Contacts of the helix formed by residues 43 - 57 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38C LEU* 4.4 1.3 - - - -
42C GLU* 1.3 77.8 - - - +
44C LEU* 1.3 62.8 + - + +
45C VAL* 3.2 29.6 - - + +
46C GLU* 3.1 27.6 + - - +
47C ALA* 2.8 26.3 + - - +
142C GLY* 6.2 1.1 - - - -
143C ASP* 3.4 33.1 + - - +
146C TRP* 3.8 16.9 + - - -
70G GLN* 3.3 7.6 - - - +
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Residues in contact with LEU 44 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6C VAL* 4.1 6.5 - - + -
8C VAL* 3.6 24.4 - - + +
38C LEU* 4.0 24.9 - - + -
43C THR* 1.3 74.6 - - + +
45C VAL* 1.3 59.1 + - + +
47C ALA* 3.0 6.4 + - - +
48C ALA* 2.8 27.4 + - - +
82C PHE* 3.5 44.2 - - + -
84C PHE* 4.1 13.7 - - + -
141C ILE* 3.6 28.0 - - + +
68G MET* 4.2 9.6 - - + -
70G GLN* 3.2 14.3 + - - +
80G LEU* 5.2 3.1 - - + -
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Residues in contact with VAL 45 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43C THR* 3.2 16.1 - - + +
44C LEU* 1.3 76.0 - - + +
46C GLU* 1.3 62.4 + - + +
48C ALA* 2.9 8.6 + - - +
49C ALA* 2.7 37.7 + - - +
61C GLN* 4.1 18.2 - - + +
62C PRO* 4.0 14.4 - - + +
84C PHE* 4.7 7.4 - - + -
138C LEU* 4.5 34.8 - - + +
141C ILE* 6.0 2.2 - - + -
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Residues in contact with GLU 46 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41C ASP 4.5 2.1 - - - +
42C GLU* 3.8 15.9 - - + +
43C THR* 3.1 35.6 + - - +
44C LEU 3.3 0.4 - - - -
45C VAL* 1.3 87.5 - - + +
47C ALA* 1.3 53.2 + - - +
49C ALA* 3.4 6.0 + - - +
50C ARG* 2.8 35.7 + - - +
61C GLN* 5.3 3.8 - - - +
146C TRP* 4.4 9.6 + - - -
149C THR 4.1 15.4 - - - +
150C LYS* 4.4 10.6 - - - +
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Residues in contact with ALA 47 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8C VAL* 3.7 18.2 - - + -
38C LEU* 4.0 15.5 - - + -
42C GLU* 3.4 29.1 - - - +
43C THR 2.8 11.3 + - - +
44C LEU 3.2 9.4 - - - +
46C GLU* 1.3 71.4 - - - +
48C ALA* 1.3 61.7 + - - +
50C ARG* 3.1 7.0 + - - +
51C GLU* 2.8 35.9 + - - +
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Residues in contact with ALA 48 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8C VAL* 3.6 12.5 - - + +
10C CYS* 4.0 14.5 - - - -
44C LEU 2.8 13.2 + - - +
45C VAL 2.9 7.2 + - - +
47C ALA* 1.3 77.6 - - - +
49C ALA* 1.3 62.1 + - - +
51C GLU* 4.0 1.5 - - - +
52C LEU* 3.0 25.5 + - - +
62C PRO* 3.6 20.0 - - + -
84C PHE* 3.7 24.7 - - + -
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Residues in contact with ALA 49 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45C VAL 2.7 19.0 + - - +
46C GLU* 3.8 5.4 - - - +
48C ALA* 1.3 73.0 - - - +
50C ARG* 1.3 65.1 + - - +
52C LEU* 3.4 3.6 + - - +
53C TRP* 3.1 21.1 + - - +
58C ILE 4.8 0.5 - - - +
59C SER* 6.0 0.2 - - - -
60C ALA 3.9 16.7 + - - +
61C GLN* 3.6 30.1 - - - +
62C PRO* 4.1 6.1 - - + +
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Residues in contact with ARG 50 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37C HIS 3.2 21.2 + - - -
39C GLU* 3.6 19.5 + - - +
42C GLU* 2.6 40.6 + - - +
46C GLU 2.8 20.3 + - - +
47C ALA* 3.1 6.4 + - - +
49C ALA* 1.3 74.2 - - - +
51C GLU* 1.3 82.1 + - - +
53C TRP* 3.0 11.7 + - + +
54C GLU* 2.7 69.8 + - + +
155C MN 4.3 1.2 + - - -
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Residues in contact with GLU 51 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C VAL* 4.8 2.2 - - + -
34C PRO* 5.2 1.8 - - - -
35C ALA* 4.0 6.5 - - - -
36C GLY* 3.5 31.3 - - - +
37C HIS 4.0 1.4 + - - +
47C ALA 2.8 21.7 + - - +
48C ALA 4.3 1.3 - - - +
50C ARG* 1.3 92.2 + - - +
52C LEU* 1.3 70.5 + - - +
54C GLU* 3.6 6.9 - - - +
55C GLU* 2.9 31.1 + - - +
154C MN 2.3 30.0 + - - -
155C MN 2.4 29.7 + - - -
156C SO4 3.2 6.0 + - - -
157C SO4 3.0 3.1 + - - -
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Residues in contact with LEU 52 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10C CYS* 4.7 7.6 - - - -
12C VAL* 4.5 13.9 - - + -
19C LEU* 4.3 8.7 - - + -
34C PRO* 3.7 31.0 - - + +
48C ALA 3.0 18.2 + - - +
49C ALA* 3.5 6.5 - - - +
51C GLU* 1.3 80.3 - - - +
53C TRP* 1.3 60.2 + - - +
55C GLU 3.0 6.1 + - - -
56C THR* 2.5 51.4 + - + +
58C ILE* 3.9 19.5 - - + +
60C ALA* 4.0 31.9 - - + +
86C ILE* 4.1 12.6 - - + -
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Residues in contact with TRP 53 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49C ALA 3.1 8.4 + - - +
50C ARG* 3.0 12.2 + - + +
52C LEU* 1.3 78.4 - - - +
54C GLU* 1.3 88.0 + - + +
57C GLY* 2.7 44.5 + - - +
58C ILE 3.3 10.9 + - - +
59C SER* 3.5 24.5 + - - +
97C HIS* 3.4 55.8 + + + -
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Residues in contact with GLU 54 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50C ARG* 2.7 61.7 + - + +
51C GLU* 3.2 22.6 + - - +
53C TRP* 1.3 93.2 - - + +
55C GLU* 1.3 58.2 + - + +
56C THR 3.8 0.2 - - - -
97C HIS* 3.1 24.3 + - - +
98C ASP* 3.3 33.5 + - + +
155C MN 3.9 4.9 + - - -
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Residues in contact with GLU 55 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C VAL* 4.0 9.6 - - + +
34C PRO* 3.7 5.5 - - + +
35C ALA 3.1 17.5 + - - +
51C GLU* 2.9 22.9 - - - +
52C LEU 3.0 2.7 + - - +
54C GLU* 1.3 81.2 - - - +
56C THR* 1.3 69.7 + - + +
96C PRO* 3.7 8.5 - - - +
98C ASP* 5.4 0.2 - - + -
101C ILE* 3.4 40.7 - - + +
104C CYS* 3.4 13.3 - - - -
154C MN 2.5 12.0 + - - +
157C SO4 2.3 47.4 + - - -
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Residues in contact with THR 56 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C LEU* 3.8 19.3 - - + -
21C VAL* 3.5 24.0 - - + -
34C PRO* 3.7 16.8 - - + -
52C LEU* 2.5 32.3 + - - +
53C TRP 3.4 0.2 + - - -
54C GLU 3.8 0.2 - - - -
55C GLU* 1.3 83.5 - - + +
57C GLY* 1.3 66.3 + - - +
58C ILE* 3.1 11.7 + - - +
94C THR* 3.5 9.6 - - - -
95C GLN 3.0 25.9 + - - -
96C PRO* 3.9 1.5 - - - +
104C CYS* 3.8 13.0 - - - -
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Residues in contact with GLY 57 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53C TRP* 2.7 30.8 + - - -
56C THR* 1.3 80.2 + - - +
58C ILE* 1.3 60.3 + - - +
59C SER* 4.0 1.7 + - - -
95C GLN* 3.2 19.0 + - - +
97C HIS* 3.8 12.5 + - - -
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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