Contacts of the helix formed by residues 41 - 49 (chain D) in PDB entry 2WWR
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 41 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34D TRP* 5.2 7.0 - - + -
39D PRO 3.4 6.2 - - - +
40D ILE* 1.3 93.9 - - + +
42D ALA* 1.3 67.2 + - - +
43D LYS* 3.1 12.9 + - + +
44D GLU* 3.1 19.6 + - + +
45D LEU* 3.0 20.1 + - - +
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Residues in contact with ALA 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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40D ILE 4.0 0.2 + - - -
41D PRO* 1.3 71.7 - - - +
43D LYS* 1.3 52.4 + - - +
45D LEU* 4.1 11.0 - - - -
46D GLU* 2.7 58.9 + - + +
67D ILE* 5.4 6.1 - - + -
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Residues in contact with LYS 43 (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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41D PRO* 3.1 11.1 + - + +
42D ALA* 1.3 78.8 - - - +
44D GLU* 1.3 73.6 + - - +
46D GLU* 3.9 9.9 + - - +
47D ARG* 3.6 26.3 + - - +
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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
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34D TRP* 4.7 18.2 - - + -
40D ILE* 3.6 33.0 - - + +
41D PRO* 3.1 14.6 + - + +
43D LYS* 1.3 90.0 - - - +
45D LEU* 1.3 60.5 + - - +
47D ARG* 3.4 17.4 + - - +
48D GLY* 2.9 24.8 + - - -
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Residues in contact with LEU 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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10D PHE* 4.1 6.5 - - + -
12D THR* 4.0 26.7 - - + -
40D ILE* 4.3 16.5 - - + +
41D PRO 3.0 16.7 + - - +
42D ALA* 3.7 8.1 - - - +
44D GLU* 1.3 76.6 - - - +
46D GLU* 1.4 57.0 + - - +
48D GLY* 2.9 18.4 + - - +
49D VAL* 3.0 44.1 + - + +
55D LEU* 4.5 3.8 - - + -
61D ASP* 4.3 23.1 - - + -
62D HIS 4.3 3.8 - - - +
63D VAL* 5.5 3.6 - - + -
67D ILE* 3.4 29.8 - - + -
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Residues in contact with GLU 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 ALA* 2.7 46.6 + - - +
43D LYS* 4.3 7.9 - - - +
45D LEU* 1.4 67.2 - - - +
47D ARG* 1.8 51.4 + - + +
49D VAL* 4.1 12.1 - - - +
50D ALA* 4.5 7.4 - - - +
66D ARG* 5.0 12.4 - - - +
67D ILE* 4.1 22.4 - - + +
70D ALA* 4.1 20.4 - - + +
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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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43D LYS* 3.6 19.3 + - - +
44D GLU* 3.4 19.8 + - - +
45D LEU 3.2 1.0 - - - -
46D GLU* 1.8 55.9 - - + +
48D GLY* 1.3 64.9 + - - +
49D VAL 3.5 1.6 - - - -
50D ALA* 3.8 18.9 + - - +
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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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10D PHE* 3.8 42.3 - - - +
44D GLU 2.9 13.5 + - - -
45D LEU 2.9 6.7 + - - -
47D ARG* 1.3 80.8 - - - +
49D VAL* 1.3 60.6 + - - +
50D ALA 3.4 4.3 + - - +
52D ALA* 4.7 1.9 - - - +
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Residues in contact with VAL 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 LEU* 3.0 45.4 + - + +
46D GLU* 4.1 10.1 - - - -
48D GLY* 1.3 73.5 - - - +
50D ALA* 1.3 66.7 + - - +
51D GLY 3.3 0.5 + - - -
52D ALA* 3.1 28.9 + - + +
55D LEU* 3.4 30.3 - - + -
67D ILE* 3.4 33.0 - - + +
70D ALA* 4.3 8.5 - - + -
71D ALA* 4.0 16.0 - - + +
75D LEU* 5.4 3.4 - - + -
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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