Contacts of the helix formed by residues 39 - 48 (chain A) in PDB entry 1DWK
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 ALA 39 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38A LEU* 1.3 77.1 - - - +
40A GLU* 1.4 66.6 + - - +
41A ALA* 4.1 3.4 - - + +
42A PHE* 3.0 3.7 + - - +
43A VAL* 3.0 21.0 + - - +
127A LYS* 6.1 0.7 - - - +
201A SO4 3.4 18.6 - - - +
156J PHE* 3.5 47.9 + - + +
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Residues in contact with GLU 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A PHE 5.0 4.9 - - - +
30A ALA* 4.4 20.2 + - - +
33A ALA* 4.1 18.5 - - + +
38A LEU 3.7 0.8 + - - -
39A ALA* 1.4 71.8 - - - +
41A ALA* 1.3 62.2 - - + +
44A THR* 2.7 40.4 + - - +
130A VAL* 4.2 5.0 + - - +
201A SO4 2.8 37.1 + - - +
111D LEU* 4.0 23.7 - - + +
114D GLU* 4.8 2.3 - - - +
115D LYS* 2.8 40.0 + - - +
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Residues in contact with ALA 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A ALA* 3.2 2.5 - - + +
40A GLU* 1.3 86.3 - - + +
42A PHE* 1.3 57.5 + - - +
45A ALA* 3.1 28.8 + - - +
128A LEU* 4.0 36.8 - - + +
129A ASP* 5.2 3.4 - - - -
130A VAL* 6.2 0.4 - - + -
201A SO4 5.0 0.2 + - - -
104D TYR* 4.0 5.1 - - + -
107D THR* 3.7 8.1 - - + +
111D LEU* 3.9 18.2 - - + -
156J PHE* 4.3 9.6 - - + -
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Residues in contact with PHE 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A LEU* 4.2 18.4 - - + -
39A ALA 3.0 8.7 + - - +
41A ALA* 1.3 76.5 - - - +
43A VAL* 1.4 68.2 + - - +
45A ALA* 3.3 5.7 + - - +
46A ALA* 3.0 19.8 + - - +
51A GLN* 3.5 40.1 - - + +
52A ALA 3.5 25.6 - - - -
53A LEU* 4.5 5.6 - - + -
54A PRO* 4.9 0.2 - - + -
104D TYR* 4.4 0.9 - - - -
153J THR* 5.1 1.3 - - + -
154J LYS 4.0 7.2 - - - -
155J PRO* 3.6 42.0 - - + -
156J PHE* 3.8 48.7 - + + +
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Residues in contact with VAL 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A PHE 5.6 0.4 - - - +
32A ILE* 4.5 5.2 - - + -
33A ALA* 4.0 26.0 - - + +
36A THR* 3.8 13.2 - - - +
38A LEU* 3.6 31.6 - - + -
39A ALA 3.0 14.7 + - - +
40A GLU 4.2 0.4 - - - +
42A PHE* 1.4 75.1 - - - +
44A THR* 1.3 64.8 + - - +
46A ALA* 3.1 3.8 + - - +
47A LEU* 3.0 31.1 + - + +
53A LEU* 4.3 15.7 - - + -
61A VAL* 4.3 20.9 - - + -
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Residues in contact with THR 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A PHE* 3.5 47.8 + - + +
33A ALA* 5.9 0.2 - - - +
40A GLU* 2.7 26.6 + - - -
43A VAL* 1.3 77.0 - - - +
45A ALA* 1.3 65.2 + - - +
47A LEU* 3.1 11.9 + - - +
48A LEU* 3.0 42.7 + - + +
107D THR* 3.9 17.7 - - + -
110D ALA* 4.3 4.7 - - + -
111D LEU* 3.8 10.3 - - + +
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Residues in contact with ALA 45 (chain A).
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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41A ALA 3.1 20.7 + - - +
42A PHE 3.6 4.7 - - - +
44A THR* 1.3 76.9 - - - +
46A ALA* 1.3 59.9 + - - +
48A LEU* 3.2 5.5 + - - +
49A GLY 3.1 5.9 + - - -
50A GLN* 2.8 33.2 + - + +
51A GLN* 3.7 14.1 - - + -
104D TYR* 3.7 20.0 - - + -
107D THR* 3.1 18.5 + - - +
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Residues in contact with ALA 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A ARG* 2.8 24.0 + - - +
42A PHE* 3.0 11.1 + - + +
43A VAL 3.4 8.3 - - - +
45A ALA* 1.3 77.3 - - - +
47A LEU* 1.3 63.1 + - - +
49A GLY 3.0 4.3 + - - -
51A GLN* 3.4 30.6 - - + +
52A ALA 4.5 0.2 - - - -
53A LEU* 3.6 35.4 - - + +
75A LEU* 3.9 5.4 - - + +
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Residues in contact with LEU 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A ARG* 4.8 1.7 + - - +
14A LEU* 5.6 0.3 - - - +
15A ALA* 3.3 22.9 + - - +
18A ILE* 3.9 44.1 - - + +
29A PHE* 3.9 28.5 - - + -
32A ILE* 3.9 26.2 - - + -
43A VAL* 3.0 24.1 + - + +
44A THR* 3.1 7.2 + - - +
46A ALA* 1.3 77.3 - - - +
48A LEU* 1.3 63.8 + - + +
49A GLY* 3.4 2.6 + - - -
53A LEU* 4.9 2.5 - - + -
61A VAL* 4.2 26.2 - - + -
65A LEU* 4.4 4.9 - - + -
75A LEU* 4.4 6.9 - - + +
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Residues in contact with LEU 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A LEU* 3.6 12.6 - - - +
15A ALA* 3.9 10.4 - - + +
18A ILE* 6.0 0.2 - - + -
19A LEU* 3.9 30.1 - - + -
29A PHE* 4.7 4.3 - - + -
44A THR* 3.0 22.1 + - + +
45A ALA* 3.4 8.3 - - - +
46A ALA 3.1 0.4 - - - -
47A LEU* 1.3 84.8 - - + +
49A GLY* 1.3 53.7 + - - -
50A GLN* 3.3 18.0 + - + +
83A CYS* 5.4 0.2 - - - +
6B ILE* 4.1 22.6 - - + +
106D THR* 3.6 47.4 + - - +
107D THR* 3.8 12.1 - - - +
110D ALA* 4.3 5.6 - - + -
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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