Contacts of the helix formed by residues 43 - 57 (chain D) in PDB entry 3SHD
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 THR 43 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38D LEU* 3.7 3.2 - - - +
42D GLU* 1.3 76.4 - - - +
44D LEU* 1.3 64.9 + - - +
45D VAL* 3.0 34.8 - - + +
46D GLU* 2.9 31.9 + - + +
47D ALA 3.0 19.4 + - - -
142D GLY* 6.4 0.2 - - - -
143D ASP* 3.3 35.4 + - - +
146D TRP* 3.6 13.3 + - - -
150D LYS* 4.6 5.3 - - + +
70E GLN* 3.4 9.4 + - - +
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Residues in contact with LEU 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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6D VAL* 4.1 20.6 - - + -
8D VAL* 3.7 24.8 - - + +
38D LEU* 3.9 21.8 - - + -
43D THR* 1.3 71.8 - - + +
45D VAL* 1.3 64.2 + - - +
46D GLU 3.2 0.5 + - - -
47D ALA* 3.4 2.4 + - - +
48D ALA* 3.0 19.6 + - - +
82D PHE* 3.6 38.6 - - + -
84D PHE* 4.4 12.6 - - + -
141D ILE* 3.9 23.3 - - + +
68E MET* 4.3 13.7 - - + -
70E GLN* 3.0 19.3 + - - +
80E LEU* 4.8 4.7 - - + -
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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
----------------------------------------------------------
43D THR* 3.0 14.3 - - + +
44D LEU* 1.3 74.9 - - + +
46D GLU* 1.3 69.9 + - + +
48D ALA* 3.9 6.5 - - - -
49D ALA* 3.2 17.7 + - - +
61D GLN* 4.1 15.7 - - + +
62D PRO* 3.9 26.7 - - + +
84D PHE* 4.7 5.8 - - + -
138D LEU* 4.8 24.5 - - + +
141D ILE* 4.9 10.8 - - + +
142D GLY* 6.0 3.1 - - - -
143D ASP* 5.6 1.8 - - - +
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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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41D ASP 4.5 2.6 - - - +
42D GLU* 3.5 16.8 - - + +
43D THR* 2.9 41.7 + - + +
45D VAL* 1.3 75.6 - - + +
47D ALA* 1.3 52.5 + - - +
49D ALA* 2.7 32.8 + - - +
50D ARG* 2.8 17.1 + - + +
61D GLN* 4.9 4.3 - - - +
146D TRP* 4.6 6.1 + - - -
149D THR 4.6 2.3 - - - +
150D LYS* 3.2 33.2 - - + +
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Residues in contact with ALA 47 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8D VAL* 3.6 13.5 - - + -
37D HIS 4.5 0.7 - - - +
38D LEU* 3.8 21.8 - - + -
42D GLU* 3.6 29.9 - - - +
43D THR 3.0 2.6 + - - -
44D LEU 3.7 6.7 - - - +
46D GLU* 1.3 77.3 - - - +
48D ALA* 1.3 56.6 + - - +
50D ARG* 3.6 12.7 - - - +
51D GLU* 2.8 35.0 + - - +
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Residues in contact with ALA 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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8D VAL* 3.4 13.1 - - + +
10D CYS* 3.5 23.4 - - - -
34D PRO 5.4 0.2 - - - +
44D LEU 3.0 15.5 + - - +
45D VAL* 4.0 0.7 - - - +
47D ALA* 1.3 73.9 - - - +
49D ALA* 1.3 61.3 + - - +
51D GLU* 4.5 1.0 - - - +
52D LEU* 3.2 23.9 + - - +
62D PRO* 3.7 23.1 - - + -
84D PHE* 3.7 21.1 - - + -
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Residues in contact with ALA 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 VAL 3.2 5.3 + - - +
46D GLU* 2.7 18.1 + - - +
48D ALA* 1.3 72.3 - - - +
50D ARG* 1.3 65.8 + - - +
52D LEU* 3.4 6.1 - - - +
53D TRP* 3.3 17.5 + - - +
58D ILE 4.7 0.9 - - - +
59D SER* 5.9 0.3 - - - -
60D ALA 3.9 21.1 + - - +
61D GLN* 3.5 28.9 - - - +
62D PRO* 4.2 4.3 - - + +
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Residues in contact with ARG 50 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37D HIS 3.0 28.1 + - - -
38D LEU* 4.1 0.2 - - - +
39D GLU* 3.0 30.1 + - - +
42D GLU* 2.9 35.1 + - - +
46D GLU 2.8 14.0 + - - +
47D ALA* 3.0 9.5 + - - +
49D ALA* 1.3 71.6 - - - +
51D GLU* 1.3 66.3 + - - +
53D TRP* 2.7 33.4 + - + +
54D GLU* 3.0 39.6 + - + +
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Residues in contact with GLU 51 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8D VAL* 5.0 3.1 - - + -
34D PRO 5.3 2.0 - - - +
35D ALA* 3.9 14.8 - - - +
36D GLY* 3.4 23.3 - - - +
37D HIS 3.8 8.4 - - - +
47D ALA 2.8 20.2 + - - +
48D ALA 4.5 1.3 - - - +
50D ARG* 1.3 78.8 + - - +
52D LEU* 1.3 62.8 + - - +
54D GLU* 3.5 14.9 - - - +
55D GLU* 2.7 41.2 + - - +
154D MN 2.3 33.8 + - - -
155D MN 2.2 28.0 + - - -
156D SO4 3.0 0.7 + - - -
157D SO4 3.2 0.7 + - - -
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Residues in contact with LEU 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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10D CYS* 4.7 3.1 - - - -
12D VAL* 4.3 13.7 - - + -
19D LEU* 4.4 2.2 - - + -
34D PRO* 3.7 25.4 + - + +
48D ALA 3.2 17.4 + - - +
49D ALA* 3.4 10.8 - - - +
50D ARG 3.1 0.2 + - - -
51D GLU* 1.3 75.0 - - - +
53D TRP* 1.3 53.3 + - - +
56D THR* 2.7 63.3 + - + +
58D ILE* 3.7 26.1 - - + +
60D ALA* 3.9 26.0 - - + +
86D ILE* 4.0 21.3 - - + -
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Residues in contact with TRP 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 ALA 3.9 5.8 - - - +
50D ARG* 2.7 20.5 + - + +
52D LEU* 1.3 71.0 - - - +
54D GLU* 1.3 98.3 + - + +
55D GLU 2.9 4.4 - - - -
57D GLY* 2.8 41.5 + - - +
58D ILE 3.3 13.2 - - - +
59D SER* 3.7 22.9 - - - +
97D HIS* 3.4 45.9 + + + -
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Residues in contact with GLU 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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50D ARG* 3.0 47.4 + - + +
51D GLU* 3.5 30.9 - - - +
53D TRP* 1.3 101.4 - - + +
55D GLU* 1.3 63.2 + - + +
97D HIS 3.3 6.4 + - - +
98D ASP* 3.1 44.5 + - + +
154D MN 4.3 4.3 + - - -
155D MN 4.1 4.7 + - - -
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Residues in contact with GLU 55 (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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21D VAL* 4.2 6.4 - - + +
33D GLN 4.1 0.7 - - - +
34D PRO* 3.7 6.0 - - + +
35D ALA 2.7 21.2 + - - +
51D GLU* 2.8 18.2 + - - +
54D GLU* 1.3 83.5 - - + +
56D THR* 1.3 69.3 + - + +
57D GLY 3.7 0.4 - - - -
96D PRO* 3.7 15.1 - - - +
98D ASP* 5.1 2.9 - - + +
101D ILE* 3.9 26.7 - - + +
104D CYS* 3.4 14.7 - - - -
155D MN 2.5 18.2 + - - +
157D SO4 2.2 48.6 + - - -
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Residues in contact with THR 56 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19D LEU* 3.3 24.9 - - + -
21D VAL* 3.9 9.2 - - + -
34D PRO* 3.8 13.9 - - + -
52D LEU* 2.7 32.4 + - + +
55D GLU* 1.3 81.5 - - - +
57D GLY* 1.3 58.0 + - - +
58D ILE* 2.8 36.0 + - - +
94D THR* 3.5 27.3 - - - -
95D GLN 3.7 7.1 + - - -
96D PRO* 4.5 0.4 - - - -
104D CYS* 4.0 10.8 - - - -
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Residues in contact with GLY 57 (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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52D LEU 3.6 0.2 + - - -
53D TRP* 2.8 28.7 + - - -
55D GLU 3.7 0.2 - - - -
56D THR* 1.3 75.6 - - - +
58D ILE* 1.3 63.1 + - - +
59D SER* 3.6 2.6 + - - -
94D THR 4.9 3.6 - - - -
95D GLN 3.5 16.1 + - - -
97D HIS* 3.7 16.7 + - - -
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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