Contacts of the helix formed by residues 21 - 32 (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 21 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10E A 3.8 37.3 + - - +
11E A 3.6 11.2 - - - -
19H ILE* 3.4 6.7 - - - +
20H GLU* 1.3 102.9 - - + +
22H GLN* 1.3 60.8 + - - +
23H ASP* 3.6 8.8 + - - +
24H GLU* 3.0 34.6 + - - +
25H LEU 3.0 21.5 + - - -
52H LYS* 4.9 1.6 - - - +
62H TYR* 4.0 5.6 - - - -
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Residues in contact with GLN 22 (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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11E A 2.8 34.5 + - - +
12E A 2.8 25.8 + - - -
21H THR* 1.3 67.0 - - - +
23H ASP* 1.3 69.0 + - - +
24H GLU 3.0 1.3 - - - -
25H LEU* 2.9 8.5 + - - +
26H VAL* 2.8 29.1 + - - +
38H GLN* 2.5 43.6 + - + -
41H VAL* 3.8 9.6 - - + -
42H SER* 3.4 10.1 - - - +
45H ILE* 3.2 33.7 - - + +
62H TYR* 3.3 12.9 + - - +
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Residues in contact with ASP 23 (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 4.7 17.1 + - + +
11E A 4.2 1.8 + - - -
21H THR* 3.3 9.7 + - - +
22H GLN* 1.3 77.7 - - - +
24H GLU* 1.3 62.1 + - + +
26H VAL* 3.5 9.4 - - - +
27H ASP* 3.2 30.1 + - - +
38H GLN* 3.9 22.4 - - - +
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Residues in contact with GLU 24 (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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18H GLU 4.2 4.0 - - - +
19H ILE* 4.0 12.3 - - + +
20H GLU* 3.0 36.6 + - - +
21H THR* 3.0 32.5 + - - +
22H GLN 3.0 0.8 - - - -
23H ASP* 1.3 76.1 - - + +
25H LEU* 1.3 67.1 + - - +
27H ASP* 3.1 10.6 + - - +
28H MET* 2.9 26.5 + - + +
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Residues in contact with LEU 25 (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* 3.7 27.4 - - + -
13H ILE* 3.7 40.8 - - + -
14H ILE* 3.8 12.8 - - + -
19H ILE* 4.0 13.8 - - + +
21H THR 3.0 11.0 + - - +
22H GLN* 2.9 9.0 + - - +
24H GLU* 1.3 74.3 - - - +
26H VAL* 1.3 65.4 + - - +
28H MET* 2.8 7.5 + - - +
29H LEU* 2.7 36.1 + - + +
41H VAL* 4.0 20.0 - - + -
45H ILE* 4.4 13.5 - - + -
62H TYR* 5.7 0.9 - - + -
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Residues in contact with VAL 26 (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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22H GLN 2.8 21.9 + - - +
23H ASP* 3.5 10.3 - - - +
25H LEU* 1.3 72.3 - - - +
27H ASP* 1.3 67.9 + - - +
29H LEU* 3.0 11.8 + - - +
30H LYS* 2.8 38.0 + - + +
34H TYR 4.6 0.2 - - - +
36H VAL 3.5 19.0 - - - +
37H THR* 3.9 4.3 - - - -
38H GLN* 3.7 32.5 - - + +
41H VAL* 3.8 16.1 - - + +
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Residues in contact with ASP 27 (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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23H ASP* 3.2 18.6 - - - +
24H GLU* 3.1 10.7 + - - +
25H LEU 3.1 1.2 - - - -
26H VAL* 1.3 79.5 - - - +
28H MET* 1.3 69.7 + - + +
30H LYS* 2.8 21.5 + - - +
31H GLN* 3.0 26.1 + - + +
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Residues in contact with MET 28 (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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13H ILE* 3.8 20.2 - - + -
17H ASN* 4.1 24.9 - - - +
19H ILE* 3.7 26.2 - - + -
24H GLU* 2.9 16.0 + - + +
25H LEU 2.8 11.1 + - - +
27H ASP* 1.3 72.6 - - + +
29H LEU* 1.3 60.7 + - - +
31H GLN* 3.4 26.1 + - - +
32H ASP* 3.1 44.1 + - - +
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Residues in contact with LEU 29 (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* 4.3 13.5 - - + -
9H LYS* 4.1 19.5 - - + -
10H ILE* 3.9 23.1 - - + -
13H ILE* 3.6 24.7 - - + -
25H LEU* 2.7 23.0 + - + +
26H VAL* 3.3 8.3 - - - +
28H MET* 1.3 70.9 - - - +
30H LYS* 1.3 63.8 + - - +
32H ASP* 3.2 3.7 + - - -
33H GLY 3.2 4.7 + - - -
34H TYR* 2.8 41.5 + - + +
36H VAL* 3.9 10.8 - - + -
41H VAL* 3.5 31.9 - - + -
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Residues in contact with LYS 30 (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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26H VAL* 2.8 31.5 + - + +
27H ASP* 2.8 19.5 + - - +
29H LEU* 1.3 70.7 - - - +
31H GLN* 1.3 55.9 - - + +
33H GLY* 2.8 27.4 + - - -
34H TYR 3.3 12.5 + - - +
35H LYS* 4.0 37.7 - - + +
36H VAL 4.0 15.7 - - - +
37H THR* 6.4 0.2 - - - -
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Residues in contact with GLN 31 (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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27H ASP* 3.0 24.4 + - + +
28H MET* 3.6 33.4 + - + +
30H LYS* 1.3 78.1 - - + +
32H ASP* 1.3 61.5 + - - +
33H GLY 3.3 3.1 + - - -
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Residues in contact with ASP 32 (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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9H LYS* 3.5 43.3 + - + -
13H ILE* 4.2 8.2 - - + +
28H MET* 3.1 31.4 + - - +
29H LEU* 3.2 4.2 + - - +
30H LYS 3.0 1.6 + - - -
31H GLN* 1.3 81.0 - - - +
33H GLY* 1.3 56.5 + - - +
34H TYR* 3.5 18.3 - - + -
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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