Contacts of the helix formed by residues 24 - 35 (chain B) in PDB entry 3TSO
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 GLY 24 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22B GLY 3.3 0.8 - - - -
23B VAL* 1.3 80.2 - - - +
25B LYS* 1.3 55.0 + - - +
26B THR 3.4 2.0 - - - -
27B ASN* 3.3 2.1 + - - +
28B LEU* 2.8 42.7 + - - +
125B ASN* 3.6 11.1 + - - -
201B GNP 3.1 32.3 + - - -
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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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17B LEU* 3.5 26.7 - - + +
18B ILE* 3.4 40.2 - - - +
19B GLY* 3.1 11.3 + - - +
20B GLU 3.0 19.4 + - - -
23B VAL* 3.9 10.8 - - + -
24B GLY* 1.3 76.1 - - - +
26B THR* 1.3 58.0 + - - +
28B LEU* 3.2 10.0 + - - +
29B LEU 2.9 23.6 + - - -
67B ASP* 3.7 11.0 - - - +
68B THR 3.5 19.1 - - - -
70B GLY* 3.9 3.1 - - - +
91B VAL* 4.2 7.2 - - + -
201B GNP 2.6 52.4 + - - +
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Residues in contact with THR 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B LYS* 1.3 75.7 - - - +
27B ASN* 1.3 59.8 + - - +
29B LEU* 3.3 5.4 + - + +
30B SER* 3.0 27.9 + - - +
34B ARG* 5.4 2.5 + - - +
41B SER* 5.0 11.2 - - - -
42B ARG 6.0 0.7 - - - +
44B THR* 2.8 6.2 + - - +
48B GLU* 5.0 9.0 - - - +
67B ASP* 2.7 25.4 + - - +
200B MG 2.1 30.7 - - - -
201B GNP 2.9 15.4 + - - +
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Residues in contact with ASN 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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24B GLY 3.3 2.4 + - - +
26B THR* 1.3 75.3 - - - +
28B LEU* 1.3 59.5 + - - +
30B SER* 3.3 6.4 + - - -
31B ARG* 2.9 31.7 + - - +
36B GLU 4.2 0.7 - - - +
37B PHE* 3.3 30.8 - - + +
38B SER* 2.8 41.9 - - - +
41B SER* 2.8 27.7 + - - -
156B ALA* 3.7 8.2 - - + +
201B GNP 2.9 28.6 + - + +
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Residues in contact with LEU 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B LEU* 4.9 4.5 - - + -
24B GLY 2.8 23.9 + - - +
25B LYS* 3.2 5.8 + - - +
27B ASN* 1.3 73.3 - - - +
29B LEU* 1.3 62.7 + - - +
31B ARG* 3.9 1.7 - - - +
32B PHE 3.0 18.2 + - - -
89B LEU* 5.0 4.9 - - + -
91B VAL* 3.7 43.7 - - + -
123B VAL* 4.3 8.3 - - + -
125B ASN* 3.7 12.3 - - - +
154B THR* 3.7 23.6 - - + +
156B ALA* 3.8 6.0 - - + +
162B VAL* 3.9 27.6 - - + +
165B ALA* 6.4 0.4 - - + -
166B PHE* 3.5 22.4 - - + -
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Residues in contact with LEU 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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17B LEU* 3.8 6.7 - - + +
25B LYS 2.9 12.5 + - - +
26B THR* 3.4 11.2 - - + +
27B ASN 3.2 0.2 - - - -
28B LEU* 1.3 77.7 - - - +
30B SER* 1.3 58.9 + - - +
32B PHE* 3.9 0.3 - - - +
33B THR* 2.8 47.9 + - + +
34B ARG* 4.2 6.7 - - - +
48B GLU* 5.0 7.9 - - + +
49B PHE* 4.7 3.1 - - - -
50B SER* 4.0 21.5 - - - +
65B ILE* 3.4 48.0 - - + +
67B ASP* 3.7 29.8 - - + +
166B PHE* 4.6 3.6 - - - -
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Residues in contact with SER 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 THR* 3.0 16.3 + - - -
27B ASN* 3.3 18.7 + - - -
29B LEU* 1.3 76.7 - - - +
31B ARG* 1.3 57.6 + - - +
33B THR* 4.0 0.4 - - - -
34B ARG* 2.8 65.4 + - - +
35B ASN 3.0 5.7 + - - -
36B GLU* 2.8 28.9 + - - -
37B PHE* 4.2 0.2 - - - -
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Residues in contact with ARG 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 ASN 2.9 19.6 + - - +
28B LEU* 3.9 3.8 - - - +
30B SER* 1.3 76.3 - - - +
32B PHE* 1.3 64.0 + - - +
35B ASN* 2.9 62.1 + - - +
36B GLU* 3.0 12.6 + - - +
37B PHE* 3.2 24.8 - - - +
52B ARG* 4.8 1.9 + - - -
156B ALA* 2.8 23.1 + - - +
157B LEU 3.0 23.6 + - - -
159B SER* 3.6 22.8 + - - +
162B VAL* 3.7 27.4 - - + -
163B GLU* 6.1 0.2 - - - +
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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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28B LEU 3.0 8.7 + - - +
29B LEU* 4.1 1.8 - - - +
31B ARG* 1.3 80.0 - - - +
33B THR* 1.3 64.1 + - + +
35B ASN 4.5 0.9 + - - -
52B ARG* 2.8 80.9 + - + +
54B VAL* 4.7 2.7 - - + -
63B ALA* 4.7 6.3 - - + -
65B ILE* 3.5 30.5 - - + -
162B VAL* 4.0 5.4 - - + +
163B GLU* 4.0 18.8 - - + -
166B PHE* 3.3 53.4 - + + -
167B GLU* 3.9 20.2 - - + -
170B LEU* 4.4 7.9 - - + -
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Residues in contact with THR 33 (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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29B LEU* 2.8 41.2 + - + +
32B PHE* 1.3 79.7 - - + +
34B ARG* 1.3 69.5 + - - +
50B SER* 3.4 27.8 - - - -
51B THR 3.6 34.9 - - - +
52B ARG* 4.2 8.3 - - + +
65B ILE* 4.0 15.9 - - + -
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Residues in contact with ARG 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B THR* 5.4 3.0 + - - +
29B LEU* 4.2 9.5 - - - +
30B SER* 2.8 45.1 + - - +
33B THR* 1.3 87.4 + - - +
35B ASN* 1.3 69.5 + - - +
36B GLU* 3.3 40.2 + - + +
48B GLU* 5.1 3.8 + - - -
50B SER* 3.1 27.0 + - - -
498C VAL* 4.1 26.0 + - - +
499C PRO* 5.1 8.2 - - - +
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Residues in contact with ASN 35 (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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30B SER 3.0 3.2 + - - -
31B ARG* 2.9 52.1 + - - +
32B PHE 4.5 0.6 + - - -
33B THR 3.8 0.6 - - - -
34B ARG* 1.3 80.0 - - - +
36B GLU* 1.3 60.2 + - - +
52B ARG* 6.4 0.4 - - - +
159B SER* 4.5 2.6 + - - -
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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