Contacts of the helix formed by residues 22 - 29 (chain K) in PDB entry 5OGC
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 22 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21K GLU* 1.3 72.9 - - - +
23K THR* 1.3 98.7 + - - +
24K LYS* 3.1 12.2 + - - +
25K GLU* 2.8 40.3 + - + +
26K LYS* 2.7 24.8 + - - +
118K GLY* 5.6 7.5 - - - -
119K LYS* 3.5 12.6 - - - +
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Residues in contact with THR 23 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21K GLU 3.9 1.4 + - - -
22K ASN* 1.3 86.9 + - - +
24K LYS* 1.3 68.9 + - + +
26K LYS* 3.8 9.4 + - - +
27K ALA* 3.3 22.1 + - + +
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Residues in contact with LYS 24 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22K ASN* 2.9 10.9 + - - +
23K THR* 1.3 87.4 - - + +
25K GLU* 1.3 61.2 + - + +
27K ALA* 3.5 12.2 + - - +
28K ALA* 3.2 27.3 + - - +
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Residues in contact with GLU 25 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21K GLU* 3.0 12.3 - - - +
22K ASN* 2.8 52.2 + - + +
24K LYS* 1.3 70.1 - - + +
26K LYS* 1.3 57.9 + - - +
28K ALA* 4.0 3.3 - - - +
29K GLY* 2.9 28.4 + - - -
117K ALA 5.0 2.1 - - - +
118K GLY* 5.5 1.2 - - - -
119K LYS* 3.9 2.2 + - - -
333K SER* 3.2 12.5 + - - -
335K SER* 3.1 41.1 + - - +
337K VAL* 5.5 5.1 - - + +
338K PHE* 3.2 18.7 - - - -
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Residues in contact with LYS 26 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20K PRO* 4.1 12.9 - - - +
21K GLU* 3.2 56.1 + - + +
22K ASN 2.7 14.6 + - - +
23K THR* 3.8 8.1 - - - +
25K GLU* 1.3 74.5 - - - +
27K ALA* 1.3 60.9 + - - +
28K ALA 4.3 0.3 - - - -
29K GLY* 4.2 6.2 + - - -
82K GLU* 4.2 8.9 + - - -
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Residues in contact with ALA 27 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23K THR* 3.3 16.8 + - + +
24K LYS* 3.8 16.2 - - + +
25K GLU 3.4 0.2 - - - -
26K LYS* 1.3 78.7 - - - +
28K ALA* 1.3 65.7 + - - +
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Residues in contact with ALA 28 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24K LYS* 3.2 20.5 + - - +
25K GLU* 4.0 3.8 - - - +
26K LYS 4.3 0.6 - - - +
27K ALA* 1.3 79.5 - - - +
29K GLY* 1.3 66.9 + - - +
30K PHE* 3.8 27.6 - - + -
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Residues in contact with GLY 29 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21K GLU* 4.8 6.7 - - - -
25K GLU 2.9 20.5 + - - -
26K LYS 4.6 4.7 - - - -
27K ALA 3.9 0.4 - - - -
28K ALA* 1.3 79.1 - - - +
30K PHE* 1.3 65.1 + - - +
32K LYS* 5.7 3.4 - - - -
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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