Contacts of the helix formed by residues 42 - 56 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29A HIS* 4.0 5.8 - - - -
40A VAL 4.7 0.7 - - - +
41A PRO* 1.3 77.5 - - - +
43A VAL* 1.3 63.4 + - - +
44A LYS* 3.4 18.0 + - - +
45A THR* 2.6 25.5 + - - +
46A CYS* 3.6 8.7 - - - -
22C G 3.3 53.2 + - + +
23C T 4.3 10.9 - - + +
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Residues in contact with VAL 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A ALA 4.7 1.3 - - - -
26A ALA* 3.9 35.9 - - + +
29A HIS* 3.8 33.5 + - + +
42A THR* 1.3 75.2 - - - +
44A LYS* 1.3 62.7 + - + +
46A CYS* 3.1 3.8 + - - +
47A GLU* 2.8 48.9 + - + +
30D A 6.4 0.2 - - + -
31D A 5.1 1.3 - - - +
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Residues in contact with LYS 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A THR* 3.1 11.7 + - - +
43A VAL* 1.3 83.9 - - + +
45A THR* 1.3 61.2 + - - +
47A GLU* 3.3 26.6 + - + +
48A ARG* 3.0 61.8 + - - +
51A GLN* 5.2 7.5 + - - -
22C G 5.4 0.2 - - - +
23C T 3.7 24.0 - - + +
24C C 4.8 3.8 - - - +
32D C 3.9 20.6 + - + +
33D G 3.1 43.0 + - - +
34D A 4.1 2.2 - - - +
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Residues in contact with THR 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A LEU* 5.2 0.2 - - - -
41A PRO* 3.3 16.9 - - + +
42A THR* 2.6 18.5 + - - +
44A LYS* 1.3 76.6 - - - +
46A CYS* 1.3 49.6 + - - +
48A ARG* 2.9 18.3 + - - +
49A TRP* 2.8 42.6 + - - -
21C T 3.4 45.3 - - + +
22C G 3.2 26.2 + - - +
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Residues in contact with CYS 46 (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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15A LEU* 3.8 31.2 - - + +
25A ALA* 4.2 19.5 - - + +
29A HIS* 4.1 26.5 - - - -
32A LEU* 4.4 13.0 - - - -
41A PRO* 4.9 5.8 - - - -
42A THR 3.6 14.6 - - - -
43A VAL* 3.1 8.1 + - - +
45A THR* 1.3 75.1 - - - +
47A GLU* 1.3 63.1 + - - +
49A TRP 4.0 0.2 - - - -
50A PHE* 3.1 33.1 + - + -
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Residues in contact with GLU 47 (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 ALA* 4.2 20.2 - - + +
43A VAL* 2.8 43.2 + - + +
44A LYS* 3.3 31.4 + - + +
46A CYS* 1.3 76.1 - - - +
48A ARG* 1.3 65.9 + - - +
50A PHE* 3.5 3.9 - - - +
51A GLN* 3.2 24.3 + - - +
31D A 3.4 46.7 + - + +
32D C 3.6 22.8 + - - +
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Residues in contact with ARG 48 (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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44A LYS* 3.0 50.8 + - - +
45A THR* 2.9 18.6 + - + +
47A GLU* 1.3 72.8 - - - +
49A TRP* 1.3 59.8 + - + +
51A GLN* 2.5 51.4 + - - +
52A ARG* 3.3 3.6 + - - +
21C T 3.5 43.7 + - - +
22C G 2.7 47.2 + - - -
34D A 3.9 5.5 - - - +
35D C 4.7 1.8 - - - +
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Residues in contact with TRP 49 (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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12A ARG* 3.2 52.9 - - + +
15A LEU* 4.2 19.7 - - + -
45A THR* 2.8 31.9 + - - +
48A ARG* 1.3 74.5 - - + +
50A PHE* 1.3 61.8 + - - +
52A ARG* 3.2 57.9 + - - +
53A PHE* 3.1 61.2 + + + -
59A ASP 3.3 19.3 - - - -
60A VAL* 4.0 4.0 - - - -
61A ASP 4.4 2.0 - - - -
62A ASP* 5.6 0.7 - - - -
20C A 5.2 4.5 - - - -
21C T 3.4 27.7 + - - -
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Residues in contact with PHE 50 (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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15A LEU* 4.0 32.1 - - + -
19A PHE* 3.9 32.4 - + + -
23A LYS 3.7 15.7 - - - -
24A THR* 4.4 0.2 - - - -
25A ALA* 3.4 34.5 - - + -
28A SER* 3.3 26.7 - - - -
46A CYS* 3.1 27.0 + - + +
47A GLU* 3.5 7.6 - - - +
48A ARG 2.8 0.4 + - - -
49A TRP* 1.3 75.2 - - - +
51A GLN* 1.3 63.0 + - - +
53A PHE* 2.8 28.6 + + - +
54A LYS* 3.2 27.1 + - - +
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Residues in contact with GLN 51 (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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44A LYS* 5.2 5.7 + - - -
47A GLU* 3.2 14.3 + - - +
48A ARG* 2.5 29.4 + - - +
50A PHE* 1.3 73.7 - - - +
52A ARG* 1.3 58.2 + - - +
54A LYS* 3.2 28.3 + - + +
55A SER* 3.5 6.8 + - - -
32D C 3.4 33.9 + - - +
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Residues in contact with ARG 52 (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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48A ARG 3.3 3.0 + - - +
49A TRP* 3.2 60.3 + - + +
50A PHE 3.2 0.8 - - - -
51A GLN* 1.3 79.5 - - - +
53A PHE* 1.3 62.0 + - + +
55A SER* 2.7 29.9 + - - +
57A ASP* 3.1 41.6 + - + +
59A ASP* 3.5 10.4 + - - +
61A ASP 4.1 4.0 + - - -
63A LYS* 3.8 27.9 - - - +
20C A 3.2 31.9 + - - -
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Residues in contact with PHE 53 (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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12A ARG* 4.3 6.5 - - + -
15A LEU* 3.7 26.9 - - + -
16A ILE* 3.2 29.8 - - + -
19A PHE* 3.5 41.2 - + + -
49A TRP* 3.1 52.7 - + + -
50A PHE* 2.8 19.8 + + - +
52A ARG* 1.3 76.5 - - - +
54A LYS* 1.3 59.2 + - - +
56A GLY* 3.7 8.9 + - - -
57A ASP 3.7 8.5 - - - -
58A PHE* 3.6 36.6 - + + -
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Residues in contact with LYS 54 (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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19A PHE* 4.1 23.1 - - + -
50A PHE* 3.5 25.1 - - - +
51A GLN* 3.2 16.5 + - + +
52A ARG 3.2 0.6 - - - -
53A PHE* 1.3 77.6 - - - +
55A SER* 1.3 62.5 + - - +
56A GLY* 3.2 1.9 + - - -
32D C 4.9 10.5 + - - -
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Residues in contact with SER 55 (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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51A GLN 3.5 7.5 + - - -
52A ARG* 2.7 27.4 + - - +
54A LYS* 1.3 79.0 - - - +
56A GLY* 1.3 55.7 + - - +
57A ASP* 3.5 18.0 + - - +
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Residues in contact with GLY 56 (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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52A ARG 3.4 2.9 + - - -
53A PHE 3.7 8.2 + - - -
54A LYS 3.2 3.6 - - - -
55A SER* 1.3 79.1 - - - +
57A ASP* 1.3 64.8 + - - +
58A PHE* 3.4 26.5 + - - -
4B PHE* 5.6 1.8 - - - -
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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