Contacts of the helix formed by residues 19 - 33 (chain p) in PDB entry 6AH0
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 LYS 19 (chain p).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154H C 4.2 19.9 + - - -
170H C 5.7 0.7 - - - -
17p LYS 3.6 3.4 + - - -
18p ILE* 1.3 73.7 - - - +
20p LYS* 1.3 64.8 + - - +
21p GLU 3.4 2.7 - - - -
22p GLU* 3.2 6.3 + - - +
23p LEU* 2.9 20.3 + - - -
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Residues in contact with LYS 20 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170H C 4.5 16.1 + - - -
18p ILE 3.5 2.0 + - - -
19p LYS* 1.3 69.9 - - - +
21p GLU* 1.3 56.5 + - - +
23p LEU* 3.4 2.0 + - - +
24p LYS* 3.1 24.8 + - - -
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Residues in contact with GLU 21 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19p LYS 3.4 0.8 - - - -
20p LYS* 1.3 72.5 - - - +
22p GLU* 1.3 59.7 + - - +
24p LYS* 4.1 0.8 - - - +
25p ARG* 3.1 21.8 + - - -
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Residues in contact with GLU 22 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19p LYS* 3.2 7.9 + - - +
21p GLU* 1.3 73.2 - - - +
23p LEU* 1.3 60.1 + - - +
25p ARG* 3.2 2.2 + - - +
26p SER* 2.9 26.0 + - - -
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Residues in contact with LEU 23 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18p ILE* 5.2 5.0 - - - +
19p LYS 2.9 15.8 + - - +
20p LYS* 3.4 2.4 + - - +
22p GLU* 1.3 73.4 - - - +
24p LYS* 1.3 58.5 + - - +
26p SER* 3.3 1.7 + - - +
27p LEU* 2.9 27.9 + - - -
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Residues in contact with LYS 24 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19o VAL* 6.4 1.6 - - - -
20p LYS 3.1 15.2 + - - -
21p GLU* 4.2 1.8 - - - +
23p LEU* 1.3 75.3 - - - +
25p ARG* 1.3 56.4 + - - +
27p LEU* 3.3 1.7 + - - +
28p TYR* 2.9 24.9 + - - -
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Residues in contact with ARG 25 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19o VAL* 6.3 3.6 - - - +
21p GLU 3.1 16.7 + - - -
22p GLU* 3.2 3.7 + - - +
24p LYS* 1.3 73.0 - - - +
26p SER* 1.3 62.2 + - - +
28p TYR* 3.5 1.8 + - - +
29p ALA* 3.2 17.5 + - - -
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Residues in contact with SER 26 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22p GLU 2.9 15.5 + - - -
23p LEU* 3.9 1.3 - - - +
25p ARG* 1.3 74.2 - - - +
27p LEU* 1.3 59.7 + - - +
29p ALA* 3.2 1.6 + - - +
30p LEU* 2.8 28.6 + - - -
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Residues in contact with LEU 27 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23p LEU 2.9 16.4 + - - -
24p LYS* 3.7 2.5 - - - +
26p SER* 1.3 77.5 - - - +
28p TYR* 1.3 60.9 + - - +
30p LEU* 4.0 0.8 - - - +
31p PHE* 3.0 22.2 + - - -
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Residues in contact with TYR 28 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24p LYS 2.9 15.5 + - - -
25p ARG* 3.5 2.9 + - - +
26p SER 3.2 0.4 - - - -
27p LEU* 1.3 77.6 - - - +
29p ALA* 1.3 59.0 + - - +
31p PHE* 3.9 1.1 - - - +
32p SER* 3.1 21.7 + - - -
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Residues in contact with ALA 29 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25p ARG 3.2 14.2 + - - -
26p SER* 3.7 3.4 - - - +
28p TYR* 1.3 71.4 - - - +
30p LEU* 1.3 66.2 + - - +
32p SER* 3.2 13.6 + - - +
33p GLN 4.2 2.1 + - - -
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Residues in contact with LEU 30 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26p SER 2.8 19.2 + - - -
27p LEU 4.0 0.7 - - - -
29p ALA* 1.3 72.1 - - - +
31p PHE* 1.3 58.1 + - - +
32p SER 3.5 0.2 + - - -
33p GLN* 3.8 8.8 + - - -
34p PHE 5.3 0.2 + - - -
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Residues in contact with PHE 31 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27p LEU 3.0 16.7 + - - -
28p TYR 3.9 1.6 - - - -
30p LEU* 1.3 70.9 - - - +
32p SER* 1.3 62.4 + - - +
33p GLN 3.1 2.6 + - - -
34p PHE* 3.4 11.9 + - - +
35p GLY 3.6 9.1 + - - +
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Residues in contact with SER 32 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28p TYR 3.1 17.3 + - - -
29p ALA 3.2 5.7 + - - -
31p PHE* 1.3 74.9 - - - +
33p GLN* 1.3 65.1 + - - +
34p PHE 3.1 1.3 + - - -
35p GLY* 3.4 20.2 + - - +
36p HIS* 5.8 0.2 - - - +
37p VAL 5.5 2.5 - - - +
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Residues in contact with GLN 33 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72o ASN* 5.4 13.9 - - - +
29p ALA 4.2 2.8 + - - -
30p LEU 3.8 9.0 + - - -
31p PHE 3.1 2.0 - - - -
32p SER* 1.3 77.9 - - - +
34p PHE* 1.3 56.1 + - - +
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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