Contacts of the helix formed by residues 42 - 56 (chain B) in PDB entry 4U7B
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 42 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29B HIS* 3.9 6.5 - - - -
41B PRO* 1.3 78.8 - - - +
43B VAL* 1.3 61.2 + - - +
44B LYS* 3.0 22.4 + - - +
45B THR* 2.8 26.5 + - - +
46B CYS* 3.3 12.3 - - - -
22E G 3.3 38.5 + - + +
23E T 4.2 21.4 - - + +
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Residues in contact with VAL 43 (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 ALA 4.4 1.6 - - - -
26B ALA* 3.6 38.8 - - + +
29B HIS* 3.6 33.0 + - + +
42B THR* 1.3 74.1 - - - +
44B LYS* 1.3 64.7 + - + +
46B CYS* 3.1 2.9 + - - +
47B GLU* 2.8 49.6 + - + +
31F A 5.1 0.2 - - - +
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Residues in contact with LYS 44 (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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42B THR* 3.0 7.4 + - - +
43B VAL* 1.3 83.0 - - + +
45B THR* 1.3 56.7 - - - +
47B GLU* 3.5 19.8 + - - +
48B ARG* 3.1 68.6 + - - +
51B GLN* 5.6 3.2 + - - -
22E G 5.0 0.2 - - - +
23E T 3.4 35.4 - - + +
24E C 4.7 3.1 - - - +
32F C 3.7 18.8 + - + +
33F G 3.3 41.7 + - - +
34F A 4.0 2.0 - - - +
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Residues in contact with THR 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B LEU* 6.0 0.4 - - - +
41B PRO* 3.6 12.5 - - + +
42B THR* 2.8 21.4 + - - +
44B LYS* 1.3 75.6 - - - +
46B CYS* 1.3 53.7 + - - -
48B ARG* 2.9 19.4 + - - +
49B TRP* 2.7 49.6 + - - -
20E A 6.0 0.2 - - + -
21E T 3.3 36.1 - - + +
22E G 3.1 26.5 + - - +
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Residues in contact with CYS 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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15B LEU* 3.8 26.8 - - + +
25B ALA* 4.2 17.7 - - - +
28B SER* 5.3 0.9 - - - -
29B HIS* 4.0 21.1 - - - -
32B LEU* 4.0 22.9 - - - -
41B PRO* 5.1 2.7 - - - -
42B THR 3.3 17.0 - - - -
43B VAL* 3.1 8.2 + - - +
45B THR* 1.3 81.3 + - - +
47B GLU* 1.3 53.3 + - - +
49B TRP* 3.8 0.2 - - - -
50B PHE* 2.7 44.7 + - + -
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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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25B ALA* 3.9 23.5 - - + +
43B VAL* 2.8 43.7 + - + +
44B LYS* 3.5 22.9 + - + +
46B CYS* 1.3 73.8 - - - +
48B ARG* 1.3 52.6 + - + +
50B PHE* 3.4 3.2 - - - +
51B GLN* 2.7 33.4 + - - +
30F A 5.7 0.3 - - - +
31F A 3.4 46.6 + - + +
32F C 3.5 32.4 + - - +
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Residues in contact with ARG 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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44B LYS* 3.1 47.4 + - - +
45B THR* 2.9 18.6 + - - +
47B GLU* 1.3 76.8 - - + +
49B TRP* 1.3 62.6 + - + +
51B GLN* 2.8 34.8 + - - +
52B ARG* 2.9 13.6 + - - +
21E T 3.4 37.6 + - - +
22E G 2.6 53.9 + - - -
34F A 3.8 3.2 - - - +
35F C 4.4 3.0 - - - +
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Residues in contact with TRP 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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12B ARG* 3.3 56.4 - - + +
15B LEU* 3.8 28.5 - - + -
45B THR* 2.7 37.4 + - - +
46B CYS 3.8 0.2 - - - +
48B ARG* 1.3 72.4 - - + +
50B PHE* 1.3 57.7 + - - +
52B ARG* 3.1 54.1 + - - +
53B PHE* 2.9 57.8 + + + -
57B ASP 5.7 0.2 - - - -
59B ASP 3.6 15.9 - - - -
60B VAL* 4.6 1.1 - - - -
61B ASP 4.6 3.1 - - - -
20E A 4.9 4.0 - - - -
21E T 2.7 27.8 + - - -
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Residues in contact with PHE 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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15B LEU* 3.7 29.4 - - + -
19B PHE* 3.6 40.9 - + + -
23B LYS 3.4 21.3 - - - -
24B THR* 3.7 8.3 - - - -
25B ALA* 4.1 15.7 - - + -
28B SER* 3.5 25.8 - - - -
46B CYS* 2.7 30.8 + - + +
47B GLU* 3.4 7.9 - - - +
49B TRP* 1.3 68.7 - - - +
51B GLN* 1.3 66.4 + - - +
53B PHE* 3.1 15.1 + + - +
54B LYS* 3.0 40.0 + - - +
31F A 5.9 0.2 - - - -
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Residues in contact with GLN 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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44B LYS* 5.6 3.3 + - - -
47B GLU* 2.7 15.8 + - - +
48B ARG* 2.8 31.3 + - - +
50B PHE* 1.3 73.2 - - - +
52B ARG* 1.3 57.4 + - - +
54B LYS* 3.3 17.8 + - + +
55B SER* 3.3 11.1 + - - -
32F C 4.0 32.2 + - - +
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Residues in contact with ARG 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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48B ARG 2.9 10.3 + - - +
49B TRP* 3.1 52.7 + - + +
51B GLN* 1.3 74.4 - - - +
53B PHE* 1.3 67.6 + - + +
55B SER* 3.2 23.5 - - - +
56B GLY 3.3 5.0 + - - -
57B ASP* 3.3 42.3 + - + +
59B ASP 3.6 8.5 + - - -
61B ASP 4.1 3.6 + - - -
63B LYS* 3.5 26.9 - - - +
20E A 3.1 36.7 + - - -
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Residues in contact with PHE 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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12B ARG* 4.0 9.9 - - + -
15B LEU* 3.5 32.1 - - + -
16B ILE* 3.2 34.5 - - + -
19B PHE* 3.9 34.1 - + + -
49B TRP* 2.9 48.6 + + + -
50B PHE* 3.1 16.4 + + - +
52B ARG* 1.3 76.6 - - + +
54B LYS* 1.3 60.2 + - - +
56B GLY* 3.0 20.3 + - - +
57B ASP 4.1 8.7 - - - -
58B PHE* 3.9 31.9 - + + -
59B ASP 5.7 0.2 - - - -
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Residues in contact with LYS 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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19B PHE* 3.9 26.2 - - + -
50B PHE* 3.0 31.6 + - - +
51B GLN* 3.5 11.1 - - - +
53B PHE* 1.3 76.2 - - - +
55B SER* 1.3 61.0 + - - +
56B GLY* 3.5 0.5 + - - -
31F A 6.0 0.2 + - - -
32F C 5.5 4.6 + - - -
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Residues in contact with SER 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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51B GLN 3.3 7.2 + - - -
52B ARG* 3.2 22.4 + - - +
53B PHE 3.1 0.2 - - - -
54B LYS* 1.3 79.4 - - - +
56B GLY* 1.3 55.3 + - - +
57B ASP* 3.9 12.6 + - - +
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Residues in contact with GLY 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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4A PHE* 5.4 3.5 - - - -
52B ARG 3.3 0.4 + - - -
53B PHE 3.0 14.7 + - - -
54B LYS 4.5 0.4 - - - -
55B SER* 1.3 79.4 - - - +
57B ASP* 1.3 60.3 + - - +
58B PHE* 3.7 21.7 + - - -
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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