Contacts of the helix formed by residues 21 - 26 (chain V) 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 V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33N LEU 5.5 0.8 + - - -
34N GLU* 3.6 8.4 + - - -
36N ASP* 2.8 35.0 + - - -
20V PRO* 1.3 73.0 - - - +
22V ARG* 1.3 57.8 + - - +
23V LEU 3.1 2.0 - - - -
24V PHE* 2.8 20.8 + - - +
25V ASP* 3.0 11.1 + - - +
38V PHE 3.7 2.1 + - - -
39V PRO* 2.6 35.6 + - - +
40V THR* 2.6 16.0 + - - -
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Residues in contact with ARG 22 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34N GLU* 3.2 31.4 + - - +
35N SER* 4.5 5.6 - - - +
1U MET* 4.5 14.4 - - - +
2U ASP* 4.8 1.8 + - - -
17V PHE* 4.0 22.0 - - + -
19V SER* 2.9 28.1 + - - +
21V SER* 1.3 74.1 - - - +
23V LEU* 1.3 57.7 + - + +
25V ASP* 2.7 33.5 + - - -
26V GLN* 2.7 74.3 + - + +
30V GLU* 2.7 32.5 + - - +
31V HIS* 3.6 4.0 - - - +
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Residues in contact with LEU 23 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13V PRO 3.5 20.0 - - - +
14V PHE* 3.6 31.1 - - + +
16V PRO* 3.8 18.2 - - + +
17V PHE* 3.4 46.7 - - + -
19V SER 4.2 1.5 + - - +
21V SER 3.1 1.0 + - - -
22V ARG* 1.3 77.3 - - + +
24V PHE* 1.3 56.3 + - - +
26V GLN* 5.9 0.2 - - + -
27V PHE* 3.1 38.6 - - + +
49V LEU* 4.3 0.2 - - - +
54V PHE* 3.2 19.9 - - + -
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Residues in contact with PHE 24 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14V PHE* 3.8 24.6 - + + -
21V SER 2.8 4.8 + - - +
23V LEU* 1.3 75.4 - - - +
25V ASP* 1.3 65.7 + - - +
26V GLN 3.4 0.4 - - - -
27V PHE* 3.0 14.7 + - - +
28V PHE* 3.0 59.5 + + + +
38V PHE* 3.5 36.6 - + + +
40V THR* 3.0 23.3 - - - +
44V LEU* 3.0 42.4 - - + -
46V PRO 3.6 12.6 - - - -
47V PHE* 5.4 2.0 - + - -
49V LEU* 4.0 13.1 - - + +
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Residues in contact with ASP 25 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34N GLU* 3.2 27.1 - - + +
21V SER* 3.0 14.4 + - - +
22V ARG* 2.7 37.9 + - - +
24V PHE* 1.3 81.4 - - + +
26V GLN* 1.3 56.0 + - - +
28V PHE 3.2 1.6 + - - -
29V GLY 3.1 30.1 + - - +
30V GLU* 3.5 0.3 - - - -
31V HIS* 2.9 17.5 + - - -
32V LEU 4.1 0.2 + - - -
33V LEU* 4.9 2.1 - - - +
37V LEU* 3.1 34.3 - - + +
38V PHE 5.0 3.6 + - - +
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Residues in contact with GLN 26 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22V ARG* 2.7 59.2 + - + +
23V LEU* 5.9 0.7 - - + -
25V ASP* 1.3 73.9 + - - +
27V PHE* 1.3 73.9 + - + +
29V GLY 3.1 19.4 + - - +
30V GLU* 3.6 8.2 - - - +
51V PRO* 4.9 5.2 - - - +
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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