Contacts of the helix formed by residues 35 - 47 (chain E) in PDB entry 4HHM
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 ASP 35 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33E ALA 4.1 1.8 + - - -
34E LEU* 1.3 77.9 - - - +
36E PRO* 1.3 67.1 - - - +
37E VAL* 3.1 16.4 + - - +
38E GLU* 2.7 36.8 + - + +
39E ALA 3.0 9.2 + - - -
74E ARG* 2.7 45.9 + - - -
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Residues in contact with PRO 36 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15E LEU* 4.2 13.3 - - + +
34E LEU 3.4 9.8 - - - +
35E ASP* 1.3 89.7 - - - +
37E VAL* 1.3 60.6 + - + +
39E ALA* 3.3 9.0 + - + +
40E VAL* 3.0 29.6 + - - +
57E ASP 3.7 23.1 - - - +
58E LEU* 4.3 10.8 - - + +
74E ARG* 5.1 2.2 - - - +
75E PHE* 4.1 23.1 - - + -
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Residues in contact with VAL 37 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35E ASP* 3.0 13.8 + - - +
36E PRO* 1.3 74.6 - - + +
38E GLU* 1.3 66.4 + - - +
40E VAL* 3.4 3.4 + - - +
41E GLN* 3.2 44.6 + - - +
74E ARG* 3.3 55.9 - - + +
75E PHE* 4.7 5.2 - - - -
78E ALA* 4.0 17.7 - - + -
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Residues in contact with GLU 38 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34E LEU* 3.8 21.3 - - + -
35E ASP* 2.7 30.3 + - + +
37E VAL* 1.3 71.2 - - - +
39E ALA* 1.3 63.1 + - - +
41E GLN* 3.3 15.0 + - - +
42E ARG* 2.9 64.1 + - + +
296E ILE* 6.2 0.4 - - + -
300E TRP* 4.9 1.6 + - + -
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Residues in contact with ALA 39 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15E LEU* 4.0 21.1 - - + +
18E VAL* 4.4 11.9 - - + -
34E LEU* 3.9 20.8 - - + +
35E ASP 3.0 8.1 + - - +
36E PRO* 3.5 10.3 - - + +
38E GLU* 1.3 76.8 - - - +
40E VAL* 1.3 62.6 + - - +
42E ARG* 4.0 0.5 - - - +
43E LEU* 2.9 34.2 + - + +
300E TRP* 4.1 12.3 - - - -
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Residues in contact with VAL 40 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15E LEU* 4.7 1.3 - - + -
36E PRO 3.0 16.9 + - - +
37E VAL 3.7 7.2 - - - +
38E GLU 3.3 0.2 - - - -
39E ALA* 1.3 75.4 - - - +
41E GLN* 1.3 56.9 + - - +
43E LEU* 3.8 4.3 - - - +
44E ALA* 2.9 28.6 + - - +
51E VAL* 4.3 11.4 - - + -
75E PHE* 3.7 25.8 - - + -
78E ALA* 3.8 22.4 - - + +
79E LEU* 4.1 10.3 - - + +
82E THR* 3.4 25.1 - - + +
84E MET* 3.8 17.5 - - + +
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Residues in contact with GLN 41 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37E VAL* 3.2 35.5 + - + +
38E GLU* 3.8 19.2 + - - +
40E VAL* 1.3 78.5 - - - +
42E ARG* 1.3 77.2 + - - +
44E ALA* 3.2 3.8 + - - +
45E GLU* 3.1 28.9 + - - +
78E ALA* 4.9 7.6 - - + +
82E THR* 4.1 21.1 - - + -
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Residues in contact with ARG 42 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38E GLU* 2.9 53.4 + - - +
41E GLN* 1.3 86.5 + - - +
43E LEU* 1.3 62.8 + - - +
45E GLU* 2.7 61.2 + - - +
46E LEU* 3.2 18.7 + - - +
300E TRP* 3.4 53.6 - - + +
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Residues in contact with LEU 43 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13E PHE* 3.6 50.7 - - + -
14E GLY 5.5 0.7 - - - +
15E LEU* 5.8 0.9 - - + -
18E VAL* 4.5 13.2 - - + -
39E ALA* 2.9 24.4 + - + +
40E VAL 3.8 2.7 - - - +
42E ARG* 1.3 73.2 - - - +
44E ALA* 1.3 67.3 + - - +
46E LEU* 3.0 25.3 + - + +
47E GLY 3.2 0.2 + - - -
48E ALA* 3.1 22.7 + - + +
50E GLY 4.8 0.2 - - - +
51E VAL* 3.4 29.4 - - + -
84E MET* 3.9 9.9 - - + -
300E TRP* 4.3 18.4 - - + -
303E ALA* 4.7 0.7 - - + -
307E MET* 5.2 0.4 - - + -
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Residues in contact with ALA 44 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7E PRO* 5.8 1.9 - - - +
40E VAL 2.9 18.9 + - - +
41E GLN 3.2 5.4 + - - +
43E LEU* 1.3 75.6 - - - +
45E GLU* 1.3 63.1 + - + +
47E GLY* 3.2 13.2 + - - -
48E ALA 4.2 3.2 + - - +
82E THR* 3.7 32.5 - - + +
84E MET* 4.0 16.3 - - + -
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Residues in contact with GLU 45 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4E GLN* 5.4 2.3 + - - -
41E GLN 3.1 14.8 + - - +
42E ARG* 2.7 47.1 + - - +
43E LEU 3.1 0.2 - - - -
44E ALA* 1.3 76.3 - - + +
46E LEU* 1.3 63.3 + - + +
47E GLY* 3.4 1.0 + - - -
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Residues in contact with LEU 46 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4E GLN* 4.0 4.8 + - - +
5E PRO* 3.1 24.7 - - - +
42E ARG 3.2 10.7 + - - +
43E LEU* 3.0 17.4 + - + +
45E GLU* 1.3 77.5 - - + +
47E GLY* 1.3 58.4 + - - +
48E ALA 3.6 0.2 - - - -
300E TRP* 3.7 45.5 - - + +
303E ALA* 3.9 17.5 - - + -
304E ALA* 4.3 19.7 - - + +
307E MET* 3.8 13.7 - - + +
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Residues in contact with GLY 47 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4E GLN* 4.5 1.6 - - - -
5E PRO* 3.4 18.1 - - - +
6E THR* 3.4 26.2 + - - +
7E PRO* 4.3 7.0 - - - -
11E PHE* 4.8 3.1 + - - -
44E ALA 3.2 11.3 + - - -
45E GLU 3.2 1.6 + - - -
46E LEU* 1.3 80.3 - - - +
48E ALA* 1.3 66.6 + - - +
49E TYR 3.9 0.3 + - - -
307E MET* 4.2 8.4 - - - +
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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