Contacts of the helix formed by residues 21 - 26 (chain T) in PDB entry 2YGD
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 SER 21 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33L LEU 5.7 0.2 - - - -
34L GLU* 3.6 17.5 + - - -
36L ASP* 4.1 15.0 - - - -
19T SER* 3.0 2.1 + - - -
20T PRO* 1.3 80.1 - - - +
22T ARG* 1.3 60.9 + - - +
23T LEU 3.1 2.0 - - - -
24T PHE* 2.9 21.4 + - - +
25T ASP* 3.1 11.9 + - - +
38T PHE 3.9 1.6 + - - -
39T PRO* 2.6 35.3 + - - +
40T THR* 2.7 15.5 + - - -
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Residues in contact with ARG 22 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34L GLU* 3.6 16.7 + - - +
35L SER* 5.4 2.5 - - - +
1S MET* 4.5 14.6 - - - +
2S ASP* 4.8 2.0 + - - -
17T PHE* 4.0 22.2 - - + -
19T SER* 2.9 26.2 + - - +
21T SER* 1.3 75.7 - - - +
23T LEU* 1.3 57.4 + - + +
25T ASP* 2.7 36.9 + - - -
26T GLN* 2.7 75.9 + - + +
30T GLU* 2.7 31.7 + - - +
31T HIS* 3.5 11.3 - - - +
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Residues in contact with LEU 23 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13T PRO 3.5 23.3 - - - +
14T PHE* 3.7 26.7 - - - +
16T PRO* 3.8 17.5 - - + +
17T PHE* 3.4 46.2 - - + -
19T SER 4.3 1.6 - - - +
21T SER* 3.1 1.6 - - - +
22T ARG* 1.3 77.9 - - + +
24T PHE* 1.3 57.3 + - - +
26T GLN* 5.9 0.2 - - + -
27T PHE* 3.1 38.1 - - + +
49T LEU* 4.3 0.2 - - - +
54T PHE* 3.3 19.5 - - + -
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Residues in contact with PHE 24 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14T PHE* 3.8 24.4 - + + -
21T SER 2.9 4.6 + - - +
23T LEU* 1.3 76.7 - - - +
25T ASP* 1.3 65.5 + - - +
27T PHE* 2.9 14.4 + - - +
28T PHE* 3.0 60.2 + + + +
38T PHE* 3.5 37.0 - + + +
40T THR* 3.1 23.6 - - - +
44T LEU* 3.0 42.0 - - + -
46T PRO 3.6 12.6 - - - -
47T PHE* 5.4 2.0 - + - -
49T LEU* 4.0 12.5 - - + +
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Residues in contact with ASP 25 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34L GLU* 3.7 21.0 - - + +
21T SER* 3.1 13.2 + - - +
22T ARG* 2.7 42.2 + - - +
24T PHE* 1.3 83.8 - - - +
26T GLN* 1.3 57.1 + - - +
27T PHE 3.3 0.2 + - - -
28T PHE 3.4 0.3 + - - -
29T GLY 3.1 18.7 + - - +
31T HIS* 2.8 26.3 + - - -
33T LEU* 4.5 3.5 - - - +
37T LEU* 3.1 37.3 - - + +
38T PHE 5.2 3.8 - - - +
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Residues in contact with GLN 26 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22T ARG* 2.7 60.0 + - + +
23T LEU* 5.9 0.7 - - + -
25T ASP* 1.3 74.8 + - - +
27T PHE* 1.3 73.0 + - + +
29T GLY 3.0 19.5 + - - +
30T GLU* 3.5 8.8 - - - +
51T PRO* 4.9 4.7 - - - +
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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