Contacts of the helix formed by residues 21 - 32 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10F T 3.7 38.1 - - - +
11F T 3.6 11.0 - - - -
19G ILE* 3.4 6.8 - - - +
20G GLU* 1.3 93.1 - - + +
22G GLN* 1.3 66.0 + - - +
23G ASP* 3.5 9.8 + - - +
24G GLU* 2.9 41.3 + - - +
25G LEU 3.2 8.3 + - - -
52G LYS* 5.2 0.4 - - - +
62G TYR* 4.1 4.3 - - - -
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Residues in contact with GLN 22 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11F T 2.7 29.8 + - - +
12F A 2.9 23.0 + - - -
21G THR* 1.3 73.1 - - - +
23G ASP* 1.3 51.9 + - - +
25G LEU* 3.0 7.1 + - - +
26G VAL* 2.7 38.7 + - - +
38G GLN* 2.7 41.1 + - + -
41G VAL* 3.6 14.9 - - + +
42G SER* 3.3 17.6 + - - +
45G ILE* 3.8 22.6 - - + +
62G TYR* 3.2 25.1 + - - +
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Residues in contact with ASP 23 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10F T 4.8 11.8 + - - +
11F T 4.3 12.4 + - - +
21G THR* 3.1 9.3 + - - +
22G GLN* 1.3 78.6 - - - +
24G GLU* 1.3 55.8 + - - +
26G VAL* 3.1 10.4 + - - +
27G ASP* 2.7 37.8 + - - +
38G GLN* 4.0 22.2 - - - +
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Residues in contact with GLU 24 (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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18G GLU 3.4 11.4 - - - +
19G ILE* 3.5 11.5 - - + +
20G GLU* 2.8 39.7 + - - +
21G THR* 2.9 28.1 + - - +
23G ASP* 1.3 75.0 - - - +
25G LEU* 1.3 53.2 + - - +
27G ASP* 3.0 10.4 + - + +
28G MET* 2.7 41.6 + - + +
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Residues in contact with LEU 25 (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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10G ILE* 3.7 37.0 - - + -
13G ILE* 3.9 38.6 - - + -
14G ILE* 4.4 9.9 - - + -
19G ILE* 3.8 16.3 - - + +
21G THR 3.2 3.1 + - - +
22G GLN* 3.0 10.4 + - - +
24G GLU* 1.3 75.7 - - - +
26G VAL* 1.3 61.5 + - - +
28G MET* 4.2 1.6 - - + -
29G LEU* 2.8 44.0 + - + +
41G VAL* 3.9 22.0 - - + -
45G ILE* 4.0 16.2 - - + -
50G LEU* 5.1 0.4 - - + -
62G TYR* 5.8 0.2 - - + -
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Residues in contact with VAL 26 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22G GLN 2.7 21.6 + - - +
23G ASP* 3.3 13.2 - - - +
25G LEU* 1.3 76.3 - - - +
27G ASP* 1.3 66.8 + - - +
29G LEU* 2.9 15.0 + - - +
30G LYS* 2.9 35.3 + - + +
36G VAL* 3.5 22.9 - - + +
37G THR* 4.2 3.1 - - - -
38G GLN* 3.9 22.9 - - - +
41G VAL* 3.4 24.0 - - + -
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Residues in contact with ASP 27 (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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23G ASP* 2.7 25.1 + - - +
24G GLU* 3.5 13.3 - - + +
26G VAL* 1.3 76.4 - - - +
28G MET* 1.3 61.5 + - + +
30G LYS* 4.2 7.2 - - - +
31G GLN* 3.4 29.1 + - - +
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Residues in contact with MET 28 (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 ILE* 3.8 28.5 - - + -
17G ASN* 4.2 21.5 - - - +
19G ILE* 4.0 21.5 - - + -
24G GLU* 2.7 23.1 + - + +
25G LEU 3.7 4.3 - - - +
27G ASP* 1.3 73.8 - - + +
29G LEU* 1.3 66.9 + - - +
30G LYS 3.2 0.2 - - - -
31G GLN* 3.0 21.2 + - + +
32G ASP* 2.9 43.7 + - - +
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Residues in contact with LEU 29 (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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6G ARG* 4.1 10.8 - - + -
9G LYS* 4.3 17.9 - - + -
10G ILE* 3.8 35.4 - - + -
13G ILE* 3.5 20.6 - - + -
25G LEU* 2.8 32.4 + - + +
26G VAL* 2.9 3.6 + - - +
28G MET* 1.3 72.2 - - - +
30G LYS* 1.3 53.5 + - - +
32G ASP* 3.0 4.1 + - - +
33G GLY 2.9 10.6 + - - -
34G TYR* 2.7 50.5 + - + +
36G VAL* 4.0 22.7 - - + -
41G VAL* 4.1 8.7 - - + -
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Residues in contact with LYS 30 (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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26G VAL* 2.9 33.8 + - + +
27G ASP* 4.3 7.4 - - - +
29G LEU* 1.3 75.6 - - + +
31G GLN* 1.3 59.5 + - + +
33G GLY* 3.1 16.5 + - - -
34G TYR 3.3 16.4 - - - +
35G LYS* 4.4 23.0 - - + +
36G VAL* 3.3 28.1 + - + +
37G THR* 5.2 5.9 - - - +
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Residues in contact with GLN 31 (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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27G ASP* 3.4 16.4 + - - +
28G MET* 3.0 25.4 + - + +
30G LYS* 1.3 77.8 - - + +
32G ASP* 1.3 64.8 + - - +
33G GLY 3.2 1.2 + - - -
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Residues in contact with ASP 32 (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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9G LYS* 3.8 36.1 + - + +
13G ILE* 3.9 12.0 - - + +
28G MET* 2.9 33.2 + - - +
29G LEU* 3.0 8.2 + - - +
31G GLN* 1.3 80.7 - - - +
33G GLY* 1.3 57.8 + - - +
34G TYR* 3.5 15.2 - - + -
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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