Contacts of the helix formed by residues 16 - 27 (chain B) in PDB entry 3PSM
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 16 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14B CYS* 3.7 0.7 - - - -
15B PHE* 1.3 86.7 + - - +
17B ASP* 1.3 67.7 + - - +
18B GLY* 3.9 10.1 - - - +
19B SER* 3.1 29.1 + - - +
20B CYS 3.6 3.8 + - - -
35B CYS* 3.4 10.2 - - - -
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Residues in contact with ASP 17 (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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16B THR* 1.3 72.4 - - - +
18B GLY* 1.3 58.7 + - - +
20B CYS* 3.1 5.5 + - - +
21B ASP* 2.9 28.3 + - - +
33B GLY 4.1 2.9 - - - +
34B ARG* 3.8 11.8 - - + +
35B CYS* 2.9 41.8 + - - +
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Residues in contact with GLY 18 (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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16B THR* 3.2 9.1 - - - +
17B ASP* 1.3 78.6 - - - +
19B SER* 1.3 56.1 + - - +
21B ASP* 3.8 7.4 - - - +
22B ASP* 3.0 30.5 + - - +
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Residues in contact with SER 19 (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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10B PHE* 3.8 17.5 - - - -
16B THR* 3.1 25.7 + - - +
18B GLY* 1.3 75.4 - - - +
20B CYS* 1.3 57.7 + - - +
22B ASP* 3.5 6.2 + - - +
23B HIS* 3.0 26.7 + - - +
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Residues in contact with CYS 20 (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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10B PHE* 3.9 4.4 - - - -
14B CYS* 3.5 19.3 - - - -
16B THR 3.6 1.8 + - - -
17B ASP 3.1 8.4 + - - +
19B SER* 1.3 77.1 - - - +
21B ASP* 1.4 67.2 + - - +
23B HIS* 3.2 1.6 + - - +
24B CYS* 2.9 29.1 + - - -
33B GLY 3.8 0.4 - - - -
34B ARG 3.3 28.0 - - - -
35B CYS* 4.1 0.7 - - - +
41B CYS* 2.0 55.9 - - - -
42B TRP 3.5 4.9 - - - -
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Residues in contact with ASP 21 (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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17B ASP 2.9 14.2 + - - +
18B GLY* 3.8 8.5 - - - +
20B CYS* 1.4 74.9 - - - +
22B ASP* 1.3 59.1 + - - +
24B CYS* 3.4 0.9 + - - +
25B LYS* 2.7 65.0 + - - +
32B LYS* 3.2 17.2 - - - +
33B GLY 2.9 40.0 + - - +
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Residues in contact with ASP 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B GLY 3.0 18.7 + - - +
19B SER* 3.6 7.6 - - - +
21B ASP* 1.3 77.9 + - - +
23B HIS* 1.3 57.9 + - - +
25B LYS* 4.8 1.6 - - - -
26B ASN* 2.8 62.3 + - - +
27B LYS* 5.0 8.5 + - - +
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Residues in contact with HIS 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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7B ALA* 3.8 17.5 - - + +
8B ASP 3.2 17.9 + - - -
9B THR 3.4 20.1 + - - -
10B PHE* 3.8 21.3 - + + -
19B SER 3.0 16.0 + - - +
20B CYS 3.5 6.3 - - - +
22B ASP* 1.3 78.1 + - - +
24B CYS* 1.3 68.0 + - - +
27B LYS* 2.9 50.4 + - + +
28B GLU* 2.7 40.0 + - + +
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Residues in contact with CYS 24 (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 CYS 2.9 22.6 + - - +
21B ASP 3.8 0.4 - - - +
23B HIS* 1.3 75.6 - - - +
25B LYS* 1.3 60.4 + - - +
28B GLU* 3.5 4.3 - - - +
29B HIS 3.1 6.4 + - - -
30B LEU* 2.9 26.7 + - + +
32B LYS* 3.4 21.8 - - - +
33B GLY* 3.7 6.3 - - - -
41B CYS* 3.6 15.9 - - - -
43B CYS* 2.0 56.8 - - + -
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Residues in contact with LYS 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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21B ASP* 2.7 50.6 + - - +
22B ASP* 4.1 2.0 - - - +
24B CYS* 1.3 77.7 - - - +
26B ASN* 1.3 72.6 + - - +
29B HIS* 3.2 23.6 + - - -
30B LEU 3.7 8.2 - - - +
31B ILE 3.3 31.2 - - - +
32B LYS* 4.2 3.3 - - - +
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Residues in contact with ASN 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 ASP* 2.8 50.0 + - - +
25B LYS* 1.3 86.7 + - - +
27B LYS* 1.3 72.5 + - + +
29B HIS* 3.6 16.8 - - - -
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Residues in contact with LYS 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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22B ASP* 5.0 9.4 + - - +
23B HIS* 2.9 41.8 + - + +
26B ASN* 1.3 87.2 - - + +
28B GLU* 1.3 60.2 + - + +
29B HIS* 3.5 16.6 + - - -
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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