Contacts of the helix formed by residues 35 - 46 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33D ALA 4.0 2.6 + - - -
34D LEU* 1.3 75.4 - - - +
36D PRO* 1.3 69.0 - - - +
37D VAL* 3.3 16.8 - - - +
38D GLU* 2.7 35.1 + - + +
39D ALA* 3.1 9.1 + - - +
74D ARG* 3.0 40.9 + - - -
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Residues in contact with PRO 36 (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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15D LEU* 4.0 23.6 - - + +
34D LEU 3.2 9.2 - - - +
35D ASP* 1.3 93.1 - - - +
37D VAL* 1.3 57.5 + - + +
39D ALA* 3.4 9.5 + - + +
40D VAL* 2.9 34.5 + - - +
57D ASP 3.8 22.4 - - - +
58D LEU* 4.5 11.7 - - + +
74D ARG* 5.1 2.7 - - - +
75D PHE* 4.4 12.6 - - + -
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Residues in contact with VAL 37 (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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35D ASP* 3.0 10.8 - - - +
36D PRO* 1.3 75.1 - - + +
38D GLU* 1.3 66.4 + - - +
40D VAL* 3.3 6.7 + - - +
41D GLN* 3.1 43.6 + - - +
74D ARG* 3.2 58.3 - - + +
75D PHE* 4.7 2.7 - - - +
78D ALA* 3.8 16.2 - - + -
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Residues in contact with GLU 38 (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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34D LEU* 3.3 22.4 - - + -
35D ASP* 2.7 26.7 + - + +
37D VAL* 1.3 73.8 - - - +
39D ALA* 1.3 52.2 + - - +
41D GLN* 3.1 12.6 + - - +
42D ARG* 2.7 80.1 + - + +
296D ILE* 6.2 1.1 - - + -
300D TRP* 4.9 2.0 + - + +
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Residues in contact with ALA 39 (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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15D LEU* 3.8 21.3 - - + +
18D VAL* 4.2 13.9 - - + -
34D LEU* 3.9 20.1 - - + +
35D ASP 3.1 5.1 + - - +
36D PRO* 3.7 9.6 - - + +
37D VAL 3.4 0.2 - - - -
38D GLU* 1.3 79.5 - - - +
40D VAL* 1.3 60.5 + - - +
43D LEU* 2.9 34.3 + - + +
300D TRP* 4.0 12.3 - - - -
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Residues in contact with VAL 40 (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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15D LEU* 4.7 1.8 - - + -
36D PRO 2.9 25.0 + - - +
37D VAL* 3.5 8.5 - - - +
38D GLU 3.1 0.2 - - - -
39D ALA* 1.3 78.8 - - - +
41D GLN* 1.3 60.4 + - - +
43D LEU* 3.9 1.6 - - - +
44D ALA* 3.1 27.9 + - - +
51D VAL* 4.6 12.8 - - + -
75D PHE* 3.4 33.9 - - + -
78D ALA* 3.6 34.8 - - + +
79D LEU* 4.1 9.4 - - + -
82D THR* 3.7 12.3 - - + +
84D MET* 4.0 10.4 - - + +
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Residues in contact with GLN 41 (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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37D VAL* 3.1 34.5 + - + +
38D GLU* 3.6 13.7 + - - +
40D VAL* 1.3 76.1 - - + +
42D ARG* 1.3 88.4 + - - +
44D ALA* 4.0 1.7 - - - +
45D GLU* 3.3 23.2 + - - +
78D ALA* 5.3 2.7 - - + +
82D THR* 4.3 22.4 - - + -
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Residues in contact with ARG 42 (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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38D GLU* 2.7 60.0 + - - +
41D GLN* 1.3 101.9 + - - +
43D LEU* 1.3 61.9 + - - +
45D GLU* 2.6 34.5 + - - +
46D LEU* 3.2 26.5 + - - +
300D TRP* 3.3 53.3 - - + +
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Residues in contact with LEU 43 (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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13D PHE* 3.8 42.8 - - + -
14D GLY 5.4 0.4 - - - +
15D LEU* 5.2 1.1 - - + -
18D VAL* 4.0 18.2 - - + -
39D ALA* 2.9 26.5 + - + +
42D ARG* 1.3 73.4 - - - +
44D ALA* 1.3 65.5 + - - +
45D GLU 3.1 1.8 - - - -
46D LEU* 2.8 25.6 + - + +
47D GLY 3.2 0.2 + - - -
48D ALA* 3.2 21.5 + - + +
50D GLY 5.2 0.2 - - - +
51D VAL* 3.4 27.4 - - + -
84D MET* 3.8 10.8 - - + -
300D TRP* 3.8 21.8 - - + -
303D ALA* 4.6 1.3 - - + -
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Residues in contact with ALA 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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7D PRO* 5.6 2.3 - - - +
40D VAL 3.1 18.1 + - - +
41D GLN 4.0 4.0 - - - +
43D LEU* 1.3 74.9 - - - +
45D GLU* 1.3 62.7 + - - +
47D GLY* 3.1 13.5 + - - -
48D ALA 4.4 4.7 - - - +
82D THR* 4.0 20.4 - - + +
84D MET* 3.6 30.0 - - + +
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Residues in contact with GLU 45 (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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4D GLN* 5.3 2.4 + - - -
41D GLN 3.3 12.1 + - - +
42D ARG* 2.6 47.0 + - - +
43D LEU 3.1 0.4 - - - -
44D ALA* 1.3 80.1 - - - +
46D LEU* 1.3 66.3 + - + +
47D GLY* 3.2 0.7 + - - -
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Residues in contact with LEU 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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4D GLN* 3.5 8.9 + - - +
5D PRO* 3.3 22.7 - - - +
42D ARG 3.2 17.3 - - - +
43D LEU* 2.8 15.2 + - + +
45D GLU* 1.3 84.5 - - + +
47D GLY* 1.3 57.6 + - - +
48D ALA 3.6 0.2 - - - -
300D TRP* 4.0 44.2 - - + +
303D ALA* 4.2 12.8 - - + -
304D ALA* 4.4 18.4 - - + +
307D MET* 3.7 14.6 - - + +
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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