Contacts of the helix formed by residues 74 - 84 (chain B) in PDB entry 5FQU
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 74 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69B TYR* 5.2 0.2 - - - -
72B GLY 4.5 6.1 - - - +
73B TYR* 1.3 77.0 - - - +
75B PRO* 1.3 76.1 - - + +
76B ALA* 4.0 8.6 + - - +
77B GLU* 3.0 25.8 + - - +
78B LEU* 3.0 21.1 + - - +
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Residues in contact with PRO 75 (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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40B ILE* 3.7 8.6 - - + +
43B LEU* 3.8 28.0 - - + +
44B LYS* 3.6 31.2 - - + +
47B ASP* 3.4 29.6 - - + +
69B TYR* 4.0 9.2 - - + -
73B TYR 4.1 0.2 - - - -
74B THR* 1.3 87.1 - - + +
76B ALA* 1.3 55.3 + - - +
78B LEU* 3.2 16.1 + - + +
79B GLU* 2.8 28.5 + - - +
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Residues in contact with ALA 76 (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* 5.2 5.5 - - + +
74B THR* 3.0 8.9 - - - +
75B PRO* 1.3 77.7 - - + +
77B GLU* 1.3 60.4 + - - +
79B GLU* 3.5 11.8 + - - +
80B ARG* 3.0 25.1 + - - +
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Residues in contact with GLU 77 (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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73B TYR* 3.7 29.0 - - + -
74B THR* 3.0 21.7 + - - +
76B ALA* 1.3 77.1 - - - +
78B LEU* 1.3 66.1 + - - +
80B ARG* 2.4 44.2 + - - +
81B ILE* 3.0 31.2 + - + +
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Residues in contact with LEU 78 (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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40B ILE* 4.0 17.2 - - + +
43B LEU* 4.0 21.3 - - + -
65B VAL* 4.0 26.5 - - + +
68B LEU* 3.6 37.9 - - + -
69B TYR* 4.2 10.8 - - + +
73B TYR* 3.8 18.8 - - + -
74B THR 3.0 18.8 + - - +
75B PRO* 3.4 13.0 - - + +
77B GLU* 1.3 76.9 - - - +
79B GLU* 1.3 62.4 + - - +
81B ILE* 3.3 8.6 + - + +
82B ALA* 3.0 23.6 + - - +
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Residues in contact with GLU 79 (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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40B ILE* 4.1 11.4 - - + +
44B LYS* 2.7 40.2 + - - +
75B PRO 2.8 13.1 + - - +
76B ALA* 3.5 11.5 - - - +
77B GLU 3.2 0.2 - - - -
78B LEU* 1.3 78.3 - - - +
80B ARG* 1.3 61.9 + - - +
82B ALA* 3.2 3.3 + - - +
83B LEU* 3.1 44.9 + - + +
294B ILE* 3.8 21.3 - - + +
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Residues in contact with ARG 80 (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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76B ALA 3.0 17.1 + - - +
77B GLU* 2.4 42.9 + - - +
79B GLU* 1.3 77.4 - - - +
81B ILE* 1.3 69.9 + - - +
83B LEU* 3.4 6.5 + - - -
84B GLU* 3.1 64.4 + - + +
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Residues in contact with ILE 81 (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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68B LEU* 6.2 2.7 - - + -
73B TYR* 3.7 24.5 - - + +
77B GLU* 3.0 32.5 + - - +
78B LEU* 3.7 10.3 - - + +
80B ARG* 1.3 85.7 - - - +
82B ALA* 1.3 64.3 + - - +
84B GLU* 3.4 11.6 + - - -
85B MSE 3.6 28.5 + - + +
87B TRP* 6.5 0.2 - - + -
144B LEU* 3.7 39.5 - - + -
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Residues in contact with ALA 82 (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 LEU* 4.3 12.8 - - + -
40B ILE* 4.1 17.5 - - + -
78B LEU 3.0 16.7 + - - +
79B GLU* 3.2 5.5 + - - +
81B ILE* 1.3 81.1 - - - +
83B LEU* 1.3 59.2 + - - +
84B GLU 3.5 0.5 + - - -
85B MSE 4.3 2.4 + - - +
87B TRP* 3.4 34.2 + - + -
290B VAL* 4.1 22.6 - - + +
294B ILE* 4.7 0.4 - - + -
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Residues in contact with LEU 83 (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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79B GLU* 3.1 44.4 + - + +
80B ARG* 4.0 7.0 - - - +
81B ILE 3.3 0.2 - - - -
82B ALA* 1.3 76.7 - - - +
84B GLU* 1.3 63.8 + - + +
85B MSE 3.8 1.2 + - - -
290B VAL* 3.7 27.6 - - + -
291B PRO* 3.9 27.6 - - + -
294B ILE* 4.6 1.6 - - + -
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Residues in contact with GLU 84 (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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80B ARG* 3.1 55.9 + - + +
81B ILE* 3.4 4.2 + - - +
82B ALA 3.3 1.0 - - - -
83B LEU* 1.3 85.7 - - + +
85B MSE 1.3 60.0 + - - +
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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