Contacts of the helix formed by residues 43 - 55 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70C GLN* 3.6 9.4 - - - +
38G LEU* 4.2 0.7 - - - -
42G GLU* 1.3 72.7 - - - +
44G LEU* 1.3 66.7 + - + +
45G VAL* 3.0 33.0 - - + +
46G GLU* 2.7 39.2 + - + +
47G ALA* 2.9 13.5 + - - +
141G ILE 5.9 1.1 - - - +
142G GLY* 6.2 0.7 - - - -
143G ASP* 3.3 35.2 + - - +
146G TRP* 3.9 12.6 - - - -
150G LYS* 4.2 9.6 - - - -
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Residues in contact with LEU 44 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68C MET* 4.0 20.9 - - + -
70C GLN* 3.1 19.6 + - - +
80C LEU* 4.7 4.9 - - + -
6G VAL* 4.0 16.6 - - + -
8G VAL* 3.9 17.1 - - + +
38G LEU* 3.8 32.5 - - + -
42G GLU 3.6 1.8 + - - -
43G THR* 1.3 72.8 - - + +
45G VAL* 1.3 57.5 + - - +
47G ALA* 3.5 2.8 + - - +
48G ALA* 3.0 26.6 + - - +
82G PHE* 3.6 39.9 - - + -
84G PHE* 4.6 6.3 - - + -
141G ILE* 4.0 20.2 - - + +
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Residues in contact with VAL 45 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43G THR* 3.0 15.8 - - + +
44G LEU* 1.3 72.2 - - - +
46G GLU* 1.3 71.8 + - + +
48G ALA* 3.6 7.9 - - - +
49G ALA* 3.1 20.4 + - - +
61G GLN* 4.4 14.8 - - + +
62G PRO* 3.7 18.4 - - + +
84G PHE* 4.3 9.6 - - + -
138G LEU* 4.3 24.7 - - + +
141G ILE* 4.1 22.9 - - + -
150G LYS* 6.5 0.9 - - + -
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Residues in contact with GLU 46 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41G ASP 4.6 1.9 - - - +
42G GLU* 3.5 16.4 - - + +
43G THR* 2.7 41.4 + - + +
45G VAL* 1.3 79.7 - - + +
47G ALA* 1.3 50.5 + - - +
49G ALA* 2.9 12.4 + - - +
50G ARG* 2.8 34.0 + - - +
61G GLN* 5.2 3.8 - - - +
146G TRP* 4.6 7.3 + - - -
149G THR 4.3 5.7 - - - +
150G LYS* 3.8 26.5 - - + +
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Residues in contact with ALA 47 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8G VAL* 3.6 16.1 - - + +
37G HIS 4.3 0.2 - - - +
38G LEU* 3.7 29.2 - - + -
42G GLU* 3.3 29.1 - - - +
43G THR 2.9 3.8 + - - +
44G LEU 3.8 3.4 - - - +
46G GLU* 1.3 75.8 - - - +
48G ALA* 1.3 65.0 + - - +
50G ARG* 3.7 10.7 - - - +
51G GLU* 3.0 24.3 + - - +
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Residues in contact with ALA 48 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8G VAL* 3.5 13.8 - - + +
9G ALA* 5.3 0.7 - - - +
10G CYS* 4.1 11.7 - - - -
44G LEU 3.0 15.4 + - - +
45G VAL* 3.6 4.3 - - - +
46G GLU 3.2 0.2 - - - -
47G ALA* 1.3 75.5 - - - +
49G ALA* 1.3 63.5 + - - +
51G GLU* 4.3 1.0 - - - +
52G LEU* 3.2 21.3 + - - +
62G PRO* 3.4 24.5 - - + -
84G PHE* 3.9 24.5 - - + -
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Residues in contact with ALA 49 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45G VAL 3.1 9.9 + - - +
46G GLU* 2.9 10.6 + - - +
48G ALA* 1.3 75.9 - - - +
50G ARG* 1.3 68.1 + - - +
52G LEU* 3.6 8.2 - - - +
53G TRP* 3.4 17.3 + - - +
58G ILE 4.8 0.5 - - - +
59G SER* 6.1 0.2 - - - -
60G ALA 3.8 20.8 - - - +
61G GLN* 3.8 22.4 - - - +
62G PRO* 3.8 6.0 - - + +
86G ILE* 6.1 0.2 - - - -
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Residues in contact with ARG 50 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37G HIS 3.4 22.2 + - - -
39G GLU* 3.2 24.9 + - - +
42G GLU* 2.7 38.0 + - - +
46G GLU 2.8 15.0 + - - +
47G ALA* 3.7 5.4 - - - +
48G ALA 3.2 0.2 - - - -
49G ALA* 1.3 73.2 - - - +
51G GLU* 1.3 68.2 + - - +
53G TRP* 2.6 33.4 + - + +
54G GLU* 2.6 60.2 + - + -
155G MN 4.3 0.8 + - - -
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Residues in contact with GLU 51 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8G VAL* 4.9 1.6 - - + -
35G ALA* 4.0 18.2 - - - +
36G GLY* 3.5 24.1 - - - +
37G HIS 3.9 7.3 - - - +
47G ALA 3.0 15.5 + - - +
48G ALA 4.4 1.6 - - - +
50G ARG* 1.3 84.5 + - - +
52G LEU* 1.3 66.2 + - - +
53G TRP 2.8 1.9 + - - -
54G GLU* 3.3 13.7 - - - +
55G GLU* 2.7 37.8 + - - +
154G MN 2.3 26.8 + - - -
155G MN 2.2 35.2 + - - -
156G SO4 3.2 1.7 + - - -
158G SO4 3.0 0.5 + - - -
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Residues in contact with LEU 52 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10G CYS* 4.9 5.6 - - + -
12G VAL* 3.9 25.1 - - + -
19G LEU* 4.3 2.2 - - + -
34G PRO* 3.6 32.3 - - + +
48G ALA 3.2 20.1 + - - +
49G ALA* 3.6 7.6 - - - +
50G ARG 3.1 0.4 + - - -
51G GLU* 1.3 74.8 - - - +
53G TRP* 1.3 55.7 + - - +
56G THR* 2.8 43.7 + - + +
58G ILE* 3.3 44.6 - - + +
60G ALA* 4.2 15.9 - - + +
86G ILE* 4.5 12.6 - - + -
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Residues in contact with TRP 53 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49G ALA 3.4 8.1 + - - +
50G ARG* 2.6 18.8 + - + +
52G LEU* 1.3 70.2 - - - +
54G GLU* 1.4 83.3 - - + +
55G GLU 2.7 15.7 + - - -
57G GLY* 2.8 49.2 + - - +
58G ILE 3.4 11.7 - - - +
59G SER* 3.5 20.5 + - - +
97G HIS* 3.4 51.4 + + + -
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Residues in contact with GLU 54 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50G ARG* 2.6 51.9 + - + +
51G GLU* 3.3 31.8 - - - +
53G TRP* 1.4 90.0 - - + +
55G GLU* 1.3 58.7 + - + +
97G HIS* 3.4 14.5 + - - +
98G ASP* 3.3 32.4 - - + +
154G MN 3.4 8.1 + - - -
155G MN 3.8 3.9 + - - -
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Residues in contact with GLU 55 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21G VAL* 4.0 3.8 - - + +
34G PRO* 4.2 4.1 - - + +
35G ALA 3.0 13.3 + - - +
51G GLU* 3.0 22.0 + - - +
53G TRP 2.7 3.0 + - - -
54G GLU* 1.3 83.0 - - + +
56G THR* 1.3 72.2 + - + +
96G PRO* 4.0 8.0 - - - +
98G ASP* 4.8 3.1 - - - +
100G ASP* 6.2 0.3 - - - +
101G ILE* 3.7 38.0 - - + +
104G CYS* 3.4 14.0 - - - -
154G MN 2.3 18.6 + - - +
158G SO4 2.2 52.6 + - - -
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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