Contacts of the helix formed by residues 24 - 38 (chain A) in PDB entry 3TR6
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 PRO 24 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22A ARG 3.3 8.9 - - - +
23A GLU* 1.3 89.2 - - + +
25A PRO* 1.3 77.1 - - + +
26A LEU* 3.1 5.8 - - + +
27A LEU* 2.8 41.0 + - + +
28A ALA 3.0 9.4 + - - -
81A LEU* 4.5 16.4 - - + -
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Residues in contact with PRO 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A GLU 3.5 5.8 - - - +
24A PRO* 1.3 85.1 - - + +
26A LEU* 1.3 57.3 + - - +
28A ALA* 3.2 10.8 + - + +
29A GLU* 2.9 30.4 + - - +
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Residues in contact with LEU 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A PRO* 3.0 4.8 + - + +
25A PRO* 1.3 80.5 - - - +
27A LEU* 1.3 62.9 + - + +
29A GLU* 3.3 13.2 + - - +
30A LEU* 2.9 24.3 + - - +
77A ILE* 4.5 15.9 - - + -
81A LEU* 5.9 3.4 - - + -
105A TYR* 3.9 32.9 - - + +
108A LYS* 3.8 41.7 - - + +
109A ALA* 3.9 20.4 - - + +
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Residues in contact with LEU 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A GLU* 3.9 4.0 - - + -
24A PRO* 2.8 34.0 + - + +
26A LEU* 1.3 76.7 - - + +
28A ALA* 1.3 67.2 + - - +
30A LEU* 3.1 25.0 + - + +
31A ARG* 3.2 10.4 + - - +
74A TYR* 3.5 59.8 - - + +
77A ILE* 3.8 22.2 - - + -
78A ALA* 4.0 28.3 - - + +
81A LEU* 4.4 6.3 - - + -
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Residues in contact with ALA 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A GLU* 3.4 30.1 + - + +
24A PRO 3.0 8.8 + - - +
25A PRO* 3.4 14.4 - - + +
27A LEU* 1.3 78.5 - - - +
29A GLU* 1.3 60.1 + - - +
31A ARG* 3.4 9.5 + - - +
32A GLU* 3.2 28.5 + - + +
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Residues in contact with GLU 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A PRO 2.9 12.8 + - - +
26A LEU* 3.5 14.6 - - - +
28A ALA* 1.3 76.4 - - - +
30A LEU* 1.3 62.8 + - - +
32A GLU* 3.4 9.1 + - + +
33A GLU* 3.1 22.8 + - + +
105A TYR* 3.2 25.5 + - + +
108A LYS* 3.0 31.6 + - - -
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Residues in contact with LEU 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A LEU 2.9 14.1 + - - +
27A LEU* 3.1 23.3 + - + +
29A GLU* 1.3 77.7 - - - +
31A ARG* 1.3 57.6 + - - +
33A GLU* 3.6 1.7 + - - +
34A THR* 2.8 34.9 + - - +
44A GLN* 4.3 5.6 - - - +
72A THR* 3.5 31.2 - - - +
74A TYR* 3.8 27.8 - - + -
77A ILE* 3.9 13.9 - - + -
101A LEU* 4.5 4.3 - - + -
105A TYR* 3.6 39.9 - - + -
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Residues in contact with ARG 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A LEU* 5.2 5.3 - - - +
23A GLU* 2.8 38.4 + - - +
27A LEU 3.2 11.7 + - - +
28A ALA* 3.5 13.0 + - - +
30A LEU* 1.3 73.0 - - - +
32A GLU* 1.3 85.1 + - - +
33A GLU 3.2 1.3 - - - -
34A THR* 3.9 1.6 - - - -
35A THR* 2.9 35.1 + - - +
44A GLN* 2.9 36.7 - - - +
45A THR 5.8 0.7 - - - -
47A PRO* 3.5 25.4 - - - +
74A TYR* 4.4 3.6 - - + -
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Residues in contact with GLU 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A ALA* 3.2 17.6 + - + +
29A GLU* 3.6 10.1 - - - +
31A ARG* 1.3 100.5 + - - +
33A GLU* 1.3 58.1 + - - +
35A THR* 3.7 7.3 + - - +
36A ARG* 3.1 27.8 + - - +
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Residues in contact with GLU 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A GLU 3.1 15.7 + - - +
30A LEU 3.8 3.1 - - - +
32A GLU* 1.3 76.9 - - - +
34A THR* 1.3 59.9 + - - +
36A ARG* 3.2 34.9 + - - +
37A SER* 2.9 37.6 + - - +
101A LEU* 3.8 33.8 - - + +
104A GLU* 5.5 1.3 - - - +
105A TYR* 3.0 22.3 + - - +
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Residues in contact with THR 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A LEU* 2.8 23.4 + - - +
31A ARG* 3.4 8.7 + - - -
32A GLU 3.4 0.2 - - - -
33A GLU* 1.3 76.3 - - - +
35A THR* 1.3 59.3 + - - +
38A PHE* 2.9 35.8 + - + +
41A TYR* 3.4 11.3 - - + +
44A GLN* 3.7 10.3 + - - +
71A PHE* 3.5 37.5 - - + -
72A THR* 2.8 31.3 + - + +
101A LEU* 4.5 1.3 - - - +
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Residues in contact with THR 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A ARG* 2.9 23.2 + - - +
32A GLU* 3.7 9.0 + - - +
34A THR* 1.3 79.8 - - - +
36A ARG* 1.3 61.9 + - - +
37A SER 3.5 0.2 + - - -
38A PHE 3.9 9.0 - - - +
41A TYR* 3.6 38.6 - - + +
44A GLN* 5.2 2.1 + - - -
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Residues in contact with ARG 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A GLU 3.1 16.6 + - - +
33A GLU* 3.2 41.3 + - - +
35A THR* 1.3 80.6 - - - +
37A SER* 1.3 70.3 + - - +
38A PHE 3.7 0.2 - - - -
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Residues in contact with SER 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A GLU* 2.9 28.1 + - - +
36A ARG* 1.3 96.0 + - - +
38A PHE* 1.3 80.2 + - - +
39A SER 4.3 0.7 + - - -
97A LYS* 3.7 17.5 + - - -
101A LEU* 5.6 0.2 - - - -
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Residues in contact with PHE 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A THR* 2.9 24.0 + - - +
35A THR 3.9 4.6 - - - +
36A ARG 3.7 0.8 - - - -
37A SER* 1.3 97.4 - - - +
39A SER* 1.3 62.5 + - - +
40A THR* 3.0 15.0 - - - +
41A TYR* 3.0 27.3 + - - +
71A PHE* 4.1 20.0 - + + -
72A THR* 3.9 5.8 - - + -
95A ASP* 5.1 1.1 - - - -
97A LYS* 3.8 41.5 - - + +
98A SER* 3.9 32.3 - - - -
101A LEU* 3.8 23.8 - - + -
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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