Contacts of the helix formed by residues 26 - 32 (chain B) in PDB entry 3DDT
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 CYS 26 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6B CYS* 3.7 12.3 - - + -
9B HIS* 3.3 7.2 - - - -
12B GLU* 3.7 19.3 - - + -
13B LYS 3.4 19.5 - - - +
14B ILE* 4.3 1.4 - - - +
15B ASN* 3.5 4.9 - - - -
16B ILE* 3.4 12.3 - - - +
25B THR* 1.3 81.2 + - - +
27B SER* 1.3 62.1 + - - +
28B MET* 3.4 15.3 - - - -
29B CYS* 2.9 17.7 + - - +
30B LYS 3.4 0.3 + - - -
46B ZN 2.3 37.6 - - - -
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Residues in contact with SER 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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27A SER* 2.6 31.5 + - - -
28A MET* 3.7 28.2 - - - -
31A VAL* 3.8 8.5 - - - +
12B GLU* 4.1 5.0 + - - -
15B ASN* 2.9 18.7 + - - -
16B ILE* 3.9 11.2 - - - +
26B CYS* 1.3 73.3 - - - +
28B MET* 1.3 56.4 + - - +
30B LYS* 3.2 5.5 + - - +
31B VAL* 2.9 31.3 + - - +
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Residues in contact with MET 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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15A ASN* 3.6 21.5 - - + +
16A ILE* 4.0 9.2 - - + -
27A SER* 3.7 14.1 - - - +
42A PRO* 4.3 14.4 - - + -
9B HIS* 3.6 25.2 - - + +
12B GLU* 3.5 30.5 - - + +
26B CYS* 3.2 12.1 - - - -
27B SER* 1.3 74.6 + - - +
29B CYS* 1.3 60.8 + - - +
30B LYS 3.2 0.2 - - - -
31B VAL* 4.2 2.0 - - - +
32B PHE* 2.9 62.4 + - + +
33B GLY 3.3 3.8 + - - -
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Residues in contact with CYS 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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6B CYS* 3.7 7.2 - - - -
8B GLU* 4.5 10.3 - - - -
9B HIS* 3.2 12.1 - - - -
25B THR* 3.4 20.6 - - - +
26B CYS* 2.9 11.7 + - - +
28B MET* 1.3 77.5 - - - +
30B LYS* 1.3 58.2 + - - +
33B GLY* 3.0 31.8 + - - +
34B ILE* 4.7 9.4 - - - +
35B HIS* 3.0 23.7 + - + +
46B ZN 2.3 33.0 - - - -
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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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31A VAL* 3.6 31.6 - - + +
36A LYS* 5.9 5.1 - - - +
16B ILE* 3.8 20.0 - - + -
26B CYS 3.4 1.6 + - - -
27B SER 3.2 8.0 + - - +
29B CYS* 1.3 76.8 - - - +
31B VAL* 1.3 65.6 + - - +
35B HIS* 3.3 19.4 - - + +
36B LYS* 2.6 45.6 + - - +
37B ALA 4.2 1.4 + - - -
38B CYS 2.7 25.6 + - - +
40B VAL* 3.9 19.7 - - + -
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Residues in contact with VAL 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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16A ILE* 5.3 1.1 - - + -
27A SER* 3.9 16.2 - - - +
30A LYS* 3.8 23.2 - - + +
31A VAL* 3.5 20.0 - - + -
40A VAL* 3.8 16.4 - - + -
27B SER 2.9 21.7 + - - +
28B MET* 4.2 2.0 - - - +
30B LYS* 1.3 79.6 - - - +
32B PHE* 1.3 97.7 + - + +
36B LYS* 4.6 6.1 - - - +
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Residues in contact with PHE 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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16A ILE* 3.8 7.2 - - + -
40A VAL* 3.8 22.9 - - + -
41A ALA 3.7 6.1 - - - -
42A PRO* 3.5 39.3 - - + -
9B HIS* 5.5 4.3 - - - +
28B MET* 2.9 46.0 + - + +
31B VAL* 1.3 105.0 - - + +
33B GLY* 1.3 61.6 + - - +
36B LYS* 3.4 20.4 + - - +
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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