Contacts of the helix formed by residues 21 - 30 (chain B) in PDB entry 4OA5
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 THR 21 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B VAL* 3.8 5.6 - - + +
20B ASP* 1.3 87.5 - - - +
22B GLU* 1.3 65.7 + - - +
24B ALA* 3.3 19.4 + - - +
25B LEU* 3.2 20.9 + - - +
49B GLN* 6.2 0.9 - - - +
76B HIS* 3.8 23.7 + - + +
307B IOD 4.2 13.9 - - - -
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Residues in contact with GLU 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 ASP 3.7 2.9 + - - -
21B THR* 1.3 72.3 - - - +
23B GLY* 1.3 61.2 + - - +
25B LEU* 3.3 3.4 + - - +
26B LYS* 2.9 56.3 + - + +
307B IOD 4.4 10.3 - - + +
317B IOD 3.9 19.9 - - + +
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Residues in contact with GLY 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 THR 3.3 0.8 - - - -
22B GLU* 1.3 85.7 - - - +
24B ALA* 1.3 55.1 + - - +
26B LYS* 3.5 6.9 + - - +
27B ALA* 3.0 27.9 + - - +
100B ASN* 5.7 0.2 - - - +
103B ASN* 6.1 1.1 - - - -
104B CYS* 3.5 28.7 - - - -
307B IOD 3.5 13.6 - - - +
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Residues in contact with ALA 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B VAL* 3.8 20.6 - - + -
21B THR* 3.3 21.2 + - - +
23B GLY* 1.3 71.5 - - - +
25B LEU* 1.3 66.7 + - - +
27B ALA* 3.2 4.6 + - - +
28B HIS 3.0 19.2 + - - -
69B PHE* 3.3 23.7 - - + -
72B ILE* 4.0 24.3 - - + +
73B CYS* 4.3 4.3 - - - +
76B HIS* 5.1 1.1 + - + -
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Residues in contact with LEU 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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19B VAL* 3.9 8.3 - - + +
20B ASP* 3.9 23.1 - - + +
21B THR 3.2 17.3 + - - +
22B GLU* 3.7 3.8 - - - +
24B ALA* 1.3 78.3 - - + +
26B LYS* 1.3 61.3 + - - +
28B HIS* 3.4 8.4 + - + +
29B LYS* 3.4 18.2 + - - +
42B THR* 3.6 31.6 - - + -
317B IOD 4.1 20.0 - - + -
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Residues in contact with LYS 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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22B GLU* 2.9 44.2 + - + +
23B GLY* 3.8 6.5 - - - +
25B LEU* 1.3 75.2 - - - +
27B ALA* 1.3 64.8 + - - +
29B LYS* 3.1 17.3 + - - +
30B THR* 3.4 16.4 + - + +
100B ASN* 5.3 0.4 - - - -
103B ASN* 6.3 1.1 - - - +
317B IOD 3.9 21.4 - - + +
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Residues in contact with ALA 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 GLY 3.0 17.8 + - - +
24B ALA* 3.2 5.8 + - - +
26B LYS* 1.3 76.1 - - - +
28B HIS* 1.3 64.3 + - - +
30B THR* 2.7 21.8 + - - -
39B GLN* 4.7 0.2 - - - -
67B VAL* 3.4 12.9 - - - +
69B PHE* 4.6 8.3 - - - -
72B ILE* 3.8 23.8 - - + -
100B ASN* 3.7 28.2 + - + +
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Residues in contact with HIS 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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24B ALA 3.0 12.4 + - - +
25B LEU* 3.5 12.6 - - + +
26B LYS 3.2 0.2 - - - -
27B ALA* 1.3 75.8 - - - +
29B LYS* 1.3 61.7 + - - +
30B THR 3.3 1.0 + - - -
31B ALA* 3.5 6.1 + - - +
36B ARG* 3.9 11.7 - - + +
39B GLN* 3.1 46.8 + - - +
40B LEU 2.9 28.5 + - - -
41B GLY* 4.4 6.0 - - - -
42B THR* 5.4 3.8 - - + -
69B PHE* 3.6 29.3 - + + -
308B IOD 4.2 18.4 - - + -
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Residues in contact with LYS 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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25B LEU 3.4 7.7 + - - +
26B LYS* 3.1 12.7 + - - +
28B HIS* 1.3 80.8 + - - +
30B THR* 1.3 60.0 + - + +
31B ALA 3.3 5.1 + - - +
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Residues in contact with THR 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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26B LYS* 3.4 15.7 - - + +
27B ALA 2.7 18.4 + - - -
29B LYS* 1.3 74.9 - - + +
31B ALA* 1.3 65.9 + - - +
32B PRO* 3.6 3.5 - - - +
67B VAL* 3.4 5.5 - - - +
96B THR* 3.5 21.4 - - + +
100B ASN* 2.9 31.6 + - - +
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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