Contacts of the helix formed by residues 25 - 29 (chain B) in PDB entry 1TVK
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 25 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B TRP 2.6 27.0 + - - -
22B GLU* 3.2 14.4 - - - -
24B ILE* 1.3 78.2 - - - +
26B ASP* 1.3 63.7 + - - -
27B GLU 3.1 0.7 - - - -
28B HIS* 2.6 30.7 + - - +
29B GLY 3.1 7.3 + - - -
30B ILE* 3.4 14.9 + - - +
51B TYR* 3.3 15.3 - - - -
81B PHE* 3.4 24.8 - - - -
84B ILE* 6.1 2.5 - - - -
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Residues in contact with ASP 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B GLU 4.3 10.3 - - - +
23B VAL* 3.6 6.2 + - - +
25B SER* 1.3 83.0 + - - +
27B GLU* 1.3 59.9 + - - +
28B HIS 2.8 1.7 + - - -
29B GLY* 2.7 24.9 + - - +
30B ILE 4.6 4.0 - - - +
39B ASP* 5.6 0.9 - - - +
43B GLN* 4.1 1.6 + - - -
81B PHE* 5.0 4.4 - - + -
359B ARG* 3.7 20.8 - - - +
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Residues in contact with GLU 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B VAL* 2.9 20.6 + - + +
24B ILE* 3.6 16.1 - - - +
25B SER 3.1 0.2 + - - -
26B ASP* 1.3 80.0 + - - +
28B HIS* 1.3 63.7 + - + +
43B GLN* 3.2 20.0 + - - +
234B SER* 2.9 23.1 + - - -
238B THR* 4.3 7.4 + - - -
239B CYS* 4.9 2.5 - - - +
242B PHE* 4.9 11.9 - - + -
318B ARG* 2.6 45.4 + - - +
357B PRO 5.6 1.1 - - - +
358B PRO* 4.7 11.1 - - + +
359B ARG* 4.9 11.8 - - + +
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Residues in contact with HIS 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B ILE* 3.1 21.8 - - + +
25B SER 2.6 15.5 + - - +
27B GLU* 1.3 78.9 + - + +
29B GLY* 1.3 65.2 + - - +
30B ILE* 3.3 19.8 - - + +
36B TYR* 3.4 14.9 - - - -
43B GLN* 2.6 44.4 + - - +
44B LEU 4.6 0.2 - - - -
46B ARG* 5.3 3.1 + - + -
47B ILE* 3.4 31.3 - - + +
50B TYR* 6.1 1.9 - + - +
51B TYR* 4.4 7.6 - + - -
238B THR* 4.2 19.0 + - - -
242B PHE* 4.0 25.7 - + - -
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Residues in contact with GLY 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B ASP* 2.7 16.5 + - - -
28B HIS* 1.3 80.5 - - - +
30B ILE* 1.3 59.8 + - - +
31B ASP* 4.0 2.0 - - - -
35B SER 3.2 1.2 - - - +
36B TYR 3.6 0.2 - - - -
37B HIS* 3.0 33.3 + - - +
38B GLY* 3.5 9.9 + - - -
39B ASP* 5.0 5.6 - - - -
43B GLN* 3.0 8.6 - - - +
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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