Contacts of the helix formed by residues 21 - 32 (chain B) in PDB entry 1JDH
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 PHE 21 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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386A ARG* 3.6 53.6 - - + +
387A ASN* 4.0 13.0 - - - +
390A ASP* 5.6 1.0 + - - -
422A GLY* 3.7 29.4 - - - -
426A ASN* 3.3 26.9 - - - -
459A ASP 6.2 0.4 - - - -
463A PRO* 5.1 5.8 - - + -
19B ILE* 3.7 31.9 - - + -
20B SER* 1.3 74.7 - - - +
22B LYS* 1.3 64.4 + - - +
24B GLU* 3.1 34.9 + - + +
25B GLY* 2.9 21.0 + - - -
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Residues in contact with LYS 22 (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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20B SER* 3.4 13.8 + - - +
21B PHE* 1.3 78.6 - - - +
23B ASP* 1.3 64.2 + - - +
25B GLY* 3.3 0.7 + - - -
26B GLU* 2.9 48.0 + - - +
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Residues in contact with ASP 23 (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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21B PHE 3.4 0.4 - - - -
22B LYS* 1.3 77.0 - - - +
24B GLU* 1.3 73.3 + - - +
26B GLU* 3.3 9.3 + - - +
27B GLN* 3.0 28.0 + - - +
30B LYS* 5.9 0.5 + - - -
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Residues in contact with GLU 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386A ARG* 3.7 29.6 + - - +
387A ASN* 5.6 0.2 - - - +
459A ASP* 6.1 1.0 - - - +
20B SER 3.8 5.7 - - - +
21B PHE* 3.1 42.5 - - + +
23B ASP* 1.3 81.0 + - - +
25B GLY* 1.3 61.3 + - - +
27B GLN* 3.6 15.1 - - - +
28B GLU 4.8 0.9 + - - -
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Residues in contact with GLY 25 (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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349A VAL* 3.7 21.9 - - - +
386A ARG* 5.9 0.2 - - - -
387A ASN* 3.7 22.4 + - - -
21B PHE 2.9 13.2 + - - -
22B LYS 3.8 0.7 - - - -
24B GLU* 1.3 77.1 - - - +
26B GLU* 1.3 58.5 + - - +
27B GLN 3.2 3.0 + - - -
28B GLU* 4.3 8.8 + - - +
29B GLU* 4.4 6.1 + - - +
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Residues in contact with GLU 26 (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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349A VAL* 4.5 23.3 - - + +
22B LYS* 2.9 33.7 + - - +
23B ASP* 3.8 8.2 - - - +
25B GLY* 1.3 76.5 - - - +
27B GLN* 1.3 63.4 + - - +
28B GLU 3.5 0.4 - - - -
29B GLU* 3.9 10.3 + - - +
30B LYS* 2.8 61.0 + - + +
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Residues in contact with GLN 27 (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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23B ASP* 3.0 16.8 + - - +
24B GLU* 3.6 12.8 - - - +
25B GLY 3.2 0.8 - - - -
26B GLU* 1.3 77.1 - - - +
28B GLU* 1.3 60.0 + - - +
30B LYS* 3.1 5.8 + - - +
31B SER* 2.9 65.3 + - - +
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Residues in contact with GLU 28 (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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306A TYR* 3.2 28.5 + - + +
345A LYS* 3.2 34.2 + - - +
24B GLU 4.8 0.6 + - - -
25B GLY 4.3 7.0 + - - +
26B GLU 3.5 0.4 - - - -
27B GLN* 1.3 79.2 - - - +
29B GLU* 1.3 59.2 + - + +
30B LYS 2.8 3.3 + - - -
31B SER* 4.2 1.8 - - - -
32B SER* 2.8 49.7 + - - +
33B GLU 5.1 3.0 - - - +
34B ASN* 5.1 1.7 - - - +
35B SER* 5.4 4.5 + - - -
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Residues in contact with GLU 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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306A TYR* 3.4 35.6 - - + -
307A GLY* 2.8 34.2 + - - +
312A LYS* 2.6 34.0 + - - -
346A VAL* 3.5 16.1 - - + +
349A VAL* 3.3 21.1 - - - +
25B GLY 4.4 5.9 + - - +
26B GLU* 3.9 8.9 + - - +
27B GLN 3.5 0.6 - - - -
28B GLU* 1.3 80.7 - - + +
30B LYS* 1.3 61.4 + - + +
32B SER 4.4 2.4 - - - +
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Residues in contact with LYS 30 (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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23B ASP* 5.9 0.6 + - - -
26B GLU* 2.8 53.6 + - - +
27B GLN* 3.1 5.5 + - - +
28B GLU 2.8 1.8 + - - -
29B GLU* 1.3 83.9 - - + +
31B SER* 1.3 62.1 + - - +
32B SER 5.0 0.2 - - - -
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Residues in contact with SER 31 (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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27B GLN* 2.9 46.1 + - - +
28B GLU* 4.0 0.5 + - - -
30B LYS* 1.3 79.5 - - - +
32B SER* 1.3 63.6 + - - +
33B GLU 4.3 0.2 + - - -
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Residues in contact with SER 32 (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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306A TYR* 2.6 28.4 + - - -
28B GLU* 2.8 42.6 + - - +
29B GLU* 4.4 2.6 - - - +
30B LYS 5.0 0.2 - - - -
31B SER* 1.3 78.6 + - - +
33B GLU* 1.3 61.4 + - - +
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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