Contacts of the helix formed by residues 30 - 36 (chain C) in PDB entry 2VK1
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 ASN 30 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25C LEU 3.3 22.6 + - - -
26C PRO* 3.4 7.2 - - - +
27C GLY* 2.8 30.7 + - - +
29C PHE* 1.3 80.5 - - - +
31C LEU* 1.3 64.1 + - - +
32C SER 3.3 2.7 - - - -
33C LEU* 3.0 13.6 + - + +
34C LEU* 2.9 27.4 + - - +
71C ILE* 3.7 22.1 - - + +
72C THR 3.2 23.4 + - - -
73C THR* 3.8 2.3 - - - +
100C GLY* 4.1 14.1 - - - -
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Residues in contact with LEU 31 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26C PRO* 3.5 29.8 - - + -
27C GLY 3.2 21.1 - - - +
28C ALA* 3.6 14.5 + - - +
30C ASN* 1.3 78.4 + - - +
32C SER* 1.3 61.7 + - - +
34C LEU* 3.2 4.4 + - + +
35C ASP* 3.1 18.2 + - - +
477D GLU* 4.0 17.3 - - + +
480D ILE* 4.0 18.6 - - + -
481D HIS* 3.7 46.4 - - + +
487D TYR* 3.5 25.4 + - + +
488D ASN* 4.3 1.8 - - - +
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Residues in contact with SER 32 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28C ALA 5.0 1.4 + - - -
29C PHE 5.6 0.2 - - - -
30C ASN 3.3 0.6 - - - -
31C LEU* 1.3 79.3 - - - +
33C LEU* 1.3 62.1 + - - +
35C ASP* 3.4 10.4 + - - +
36C LYS* 2.9 25.9 + - - -
169C ALA* 5.1 4.3 - - - -
172C VAL* 4.1 7.2 - - - -
173C ASP* 2.5 35.7 + - - -
481D HIS* 4.2 19.0 + - - -
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Residues in contact with LEU 33 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7C GLY* 3.5 30.3 - - - -
10C LEU* 4.2 5.2 - - + -
11C PHE* 3.3 33.3 - - + -
30C ASN* 3.0 17.5 + - + +
32C SER* 1.3 80.1 - - - +
34C LEU* 1.3 63.1 + - - +
36C LYS* 3.0 16.0 + - - +
71C ILE* 4.0 28.9 - - + -
98C VAL* 4.1 10.5 - - + -
100C GLY* 5.6 3.4 - - - -
167C LEU* 3.9 31.0 - - + -
172C VAL* 3.9 21.2 - - + +
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Residues in contact with LEU 34 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26C PRO* 3.7 23.8 - - + -
30C ASN* 2.9 33.2 + - - +
31C LEU* 3.2 5.6 + - - +
33C LEU* 1.3 76.2 - - + +
35C ASP* 1.3 63.0 + - - +
36C LYS 3.0 1.2 + - - -
37C ILE* 3.0 29.7 + - + +
38C TYR* 4.0 6.8 - - - -
45C TRP* 3.5 44.0 - - + -
71C ILE* 3.9 28.3 - - + -
487D TYR* 3.6 27.4 - - + -
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Residues in contact with ASP 35 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31C LEU 3.1 10.2 + - - -
32C SER* 3.4 12.5 + - - +
33C LEU 3.2 0.2 - - - -
34C LEU* 1.3 75.8 - - - +
36C LYS* 1.3 69.1 + - - +
38C TYR* 3.2 29.0 + - - +
39C GLU* 3.8 12.5 + - - +
481D HIS* 2.6 32.0 + - - -
482D GLY* 5.2 1.2 - - - -
485D ALA* 4.7 3.1 - - - +
487D TYR* 2.6 29.8 + - - -
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Residues in contact with LYS 36 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5C THR* 3.3 30.7 - - + +
7C GLY* 3.8 6.5 - - - -
8C LYS* 3.7 24.2 - - + +
11C PHE* 3.8 10.3 - - + -
32C SER* 2.9 27.5 + - - +
33C LEU 3.0 15.7 + - - +
35C ASP* 1.3 82.7 + - - +
37C ILE* 1.3 65.1 + - - +
39C GLU* 3.0 40.5 + - - +
40C VAL* 3.6 12.0 + - - +
172C VAL* 4.2 6.7 - - - -
173C ASP* 2.9 28.9 + - - -
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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