* 1.3 61.0 + - - +
49D MET* 3.1 20.9 + - - +
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Residues in contact with GLY 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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20D GLU* 3.2 38.0 - - - +
44D VAL 2.7 24.4 + - - -
47D GLU* 1.3 69.1 - - - +
49D MET* 1.3 69.8 + - - +
50D LEU* 3.3 7.4 + - - +
53D LYS* 3.4 15.6 + - - -
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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