Contacts of the helix formed by residues 47 - 58 (chain B) in PDB entry 1FUU
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 ILE 47 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B ILE* 4.5 15.5 - - + -
45B SER* 3.3 5.6 + - - +
46B ALA* 1.3 79.0 - - + +
48B GLN* 1.3 60.7 + - + +
50B ARG* 3.2 1.7 + - - +
51B ALA* 2.8 41.6 + - + +
63B ALA* 4.9 6.5 - - + -
64B GLN 3.6 20.6 - - - +
65B ALA* 4.1 27.1 - - + -
70B GLY 5.8 1.1 - - - +
71B LYS* 5.4 4.3 - - + -
74B THR* 4.0 15.5 - - + +
199B LEU* 5.8 0.7 - - + -
221B ILE* 4.0 22.7 - - + -
223B VAL* 6.1 0.4 - - + -
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Residues in contact with GLN 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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23B PHE* 3.4 14.3 - - - -
26B MSE 3.9 4.2 - - - +
41B PHE* 3.5 30.1 - - - -
43B GLU 4.4 0.5 - - - +
44B PRO* 3.4 14.5 - - + +
45B SER* 3.0 35.5 + - - +
47B ILE* 1.3 72.5 - - + +
49B GLN* 1.3 61.0 + - - +
50B ARG 3.0 6.2 + - - -
52B ILE* 3.3 38.0 + - + +
53B MSE 5.1 0.5 + - - +
70B GLY* 3.1 20.3 + - - +
73B GLY 3.9 4.9 - - - -
74B THR* 3.2 29.1 - - - +
77B ILE* 4.3 3.8 - - - +
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Residues in contact with GLN 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B LYS 3.9 0.9 - - - +
19B VAL* 3.4 17.6 - - + +
20B VAL* 3.1 41.2 + - - +
21B TYR* 3.9 28.8 + - - -
26B MSE 4.8 1.1 - - - -
43B GLU* 2.6 31.1 + - - -
44B PRO* 3.0 20.0 + - + +
45B SER 2.8 24.0 + - - +
46B ALA* 3.8 14.7 - - - +
47B ILE 3.3 0.4 - - - -
48B GLN* 1.3 75.5 - - - +
50B ARG* 1.3 65.6 + - - +
53B MSE 5.7 2.3 - - - +
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Residues in contact with ARG 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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12B ILE* 3.9 38.3 + - - +
14B THR* 4.1 26.7 - - + +
16B TYR* 4.2 9.1 - - + -
18B LYS 4.0 15.4 - - - +
19B VAL* 4.2 23.7 - - - +
46B ALA* 3.3 26.8 + - - +
47B ILE 3.2 5.0 + - - +
48B GLN 3.0 0.4 - - - -
49B GLN* 1.3 92.0 + - - +
51B ALA* 1.3 60.5 + - - +
52B ILE 3.6 1.6 - - - -
53B MSE 4.9 1.1 - - - -
54B PRO* 2.8 26.7 - - - +
221B ILE* 3.9 23.7 - - + +
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Residues in contact with ALA 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 ILE* 2.8 29.1 + - + +
50B ARG* 1.3 74.9 - - - +
52B ILE* 1.3 62.0 + - - +
54B PRO* 3.0 9.0 - - - +
55B ILE* 3.0 28.9 - - + +
61B VAL* 4.9 2.7 - - + -
63B ALA* 4.6 9.4 - - + -
74B THR* 3.7 17.3 - - + -
199B LEU* 5.9 0.2 - - + -
221B ILE* 3.6 20.2 - - + -
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Residues in contact with ILE 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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23B PHE* 3.9 13.9 - - + -
26B MSE 3.7 16.6 - - - -
28B LEU* 5.1 0.9 - - + -
48B GLN* 3.3 43.1 + - + +
50B ARG 3.6 0.2 - - - -
51B ALA* 1.3 74.8 - - - +
53B MSE 1.3 87.2 + - + +
55B ILE* 3.2 7.0 + - - +
56B ILE* 2.9 32.6 + - + +
74B THR* 3.9 21.8 - - - +
77B ILE* 4.3 26.7 - - + -
78B ALA* 4.0 7.4 - - + +
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Residues in contact with MSE 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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16B TYR* 4.2 6.7 - - + +
18B LYS* 5.4 4.0 - - + +
20B VAL* 3.5 30.5 - - + -
26B MSE 3.3 52.3 - - + +
27B GLU* 4.3 6.3 - - - +
28B LEU* 4.3 1.8 - - + -
48B GLN 5.1 0.6 + - - +
49B GLN 5.7 2.9 - - - +
50B ARG 4.5 1.3 + - - -
52B ILE* 1.3 112.5 - - + +
54B PRO* 1.3 65.5 - - + +
56B ILE* 3.1 17.4 + - + +
57B GLU* 2.8 47.5 + - - +
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Residues in contact with PRO 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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16B TYR* 3.7 34.1 - - + +
50B ARG 2.8 28.5 - - - +
51B ALA* 3.0 18.2 - - - +
53B MSE 1.3 92.7 - - + +
55B ILE* 1.3 60.1 + - - +
57B GLU* 3.3 1.1 + - + -
58B GLY 3.2 4.7 + - - -
59B HIS* 3.2 29.5 + - - +
61B VAL* 4.2 6.5 - - + -
219B VAL* 4.1 28.3 - - + -
221B ILE* 4.7 0.7 - - + -
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Residues in contact with ILE 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 ALA* 3.0 24.0 + - + +
52B ILE 3.5 6.3 - - - +
53B MSE 3.2 0.4 - - - -
54B PRO* 1.3 73.6 - - - +
56B ILE* 1.3 66.8 + - - +
58B GLY 3.0 3.1 + - - -
61B VAL* 3.8 21.1 - - + -
74B THR* 4.2 21.8 - - + -
75B PHE* 4.4 8.1 - - + -
78B ALA* 3.3 20.4 - - + -
82B ARG* 3.6 3.5 + - - -
165B MSE 3.2 29.6 - - + +
167B ILE* 5.4 0.9 - - + -
195B GLN* 2.7 25.5 - - - +
197B VAL* 3.7 33.0 - - + -
199B LEU* 5.6 1.3 - - + -
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Residues in contact with ILE 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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26B MSE 5.7 1.8 - - - +
28B LEU* 5.4 2.5 - - + -
52B ILE* 2.9 21.2 + - + +
53B MSE 3.4 28.3 - - + +
55B ILE* 1.3 75.3 - - - +
57B GLU* 1.3 62.3 + - + +
58B GLY 3.0 0.2 + - - -
78B ALA* 3.1 36.8 - - - +
81B GLN* 3.2 33.9 - - + -
82B ARG* 2.6 36.0 + - + +
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Residues in contact with GLU 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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16B TYR* 2.5 33.4 + - - -
18B LYS* 4.2 11.4 + - - +
53B MSE 2.8 30.6 + - - +
54B PRO 3.7 4.9 - - - +
55B ILE 3.2 0.2 - - - -
56B ILE* 1.3 76.8 - - + +
58B GLY* 1.3 56.9 + - - +
59B HIS* 3.6 22.5 + - + +
82B ARG* 3.7 6.4 + - - -
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Residues in contact with GLY 58 (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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54B PRO 3.2 0.2 + - - -
55B ILE 3.0 8.2 + - - -
56B ILE 3.0 0.8 + - - -
57B GLU* 1.3 77.9 - - - +
59B HIS* 1.3 62.6 + - - +
60B ASP* 3.8 1.6 + - - +
82B ARG* 3.3 17.3 - - - -
195B GLN* 3.0 28.5 - - - +
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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