Contacts of the helix formed by residues 44 - 59 (chain F) in PDB entry 4P9U
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 44 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38F SER* 4.9 0.9 - - - -
43F VAL* 1.3 80.2 - - - +
45F ARG* 1.3 67.2 + - - +
46F THR* 3.9 2.9 - - - +
47F THR* 3.3 22.0 - - - +
48F LEU* 3.3 17.5 + - - +
15H T 3.1 53.2 + - + +
16H T 3.0 41.1 + - - +
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Residues in contact with ARG 45 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34F GLU* 2.7 44.2 + - + +
35F ARG* 4.0 35.4 - - - +
38F SER* 4.0 17.7 - - - +
44F THR* 1.3 77.0 + - - +
46F THR* 1.3 64.6 + - - +
48F LEU* 3.1 7.3 + - + +
49F ARG* 2.9 36.8 + - + +
12G G 3.6 18.6 + - - -
13G G 3.0 45.2 + - - -
14G T 4.0 5.3 + - - -
16H T 4.2 12.0 - - + +
18H A 3.8 15.2 - - - +
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Residues in contact with THR 46 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46E THR* 3.6 31.6 - - + +
50E GLU* 4.4 2.1 - - - +
44F THR* 3.4 1.9 + - - +
45F ARG* 1.3 78.9 - - - +
47F THR* 1.3 58.0 + - - +
49F ARG* 2.9 26.1 + - - +
50F GLU* 2.9 25.7 + - + +
14G T 5.9 2.8 - - + +
15G C 4.2 8.3 + - - -
14H T 5.5 1.6 - - + -
15H T 3.6 26.3 + - + +
16H T 2.5 28.3 + - - +
17H G 4.4 0.3 + - - -
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Residues in contact with THR 47 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8F PRO* 4.3 8.5 - - + -
9F ALA* 3.7 38.8 - - + +
43F VAL* 4.7 5.6 - - + -
44F THR* 3.3 15.4 - - - +
45F ARG 3.3 0.4 - - - -
46F THR* 1.3 78.1 - - - +
48F LEU* 1.3 63.9 + - - +
50F GLU* 3.0 14.6 + - - +
51F VAL* 3.0 22.5 + - + +
14H T 3.7 24.3 + - - +
15H T 3.2 20.5 + - - +
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Residues in contact with LEU 48 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12F ALA* 4.4 8.5 - - + -
16F ILE* 3.8 28.5 - - + -
34F GLU* 4.0 26.2 - - + +
37F LEU* 4.2 18.4 - - + -
38F SER* 4.6 4.3 - - - +
41F ILE* 4.2 14.8 - - + -
43F VAL* 4.0 12.5 - - + +
44F THR 3.3 11.4 + - - +
45F ARG* 3.1 11.6 + - - +
47F THR* 1.3 78.1 - - - +
49F ARG* 1.3 57.9 + - - +
51F VAL* 3.4 5.8 + - + -
52F LEU* 2.9 54.3 + - + +
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Residues in contact with ARG 49 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50E GLU* 2.6 46.8 + - - +
34F GLU* 2.9 33.9 + - + +
45F ARG* 2.9 39.3 + - + +
46F THR* 2.9 11.9 + - - +
48F LEU* 1.3 74.6 - - - +
50F GLU* 1.3 57.5 + - - +
52F LEU* 3.3 7.8 + - - +
53F GLN* 2.9 43.4 + - - +
13G G 2.3 61.9 + - - +
14G T 3.6 23.7 + - - +
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Residues in contact with GLU 50 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46E THR* 4.9 1.9 - - - +
49E ARG* 2.5 45.2 + - - +
50E GLU* 4.0 20.2 - - + -
53E GLN* 4.0 26.2 + - + +
9F ALA* 5.6 1.0 - - + +
46F THR* 2.9 27.1 + - + +
47F THR* 3.0 14.0 + - + +
49F ARG* 1.3 77.0 - - - +
51F VAL* 1.3 62.3 + - - +
53F GLN* 3.2 7.5 + - - +
54F ARG* 3.0 35.3 + - - +
14H T 4.1 18.8 + - - +
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Residues in contact with VAL 51 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9F ALA* 3.4 32.3 - - + +
12F ALA* 3.9 10.1 - - + -
13F GLU* 3.5 32.1 - - + +
16F ILE* 4.1 11.2 - - + -
47F THR 3.0 17.3 + - - +
48F LEU* 3.5 9.0 - - + +
50F GLU* 1.3 76.5 - - - +
52F LEU* 1.3 56.7 + - - +
54F ARG* 3.2 21.1 + - - +
55F LEU* 2.9 41.4 + - + +
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Residues in contact with LEU 52 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16F ILE* 3.8 22.4 - - + -
31F LEU* 3.7 19.5 - - + -
32F PRO 6.1 0.9 - - - +
34F GLU* 3.7 31.0 - - + +
37F LEU* 5.4 0.9 - - + -
48F LEU* 2.9 44.0 + - + +
49F ARG* 3.6 7.0 - - - +
51F VAL* 1.3 73.7 - - - +
53F GLN* 1.3 60.9 + - + +
55F LEU* 3.9 3.2 - - + +
56F ALA* 2.9 32.4 + - - +
61F LEU* 3.6 23.0 - - + +
63F ILE* 3.9 17.4 - - + +
69F THR* 5.0 3.8 - - - +
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Residues in contact with GLN 53 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50E GLU* 3.7 33.0 + - + +
53E GLN* 5.6 0.2 - - + -
54E ARG* 3.0 49.6 + - + +
49F ARG* 2.9 24.9 + - - +
50F GLU* 3.6 6.1 - - - +
52F LEU* 1.3 76.6 - - - +
54F ARG* 1.3 64.2 + - + +
56F ALA* 3.8 5.6 - - - +
57F ARG* 2.9 24.9 + - - +
63F ILE* 4.8 11.5 - - - +
13G G 3.7 27.1 + - - -
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Residues in contact with ARG 54 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53E GLN* 2.9 61.6 + - + +
54E ARG* 5.1 0.9 - - - +
57E ARG* 3.1 46.9 - - - +
9F ALA* 3.8 23.2 + - - +
10F GLY* 4.8 1.4 - - - +
13F GLU* 3.0 20.0 + - - +
50F GLU* 3.0 27.1 + - - +
51F VAL* 3.5 31.8 - - - +
53F GLN* 1.3 75.7 - - - +
55F LEU* 1.3 57.3 + - + +
57F ARG* 3.0 9.2 + - - +
58F ASP* 2.9 26.3 + - - +
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Residues in contact with LEU 55 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57E ARG* 4.7 2.2 - - - +
13F GLU* 3.6 29.6 - - + +
16F ILE* 3.7 36.1 - - + -
17F ILE* 3.6 26.9 - - + -
51F VAL* 2.9 38.5 + - + +
52F LEU 3.9 2.9 - - - +
54F ARG* 1.3 77.4 - - - +
56F ALA* 1.3 58.7 + - - +
58F ASP* 3.0 5.9 + - - +
59F GLY 2.9 22.2 + - - -
60F TRP* 3.0 26.6 + - + -
61F LEU* 4.2 12.8 - - + -
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Residues in contact with ALA 56 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52F LEU 2.9 19.7 + - - +
53F GLN* 3.8 6.3 - - - +
55F LEU* 1.3 76.0 - - - +
57F ARG* 1.3 58.6 + - - +
59F GLY* 3.1 17.2 + - - -
61F LEU* 3.9 24.8 - - + +
63F ILE* 3.8 27.4 - - + +
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Residues in contact with ARG 57 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13E GLU* 2.9 28.3 + - - -
54E ARG* 3.2 54.5 + - + +
55E LEU* 4.8 0.4 - - - +
57E ARG* 4.7 6.5 - - + -
58E ASP* 2.5 55.4 + - - +
53F GLN 2.9 15.4 + - - +
54F ARG* 3.0 11.0 + - - +
56F ALA* 1.3 76.1 - - - +
58F ASP* 1.3 61.3 + - - +
59F GLY* 4.6 0.2 - - - -
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Residues in contact with ASP 58 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57E ARG* 2.8 52.8 + - - +
13F GLU* 4.7 0.3 - - - +
54F ARG 2.9 6.3 + - - +
55F LEU* 3.0 10.8 + - - +
57F ARG* 1.3 79.4 - - - +
59F GLY* 1.3 56.5 + - - +
60F TRP* 3.5 18.7 + - + -
77F THR 4.8 0.2 - - - +
78F SER* 2.9 20.7 + - - -
79F GLY 4.6 0.2 + - - -
81F HIS* 3.1 42.3 + - + -
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Residues in contact with GLY 59 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55F LEU 2.9 1.8 + - - -
56F ALA 3.1 13.6 + - - -
57F ARG 3.3 0.6 - - - -
58F ASP* 1.3 78.9 - - - +
60F TRP* 1.3 62.6 + - - +
61F LEU 3.3 2.0 - - - -
72F ASN* 3.5 11.2 + - - +
74F PHE* 4.6 1.6 - - - -
77F THR* 2.4 39.0 + - - -
78F SER* 3.5 8.2 + - - -
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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