Contacts of the helix formed by residues 24 - 32 (chain G) in PDB entry 2P5V
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 24 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22G ARG 3.8 3.0 + - - +
23G LEU* 1.3 78.3 - - - +
25G ASN* 1.3 60.7 + - - +
26G VAL* 3.0 27.8 - - + +
27G GLU* 3.2 25.9 + - - +
28G LEU* 2.9 24.7 + - - +
22H ARG* 5.1 1.3 - - - +
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Residues in contact with ASN 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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24G THR* 1.3 74.5 - - - +
26G VAL* 1.3 54.6 + - + +
28G LEU* 3.3 9.2 + - - +
29G SER* 2.8 38.2 + - - -
36G PRO* 2.7 46.2 + - - +
39G CYS* 3.7 9.4 - - - +
40G LEU* 3.4 48.7 + - + +
43G LEU* 5.0 3.0 - - - +
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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
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24G THR* 3.0 24.7 - - + +
25G ASN* 1.3 78.7 - - + +
27G GLU* 1.3 62.0 + - + +
29G SER* 2.8 19.7 + - - -
30G GLU* 3.2 14.0 + - - +
36G PRO* 4.6 18.6 - - + -
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Residues in contact with GLU 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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22G ARG 4.2 2.4 - - - +
23G LEU* 3.1 33.2 - - + +
24G THR* 3.2 36.3 + - - +
25G ASN 3.3 0.4 - - - -
26G VAL* 1.3 78.8 - - + +
28G LEU* 1.3 66.0 + - - +
30G GLU* 3.0 17.0 + - - +
31G ARG* 3.1 33.1 + - - +
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Residues in contact with LEU 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* 4.2 13.7 - - + -
16G VAL* 3.7 26.0 - - + -
17G LEU* 3.9 25.6 - - + -
23G LEU* 4.2 13.2 - - + +
24G THR 2.9 18.8 + - - +
25G ASN* 3.7 7.2 - - - +
27G GLU* 1.3 75.9 - - - +
29G SER* 1.3 61.8 + - - +
31G ARG* 3.2 8.6 + - - +
32G VAL* 3.2 34.4 - - + +
39G CYS* 3.8 20.6 - - - -
43G LEU* 3.7 30.7 - - + -
22H ARG* 5.3 1.3 - - - +
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Residues in contact with SER 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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25G ASN 2.8 18.7 + - - -
26G VAL* 2.8 26.2 + - - -
28G LEU* 1.3 72.2 - - - +
30G GLU* 1.3 60.7 + - - +
32G VAL* 3.4 1.6 + - - +
33G ALA* 3.2 5.5 + - - -
34G LEU* 3.0 45.4 + - - +
36G PRO* 4.0 16.6 - - - +
39G CYS* 3.7 26.7 - - - -
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Residues in contact with GLU 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 3.4 11.1 - - - +
27G GLU* 3.0 13.5 + - - +
29G SER* 1.3 81.1 + - - +
31G ARG* 1.3 70.5 - - - +
32G VAL 3.4 0.4 + - - -
33G ALA* 4.0 6.4 + - - +
34G LEU 5.5 1.2 - - - +
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Residues in contact with ARG 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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12G LYS* 3.6 21.0 - - - -
16G VAL* 4.3 19.3 - - + -
20G ASN* 5.7 4.3 - - - +
23G LEU* 3.6 38.7 - - + +
27G GLU* 3.1 37.3 + - - +
28G LEU* 3.2 8.6 + - - +
30G GLU* 1.3 88.0 - - - +
32G VAL* 1.3 60.3 + - - +
33G ALA 3.5 0.7 - - - -
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Residues in contact with VAL 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 THR* 3.8 25.3 - - - +
12G LYS* 4.0 21.8 - - + +
13G ILE* 3.7 38.6 - - + -
16G VAL* 4.4 5.2 - - + -
28G LEU* 3.2 28.5 + - + +
29G SER* 3.4 3.8 + - - +
31G ARG* 1.3 80.5 - - - +
33G ALA* 1.3 71.7 + - - +
34G LEU* 3.2 13.6 + - + +
39G CYS* 5.5 0.4 - - - -
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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