Contacts of the helix formed by residues 35 - 47 (chain G) 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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33G ALA 4.1 1.6 + - - -
34G LEU* 1.3 76.7 - - - +
36G PRO* 1.3 67.7 - - - +
37G VAL* 3.2 9.4 + - - +
38G GLU* 2.7 40.8 + - + +
39G ALA* 2.9 10.4 + - - +
74G ARG* 3.1 39.8 + - - -
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Residues in contact with PRO 36 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15G LEU* 4.0 24.2 - - + +
34G LEU 3.4 9.0 - - - +
35G ASP* 1.3 91.6 - - - +
37G VAL* 1.3 59.5 + - + +
39G ALA* 3.3 10.1 + - + +
40G VAL* 3.0 29.1 + - - +
57G ASP 3.8 22.7 - - - +
58G LEU* 4.1 21.1 - - + +
74G ARG* 5.3 1.6 - - - +
75G PHE* 4.4 4.9 - - + -
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Residues in contact with VAL 37 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35G ASP* 3.1 10.3 + - - +
36G PRO* 1.3 80.6 - - + +
38G GLU* 1.3 62.8 + - - +
40G VAL* 3.4 9.8 + - - +
41G GLN* 3.4 33.8 + - - +
71G HIS 5.5 0.2 - - - +
74G ARG* 3.1 62.1 - - + +
75G PHE* 3.7 10.1 - - + +
78G ALA* 4.0 13.9 - - + +
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Residues in contact with GLU 38 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34G LEU* 3.8 18.8 - - + -
35G ASP* 2.7 30.9 + - + +
37G VAL* 1.3 79.5 - - - +
39G ALA* 1.3 61.8 + - - +
41G GLN* 3.4 13.1 + - - +
42G ARG* 3.0 61.0 + - + +
300G TRP* 5.3 0.7 - - + -
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Residues in contact with ALA 39 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15G LEU* 4.3 19.3 - - + +
18G VAL* 4.3 12.8 - - + -
34G LEU* 3.9 20.4 - - + +
35G ASP 2.9 7.6 + - - +
36G PRO* 3.3 11.2 + - + +
38G GLU* 1.3 76.2 - - - +
40G VAL* 1.3 57.0 + - - +
43G LEU* 3.0 39.3 + - + +
51G VAL* 5.5 0.2 - - - -
300G TRP* 4.2 11.4 - - - -
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Residues in contact with VAL 40 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15G LEU* 5.0 1.1 - - + -
36G PRO 3.0 18.6 - - - +
37G VAL* 3.6 9.9 - - - +
39G ALA* 1.3 78.7 - - - +
41G GLN* 1.3 57.0 + - - +
44G ALA* 3.0 31.6 + - - +
51G VAL* 4.8 10.1 - - + -
75G PHE* 3.9 22.9 - - + -
78G ALA* 3.9 21.8 - - + -
79G LEU* 4.2 7.6 - - + +
82G THR* 3.4 21.5 - - - +
84G MET* 3.6 25.7 - - + +
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Residues in contact with GLN 41 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37G VAL* 3.4 26.1 + - - +
38G GLU* 3.4 15.5 + - - +
39G ALA 3.4 0.4 - - - -
40G VAL* 1.3 74.1 - - - +
42G ARG* 1.3 90.0 + - - +
44G ALA* 3.3 2.8 + - - +
45G GLU* 3.1 27.0 + - - +
78G ALA* 4.9 6.8 - - + +
82G THR* 4.2 21.1 - - + -
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Residues in contact with ARG 42 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38G GLU* 3.0 41.0 + - - +
41G GLN* 1.3 101.3 + - - +
43G LEU* 1.3 63.1 + - - +
45G GLU* 2.4 57.6 + - - +
46G LEU* 3.3 16.2 + - - +
300G TRP* 3.3 59.0 - - + +
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Residues in contact with LEU 43 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13G PHE* 3.8 49.4 - - + +
14G GLY 5.5 0.4 - - - +
15G LEU* 5.7 1.3 - - + -
18G VAL* 4.2 28.3 - - + -
39G ALA* 3.0 24.9 + - + +
42G ARG* 1.3 73.3 - - - +
44G ALA* 1.3 66.3 + - - +
46G LEU* 3.0 30.1 + - + +
47G GLY 3.3 0.2 + - - -
48G ALA* 3.2 21.8 + - + +
51G VAL* 3.9 19.7 - - + -
84G MET* 3.7 11.9 - - + -
300G TRP* 4.2 9.0 - - + -
303G ALA* 4.4 0.9 - - + -
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Residues in contact with ALA 44 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7G PRO* 5.4 3.3 - - - +
40G VAL 3.0 21.1 + - - +
41G GLN 3.3 4.2 + - - +
43G LEU* 1.3 75.7 - - - +
45G GLU* 1.3 63.9 + - + +
47G GLY* 3.2 13.0 + - - -
48G ALA 4.5 3.4 - - - +
82G THR* 3.7 23.6 - - + +
84G MET* 3.6 26.6 - - + +
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Residues in contact with GLU 45 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4G GLN* 5.1 3.6 + - - -
41G GLN* 3.1 10.7 + - - +
42G ARG* 2.4 46.4 + - - +
44G ALA* 1.3 79.6 - - + +
46G LEU* 1.3 63.1 + - + +
47G GLY 3.5 0.5 + - - -
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Residues in contact with LEU 46 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4G GLN* 3.8 10.8 + - - +
5G PRO* 3.1 25.6 - - - +
42G ARG 3.3 12.7 + - - +
43G LEU* 3.0 22.2 + - + +
45G GLU* 1.3 80.4 - - + +
47G GLY* 1.3 57.5 + - - +
48G ALA 3.6 0.2 - - - -
300G TRP* 3.8 36.1 - - + +
303G ALA* 4.0 18.4 - - + -
304G ALA* 4.1 19.3 - - + +
307G MET* 3.6 12.6 - - + -
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Residues in contact with GLY 47 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5G PRO* 3.2 19.7 - - - +
6G THR* 3.1 8.7 + - - +
7G PRO* 3.0 28.1 - - - -
11G PHE* 5.1 1.9 + - - +
44G ALA 3.2 10.9 + - - -
45G GLU 3.3 0.8 - - - -
46G LEU* 1.3 79.4 - - - +
48G ALA* 1.3 66.9 + - - +
307G MET* 4.4 4.6 - - - +
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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