Contacts of the helix formed by residues 37 - 49 (chain H) in PDB entry 2P5L
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 37 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4F G 2.7 68.9 + - + +
5F A 3.5 12.8 + - - +
26H VAL* 3.9 6.3 - - - -
30H LYS* 6.4 0.4 - - - -
36H VAL* 1.3 77.1 - - - +
38H GLN* 1.3 69.0 + - - +
39H ALA* 3.9 8.0 + - - +
40H THR* 2.9 14.0 + - - -
41H VAL* 3.0 9.0 + - - +
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Residues in contact with GLN 38 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10E A 6.4 0.2 - - + -
11E A 3.7 17.3 + - + +
12E A 2.8 48.3 + - - -
6F A 4.8 0.5 + - - -
22H GLN* 2.5 38.8 + - + +
23H ASP* 3.9 23.6 - - - +
26H VAL* 3.7 15.6 - - + +
37H THR* 1.3 72.6 - - - +
39H ALA* 1.3 52.8 + - - +
41H VAL* 2.6 8.4 + - - +
42H SER* 2.6 45.0 + - - -
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Residues in contact with ALA 39 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13E T 3.1 28.8 - - + +
4F G 4.4 1.8 - - - +
5F A 3.6 20.0 - - - +
6F A 4.0 5.6 - - - +
37H THR* 3.3 8.7 + - - +
38H GLN* 1.3 85.2 + - - +
40H THR* 1.3 63.7 - - - +
42H SER* 2.9 6.8 + - - -
43H ARG* 2.8 37.3 + - - +
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Residues in contact with THR 40 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3F T 3.3 25.9 + - - +
4F G 3.0 23.5 + - - -
6H ARG* 3.3 35.2 - - - +
36H VAL* 3.9 13.0 - - + -
37H THR* 2.9 6.5 + - - -
39H ALA* 1.3 78.1 - - - +
41H VAL* 1.3 60.4 + - - +
43H ARG* 3.0 19.1 + - - +
44H ASP* 2.8 31.8 + - - +
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Residues in contact with VAL 41 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10H ILE* 4.8 1.3 - - + -
22H GLN* 3.8 17.0 - - + +
25H LEU* 4.0 18.8 - - + -
26H VAL* 3.8 16.8 - - + +
29H LEU* 3.5 30.7 - - + -
36H VAL* 3.8 16.2 - - + -
37H THR 3.0 3.6 + - - -
38H GLN 2.6 13.5 + - - +
40H THR* 1.3 72.7 - - - +
42H SER* 1.3 56.8 + - - +
44H ASP* 3.4 10.2 - - + +
45H ILE* 2.7 48.7 + - + +
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Residues in contact with SER 42 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12E A 2.8 37.9 + - - +
13E T 3.8 6.5 - - - +
22H GLN* 3.4 27.8 + - - +
38H GLN* 2.6 22.4 + - - -
39H ALA* 2.9 10.3 + - - -
41H VAL* 1.3 73.9 - - - +
43H ARG* 1.3 57.4 + - - +
45H ILE* 3.2 3.0 + - - +
46H LYS* 2.9 27.0 + - - +
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Residues in contact with ARG 43 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13E T 4.6 12.9 + - + +
14E T 2.7 26.3 + - - +
15E C 4.1 2.4 - - - +
3F T 3.4 33.5 - - - +
4F G 2.5 48.0 + - - -
5F A 3.5 5.7 - - - +
39H ALA* 2.8 22.5 + - - +
40H THR* 3.5 23.5 + - - +
42H SER* 1.3 68.5 - - - +
44H ASP* 1.3 67.3 + - - +
46H LYS* 3.1 9.1 + - - +
47H GLU* 3.0 36.1 + - - +
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Residues in contact with ASP 44 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6H ARG* 2.7 43.3 + - - -
7H HIS* 2.5 32.1 + - + +
10H ILE* 3.3 26.7 - - + +
40H THR* 2.8 22.5 + - - +
41H VAL* 3.4 10.2 - - - +
43H ARG* 1.3 71.9 - - - +
45H ILE* 1.3 66.4 + - - +
47H GLU* 3.0 11.5 + - - +
48H LEU* 2.8 28.6 + - - +
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Residues in contact with ILE 45 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12E A 5.1 4.5 - - - +
60G TYR* 5.7 1.8 - - - +
10H ILE* 5.3 1.1 - - + -
22H GLN* 3.2 42.0 - - + +
25H LEU* 4.4 10.8 - - + -
41H VAL* 2.7 25.4 + - + +
42H SER* 3.5 4.3 - - - +
44H ASP* 1.3 79.0 - - + +
46H LYS* 1.3 67.5 + - - +
48H LEU* 3.1 5.3 + - - -
49H HIS* 2.9 18.2 + - - -
50H LEU* 3.4 42.7 + - + +
62H TYR* 3.6 25.6 - - + -
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Residues in contact with LYS 46 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12E A 6.2 0.2 - - - +
13E T 4.4 19.1 + - - +
58G GLY* 2.8 40.1 + - - -
60G TYR* 3.4 36.7 + - + +
42H SER* 2.9 13.2 + - - +
43H ARG* 3.1 10.7 + - - +
45H ILE* 1.3 76.8 - - - +
47H GLU* 1.3 63.4 + - + +
49H HIS* 3.1 23.1 + - - +
50H LEU 5.9 0.2 - - - -
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Residues in contact with GLU 47 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3H LYS* 2.8 43.4 + - - +
7H HIS* 3.3 21.1 + - + -
43H ARG* 3.0 27.2 + - + +
44H ASP* 3.6 8.7 - - - +
46H LYS* 1.3 78.3 - - + +
48H LEU* 1.3 62.9 + - - +
49H HIS* 3.4 20.6 + - - -
101H SO4 5.0 5.8 + - - +
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Residues in contact with LEU 48 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7H HIS* 3.5 34.8 - - + +
10H ILE* 3.7 40.8 - - + -
11H ARG* 3.5 38.7 + - + +
44H ASP 2.8 19.0 + - - +
47H GLU* 1.3 77.2 - - - +
49H HIS* 1.3 74.8 + - - +
50H LEU* 3.3 27.3 + - + +
64H LEU* 5.4 1.4 - - - +
101H SO4 3.6 3.6 - - - +
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Residues in contact with HIS 49 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54G PRO* 4.3 25.3 - - + +
60G TYR* 6.2 0.2 - - - -
45H ILE 2.9 5.1 + - - -
46H LYS* 3.1 14.6 + - - +
47H GLU* 3.4 21.4 + - - -
48H LEU* 1.3 82.1 - - - +
50H LEU* 1.3 68.2 + - - +
51H VAL* 3.7 10.7 - - - +
64H LEU* 4.1 9.3 - - - +
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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