Contacts of the helix formed by residues 23 - 31 (chain A) in PDB entry 6V99
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 GLY 23 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21A GLY* 3.4 3.0 - - - -
22A ARG* 1.3 75.1 - - - +
24A SER* 1.3 65.5 + - - +
25A ARG 3.2 3.1 - - - -
26A LEU* 3.0 18.7 + - - +
30A THR* 3.0 14.0 + - - -
35A LYS* 4.0 25.2 - - - +
271A GLY* 5.6 2.0 - - - -
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Residues in contact with SER 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A ARG* 3.5 10.9 - - - +
23A GLY* 1.3 75.5 - - - +
25A ARG* 1.3 63.5 + - - +
27A LYS* 2.9 29.2 + - - +
30A THR* 4.5 2.7 - - - -
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Residues in contact with ARG 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A GLY 3.1 1.2 + - - -
24A SER* 1.3 79.3 - - - +
26A LEU* 1.3 58.7 + - - +
27A LYS* 3.1 36.2 + - - +
271A GLY 3.4 19.5 - - - +
272A THR* 3.7 30.3 - - - +
273A ILE* 4.2 11.4 + - - +
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Residues in contact with LEU 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A GLY* 3.0 14.2 + - - +
25A ARG* 1.3 76.1 - - - +
27A LYS* 1.3 67.3 + - - +
28A GLU 3.3 1.0 + - - -
29A LEU* 3.2 28.9 + - + +
30A THR* 3.8 17.0 - - + +
35A LYS* 3.8 31.0 - - + -
38A VAL* 4.4 13.2 - - + -
46A ILE* 5.6 0.9 - - + -
270A VAL 3.3 25.4 - - - +
271A GLY* 3.8 12.5 + - - +
272A THR 3.8 17.5 - - - +
273A ILE* 3.9 16.2 - - - +
276A TYR* 4.3 12.8 - - + -
409A LEU* 4.4 0.3 - - - +
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Residues in contact with LYS 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A SER 2.9 17.9 + - - +
25A ARG* 3.4 36.2 - - - +
26A LEU* 1.3 73.8 - - - +
28A GLU* 1.3 70.7 + - - +
29A LEU 2.8 8.1 + - - -
30A THR* 2.8 20.3 + - - -
31A ASP* 3.6 11.3 - - - +
273A ILE* 4.2 8.3 - - + -
401A ARG* 3.8 34.6 - - - +
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Residues in contact with GLU 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A LEU 3.3 1.0 + - - -
27A LYS* 1.3 77.6 - - - +
29A LEU* 1.3 61.5 + - - +
30A THR 3.2 0.6 + - - -
31A ASP* 3.4 35.3 + - + +
32A ARG* 4.9 0.9 + - - +
378A ASP* 5.1 3.2 - - - +
401A ARG* 2.7 55.4 + - - +
409A LEU* 3.7 7.9 - - + +
411A THR* 3.6 30.8 + - + +
413A SER* 6.4 1.6 - - - -
414A MET* 3.9 17.2 - - + +
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Residues in contact with LEU 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A LEU* 3.2 29.0 + - + +
27A LYS 2.8 1.2 + - - -
28A GLU* 1.3 77.8 - - - +
30A THR* 1.3 60.5 + - + +
31A ASP 3.5 0.4 + - - -
32A ARG 5.0 0.5 + - - -
33A ARG* 3.4 31.5 + - - +
38A VAL* 4.5 13.3 - - + +
273A ILE* 5.4 5.6 - - + -
276A TYR* 3.8 39.7 - - + -
361A LEU* 4.3 14.6 - - + -
376A VAL* 4.4 2.5 - - + -
378A ASP* 3.4 26.2 - - + +
409A LEU* 3.7 31.2 - - + +
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Residues in contact with THR 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A ARG* 3.3 23.5 + - - +
23A GLY 3.0 17.3 + - - -
24A SER* 4.5 2.8 - - - -
26A LEU* 3.8 20.4 - - + +
27A LYS 2.8 13.2 + - - -
29A LEU* 1.3 78.8 - - - +
31A ASP* 1.3 64.0 + - - +
32A ARG 3.4 0.7 - - - -
33A ARG 3.0 26.0 + - - +
35A LYS* 3.7 20.9 - - - +
38A VAL* 3.9 6.1 - - + -
69A LYS* 5.0 2.3 - - - +
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Residues in contact with ASP 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A LYS* 3.6 10.7 - - - +
28A GLU* 3.4 39.4 + - - +
29A LEU 3.5 0.2 - - - -
30A THR* 1.3 79.0 - - - +
32A ARG* 1.3 71.6 + - + +
69A LYS* 2.9 20.3 + - - -
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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