Contacts of the helix formed by residues 35 - 46 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33C ALA 3.9 3.0 + - - -
34C LEU* 1.3 73.1 - - - +
36C PRO* 1.3 70.0 - - - +
37C VAL* 3.1 25.2 + - - +
38C GLU* 2.7 41.3 + - + +
39C ALA 3.1 4.5 + - - -
74C ARG* 3.1 34.8 + - - -
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Residues in contact with PRO 36 (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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15C LEU* 4.0 20.9 - - + +
34C LEU 3.4 8.7 - - - +
35C ASP* 1.3 91.9 - - - +
37C VAL* 1.3 61.3 + - + +
39C ALA* 3.3 10.6 + - + +
40C VAL* 3.1 29.6 + - - +
57C ASP 3.8 22.7 - - - +
58C LEU* 4.6 9.4 - - + +
74C ARG* 5.4 1.8 - - - +
75C PHE* 4.5 13.0 - - + -
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Residues in contact with VAL 37 (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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35C ASP* 2.9 17.0 + - - +
36C PRO* 1.3 78.7 - - + +
38C GLU* 1.3 63.1 + - - +
40C VAL* 3.4 2.1 + - - +
41C GLN* 3.1 42.5 + - - +
74C ARG* 3.8 48.0 - - + +
75C PHE* 4.8 2.9 - - - +
78C ALA* 3.8 22.2 - - + -
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Residues in contact with GLU 38 (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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34C LEU* 4.0 18.4 - - + -
35C ASP* 2.7 32.8 + - + +
37C VAL* 1.3 76.1 - - - +
39C ALA* 1.3 59.2 + - - +
41C GLN* 3.7 14.1 + - - +
42C ARG* 2.8 73.4 + - + +
296C ILE* 6.1 0.2 - - + -
300C TRP* 4.8 1.8 + - + -
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Residues in contact with ALA 39 (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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15C LEU* 3.7 22.7 - - + +
18C VAL* 4.4 10.3 - - + -
34C LEU* 3.6 26.4 - - + +
35C ASP 3.1 4.4 + - - +
36C PRO* 3.4 11.7 - - + +
38C GLU* 1.3 75.9 - - - +
40C VAL* 1.3 58.6 + - - +
42C ARG* 3.8 0.7 - - - +
43C LEU* 2.9 40.0 + - + +
300C TRP* 4.1 6.1 - - - -
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Residues in contact with VAL 40 (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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15C LEU* 4.7 2.0 - - + -
36C PRO 3.1 15.0 + - - +
37C VAL 3.7 5.6 - - - +
39C ALA* 1.3 76.7 - - - +
41C GLN* 1.3 58.2 + - - +
43C LEU* 4.7 0.2 - - - -
44C ALA* 2.9 29.5 + - - +
51C VAL* 4.4 9.4 - - + -
75C PHE* 3.7 28.5 - - + -
78C ALA* 4.0 22.2 - - + +
79C LEU* 4.1 8.5 - - + -
82C THR* 3.3 23.8 - - + +
84C MET* 3.6 24.7 - - + +
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Residues in contact with GLN 41 (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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37C VAL* 3.1 35.0 + - + +
38C GLU* 3.7 24.1 + - - +
40C VAL* 1.3 80.1 - - - +
42C ARG* 1.3 80.6 + - - +
44C ALA* 3.4 2.4 + - - +
45C GLU* 3.1 22.0 + - - +
78C ALA* 5.0 4.3 - - + -
82C THR* 4.0 22.3 - - + +
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Residues in contact with ARG 42 (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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38C GLU* 2.8 65.7 + - - +
41C GLN* 1.3 98.6 + - - +
43C LEU* 1.3 63.0 + - - +
45C GLU* 2.9 47.5 + - - +
46C LEU* 3.2 19.7 + - - +
300C TRP* 3.4 48.2 - - + +
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Residues in contact with LEU 43 (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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13C PHE* 3.6 49.1 - - + +
14C GLY 5.4 0.7 - - - +
15C LEU* 5.7 1.1 - - + -
18C VAL* 4.4 13.9 - - + -
39C ALA* 2.9 24.6 + - + +
42C ARG* 1.3 73.9 - - - +
44C ALA* 1.3 58.6 + - - +
46C LEU* 2.8 35.7 + - + +
47C GLY 3.1 0.3 + - - -
48C ALA* 3.1 27.2 + - + +
51C VAL* 3.4 30.5 - - + -
84C MET* 3.6 5.8 - - + -
300C TRP* 4.3 18.2 - - + -
303C ALA* 4.4 1.3 - - + -
307C MET* 5.4 0.2 - - + -
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Residues in contact with ALA 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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7C PRO* 6.1 0.5 - - - +
40C VAL 2.9 18.8 + - - +
41C GLN 3.7 4.3 - - - +
43C LEU* 1.3 76.1 - - - +
45C GLU* 1.3 60.9 + - - +
47C GLY* 3.2 12.3 + - - -
48C ALA 4.3 5.2 - - - +
82C THR* 3.8 21.5 - - + +
84C MET* 3.7 29.5 - - + +
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Residues in contact with GLU 45 (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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4C GLN* 5.2 2.6 + - - -
41C GLN 3.1 11.8 + - - +
42C ARG* 2.9 46.5 + - - +
43C LEU 3.0 0.8 - - - -
44C ALA* 1.3 78.3 - - - +
46C LEU* 1.3 60.8 + - + +
47C GLY 3.2 1.1 + - - -
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Residues in contact with LEU 46 (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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4C GLN* 3.5 10.7 + - - +
5C PRO* 3.2 22.7 - - - +
42C ARG 3.2 13.9 + - - +
43C LEU* 2.8 15.7 + - + +
45C GLU* 1.3 78.6 - - + +
47C GLY* 1.3 56.6 + - - +
300C TRP* 3.8 41.5 - - + +
303C ALA* 4.1 17.9 - - + -
304C ALA* 4.2 20.2 - - + +
307C MET* 3.8 14.1 - - + +
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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