Contacts of the helix formed by residues 43 - 57 (chain L) 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 L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70B GLN* 3.4 7.9 - - - +
38L LEU* 4.3 1.3 - - - -
42L GLU* 1.3 76.7 - - - +
44L LEU* 1.3 68.4 + - + +
45L VAL* 3.0 37.7 - - + +
46L GLU* 3.3 27.5 + - + +
47L ALA* 2.9 21.8 + - - +
141L ILE* 6.2 0.7 - - + -
142L GLY* 6.2 2.0 - - - -
143L ASP* 3.7 31.1 + - + +
146L TRP* 3.8 10.5 + - - -
150L LYS* 4.3 6.1 + - - +
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Residues in contact with LEU 44 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B MET* 4.2 5.8 - - + -
70B GLN* 3.4 16.8 + - - +
80B LEU* 4.9 3.6 - - + -
6L VAL* 3.9 27.8 - - + -
8L VAL* 3.8 9.4 - - + +
38L LEU* 4.0 17.5 - - + -
43L THR* 1.3 73.5 - - - +
45L VAL* 1.3 66.3 + - - +
47L ALA* 2.9 6.6 + - - +
48L ALA* 2.8 22.7 + - - +
82L PHE* 3.6 40.4 - - + -
84L PHE* 4.0 7.6 - - + -
141L ILE* 3.6 39.9 + - + +
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Residues in contact with VAL 45 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43L THR* 3.0 19.8 - - + +
44L LEU* 1.3 76.0 - - - +
46L GLU* 1.3 72.7 + - + +
48L ALA* 3.1 4.0 + - - +
49L ALA* 3.0 22.3 + - - +
61L GLN* 4.0 20.9 - - - +
62L PRO* 3.8 19.1 - - + +
84L PHE* 3.7 23.3 - - + -
138L LEU* 4.2 29.4 - - + +
141L ILE* 4.5 6.5 - - + -
150L LYS* 6.3 0.7 - - - +
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Residues in contact with GLU 46 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41L ASP 4.4 4.5 - - - +
42L GLU* 4.1 13.4 - - + +
43L THR* 3.3 38.0 + - + +
44L LEU 3.2 0.6 - - - -
45L VAL* 1.3 82.8 - - + +
47L ALA* 1.3 66.0 + - - +
49L ALA* 3.1 5.0 + - - +
50L ARG* 3.0 24.4 + - - +
61L GLN* 5.8 3.6 - - - +
146L TRP* 4.8 5.7 + - - -
149L THR 4.2 4.3 - - - +
150L LYS* 3.2 40.2 - - + +
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Residues in contact with ALA 47 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8L VAL* 3.9 19.1 - - + -
38L LEU* 3.8 15.0 - - + -
42L GLU* 3.1 31.1 + - - +
43L THR 2.9 12.8 + - - +
44L LEU 3.3 8.1 - - - +
46L GLU* 1.3 74.9 - - - +
48L ALA* 1.3 59.2 + - - +
50L ARG* 3.1 7.7 + - - +
51L GLU* 2.8 34.0 + - - +
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Residues in contact with ALA 48 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8L VAL* 3.8 15.9 - - + -
9L ALA 5.4 0.2 - - - +
10L CYS* 3.6 16.8 - - - -
44L LEU 2.8 18.2 + - - +
45L VAL 3.1 5.3 + - - +
47L ALA* 1.3 73.0 - - - +
49L ALA* 1.3 57.3 + - - +
51L GLU* 4.3 1.4 - - - +
52L LEU* 3.3 24.4 + - - +
62L PRO* 3.8 10.5 - - + -
84L PHE* 3.6 32.3 - - + -
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Residues in contact with ALA 49 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10L CYS* 5.6 0.2 - - - -
45L VAL 3.0 15.0 + - - +
46L GLU* 3.7 4.9 - - - +
48L ALA* 1.3 73.7 - - - +
50L ARG* 1.3 61.0 + - - +
52L LEU* 3.4 7.3 - - - +
53L TRP* 3.1 27.7 + - - +
58L ILE 4.5 0.5 - - - +
60L ALA 3.4 24.7 + - - +
61L GLN* 4.3 6.7 - - + +
62L PRO* 3.9 11.6 - - + +
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Residues in contact with ARG 50 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37L HIS 2.8 29.7 + - - -
39L GLU* 3.4 22.3 + - - +
42L GLU* 2.4 36.9 + - - +
46L GLU 3.0 15.5 + - - +
47L ALA* 3.5 4.2 - - - +
49L ALA* 1.3 74.8 - - - +
51L GLU* 1.3 91.6 + - - +
53L TRP* 3.2 6.4 + - + +
54L GLU* 2.8 67.2 + - + +
154L MN 3.7 2.0 + - - -
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Residues in contact with GLU 51 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8L VAL* 4.2 7.4 - - + -
34L PRO* 4.8 1.5 - - - +
35L ALA* 2.9 21.5 - - - +
36L GLY* 3.6 16.2 - - - -
37L HIS 3.8 2.3 - - - +
47L ALA 2.8 17.4 + - - +
48L ALA 4.4 2.9 - - - +
50L ARG* 1.3 103.9 + - - +
52L LEU* 1.3 57.7 + - - +
54L GLU* 4.1 2.5 - - - -
55L GLU* 2.6 37.0 + - - +
154L MN 2.2 31.6 + - - -
155L MN 2.5 27.5 + - - -
156L SO4 3.4 1.0 + - - -
157L SO4 2.9 9.0 + - - -
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Residues in contact with LEU 52 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10L CYS* 4.6 5.8 - - + -
12L VAL* 4.2 15.0 - - + -
19L LEU* 4.4 3.4 - - + -
34L PRO* 4.2 27.5 - - + -
48L ALA 3.3 19.0 + - - +
49L ALA* 3.4 5.8 - - - +
50L ARG 3.2 0.4 - - - -
51L GLU* 1.3 77.4 - - - +
53L TRP* 1.3 56.8 + - - +
56L THR* 3.0 47.4 + - - +
58L ILE* 3.0 42.4 - - + +
60L ALA* 3.6 29.8 - - + +
86L ILE* 4.4 12.3 - - + -
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Residues in contact with TRP 53 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49L ALA 3.1 13.0 + - - +
50L ARG* 3.6 5.2 - - + +
52L LEU* 1.3 75.7 - - - +
54L GLU* 1.3 84.5 + - + +
55L GLU 2.9 4.0 - - - -
56L THR 2.7 8.7 + - - -
57L GLY* 2.6 54.7 + - - +
58L ILE 3.2 26.5 - - - +
59L SER* 3.6 22.7 - - - -
97L HIS* 3.9 38.0 + + - +
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Residues in contact with GLU 54 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39L GLU* 5.4 0.3 - - - +
50L ARG* 2.8 64.6 + - + +
51L GLU* 3.8 4.2 - - - +
53L TRP* 1.3 85.4 - - + +
55L GLU* 1.3 59.7 + - - +
97L HIS* 3.7 8.3 + - + -
98L ASP* 3.3 36.9 + - + +
101L ILE* 4.7 0.5 - - - +
154L MN 4.1 2.6 + - - -
155L MN 3.6 21.1 + - - +
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Residues in contact with GLU 55 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21L VAL* 4.6 14.5 - - + +
23L GLU* 5.2 1.2 - - - +
33L GLN 4.8 0.2 - - - +
34L PRO* 4.0 8.0 - - + +
35L ALA 3.6 12.8 + - - +
51L GLU 2.6 25.7 + - - +
52L LEU 4.1 0.2 - - - +
53L TRP 2.8 1.2 + - - -
54L GLU* 1.3 82.9 - - - +
56L THR* 1.3 70.5 + - + +
96L PRO* 3.4 22.6 - - - +
101L ILE* 4.2 27.4 - - + +
104L CYS* 5.4 0.7 - - - +
155L MN 2.8 16.1 + - - +
157L SO4 2.2 50.1 + - - -
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Residues in contact with THR 56 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19L LEU* 4.1 8.9 - - + +
21L VAL* 3.9 25.8 - - + -
34L PRO* 4.2 12.6 - - + -
52L LEU* 3.0 22.1 + - - +
53L TRP 2.7 10.9 + - - -
55L GLU* 1.3 83.8 - - + +
57L GLY* 1.3 56.5 + - - -
58L ILE* 3.3 23.7 + - - +
93L PRO 4.5 0.5 - - - +
94L THR* 3.9 4.9 - - - -
95L GLN 2.8 30.8 + - - +
96L PRO* 4.2 5.2 - - - -
104L CYS* 4.5 13.7 - - - -
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Residues in contact with GLY 57 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53L TRP* 2.6 49.7 + - - -
56L THR* 1.3 71.7 - - - +
58L ILE* 1.3 60.3 + - - +
59L SER* 3.8 0.9 + - - -
93L PRO 5.6 2.2 - - - -
95L GLN* 3.5 18.9 + - - -
97L HIS* 4.2 7.6 - - - -
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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