Contacts of the helix formed by residues 45 - 59 (chain B) in PDB entry 5TQB
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 ASP 45 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32A ARG* 3.2 33.2 + - - +
40B LEU* 2.9 31.8 + - + +
43B GLU* 3.2 2.6 - - + +
44B GLY* 1.3 74.9 - - - +
46B ILE* 1.3 59.9 + - - +
47B GLU* 4.0 5.0 + - - +
48B THR* 2.9 33.6 + - - -
49B ALA* 3.2 18.7 + - - +
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Residues in contact with ILE 46 (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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38A HIS* 3.5 37.5 - - + +
118A GLN* 5.2 0.2 - - - +
41B LEU* 4.1 17.3 - - + +
44B GLY* 3.3 18.1 + - - +
45B ASP* 1.3 69.4 - - - +
47B GLU* 1.3 68.1 + - + +
49B ALA* 3.3 7.7 + - - +
50B ALA* 3.1 21.5 + - - +
77B ILE* 3.8 18.6 - - + +
80B GLU* 3.8 14.1 - - + +
81B LEU* 3.3 36.1 - - + -
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Residues in contact with GLU 47 (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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45B ASP* 3.4 4.9 - - - +
46B ILE* 1.3 80.9 - - + +
48B THR* 1.3 62.8 + - - +
50B ALA* 3.3 13.0 + - - +
51B LYS* 3.4 19.4 + - - +
81B LEU* 3.5 26.5 - - - +
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Residues in contact with THR 48 (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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36B ARG* 6.2 0.2 - - - +
40B LEU* 3.7 20.9 - - + -
45B ASP* 2.9 31.0 + - - +
46B ILE 3.4 0.2 - - - -
47B GLU* 1.3 76.4 - - - +
49B ALA* 1.3 60.4 + - - +
51B LYS* 3.2 14.1 + - + +
52B VAL* 2.9 34.9 + - + +
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Residues in contact with ALA 49 (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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37B ALA* 3.6 25.0 - - - +
40B LEU* 3.9 13.6 - - + +
41B LEU* 4.0 9.0 - - + +
45B ASP 3.2 14.5 + - - +
46B ILE* 3.5 12.6 - - - +
48B THR* 1.3 78.0 - - - +
50B ALA* 1.3 57.1 + - - +
52B VAL 3.7 0.2 - - - -
53B ALA* 2.8 33.8 + - - +
77B ILE* 3.9 14.1 - - + -
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Residues in contact with ALA 50 (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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46B ILE 3.1 8.7 + - - +
47B GLU* 3.6 9.6 - - - +
48B THR 3.3 0.2 - - - -
49B ALA* 1.3 75.6 - - - +
51B LYS* 1.3 59.3 + - + +
53B ALA* 3.8 0.9 - - - +
54B ARG* 2.9 31.5 + - - +
74B LEU* 4.3 4.2 - - - +
77B ILE* 3.7 28.6 - - + +
78B HIS* 4.7 10.3 - - + +
81B LEU* 4.6 11.0 - - + -
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Residues in contact with LYS 51 (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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47B GLU* 3.4 15.4 + - - +
48B THR* 3.2 15.4 + - + +
50B ALA* 1.3 79.1 - - + +
52B VAL* 1.3 64.1 + - + +
54B ARG* 3.3 5.6 + - - +
55B THR* 3.1 30.9 + - + +
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Residues in contact with VAL 52 (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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33B LEU* 3.4 35.6 - - + +
36B ARG* 4.2 12.1 - - + -
37B ALA* 4.1 11.0 - - + +
40B LEU* 3.8 16.6 - - + -
48B THR* 2.9 26.8 + - + +
49B ALA 4.0 2.7 - - - +
51B LYS* 1.3 77.1 - - + +
53B ALA* 1.3 57.5 + - - +
55B THR* 2.8 21.4 + - - +
56B ALA* 3.0 15.4 + - - +
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Residues in contact with ALA 53 (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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34B LEU* 5.2 1.9 - - + +
37B ALA* 3.9 11.6 - - + +
49B ALA 2.8 22.4 + - - +
50B ALA 3.9 0.7 - - - +
52B VAL* 1.3 70.0 - - - +
54B ARG* 1.3 65.6 + - - +
56B ALA* 3.4 7.7 - - - +
57B TYR* 3.1 23.6 + - - +
70B ALA* 5.5 1.4 - - - +
73B LEU* 4.2 10.3 - - + -
74B LEU* 3.7 20.8 - - + +
77B ILE* 3.5 22.7 - - + -
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Residues in contact with ARG 54 (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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50B ALA 2.9 19.2 + - - +
51B LYS* 3.6 6.3 - - - +
53B ALA* 1.3 73.8 - - - +
55B THR* 1.3 68.7 + - + +
57B TYR* 3.1 27.5 + - - +
58B GLU* 3.0 52.1 + - - +
74B LEU* 4.0 11.6 - - + +
90B TYR* 2.5 42.8 + - - -
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Residues in contact with THR 55 (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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33B LEU* 4.3 10.3 - - - +
51B LYS* 3.1 14.5 + - + +
52B VAL* 2.8 25.7 + - - +
54B ARG* 1.3 76.7 - - + +
56B ALA* 1.3 62.2 + - - +
58B GLU* 3.2 22.5 + - - +
59B HIS* 3.0 28.7 + - - -
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Residues in contact with ALA 56 (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 PRO* 4.1 5.1 - - - +
33B LEU* 3.7 31.0 - - + -
34B LEU* 3.9 22.9 - - + -
52B VAL 3.0 19.7 + - - +
53B ALA* 3.4 7.4 - - - +
54B ARG 3.1 0.2 - - - -
55B THR* 1.3 76.5 + - - +
57B TYR* 1.3 58.1 + - - +
59B HIS* 2.9 21.5 + - - +
60B ILE* 3.3 17.1 - - + +
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Residues in contact with TYR 57 (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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53B ALA 3.1 15.1 + - - +
54B ARG* 3.1 24.0 + - - +
56B ALA* 1.3 79.4 - - - +
58B GLU* 1.3 58.3 + - - +
60B ILE* 2.8 10.7 + - + +
61B GLY* 2.7 56.5 + - - -
62B GLU* 3.3 25.1 + - - +
67B ALA* 4.4 4.7 - - - -
70B ALA* 3.8 21.7 - - + +
71B LEU* 3.7 37.7 - - + +
74B LEU* 4.0 17.0 - - + -
90B TYR* 5.9 0.9 - + - -
93B ALA* 5.8 0.7 - - - +
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Residues in contact with GLU 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B ARG* 3.0 52.7 + - - +
55B THR* 3.4 18.6 - - - +
56B ALA 3.2 0.2 - - - -
57B TYR* 1.3 79.1 - - + +
59B HIS* 1.3 63.8 + - + +
60B ILE 3.2 2.9 + - - -
61B GLY* 4.4 4.4 + - - -
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Residues in contact with HIS 59 (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 SER* 5.1 11.5 + - - -
28B ILE* 6.0 2.2 - - + -
30B PRO* 3.7 26.4 - - + +
33B LEU* 4.9 10.3 - - + -
55B THR* 3.0 30.6 + - - -
56B ALA 2.9 8.6 + - - +
58B GLU* 1.3 83.8 + - + +
60B ILE* 1.3 59.8 + - - +
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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