Contacts of the helix formed by residues 68 - 83 (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 GLY 68 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66B GLN 3.5 2.1 + - - -
67B SER* 1.3 77.0 - - - +
69B THR* 1.3 66.2 + - - -
70B GLY 3.1 4.0 - - - -
71B LYS* 3.2 8.7 + - - +
72B THR* 3.1 26.4 + - - -
104B GLN* 5.9 4.7 - - - -
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Residues in contact with THR 69 (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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39B TYR* 3.6 32.4 + - + -
41B PHE* 3.3 16.8 - - + -
68B GLY* 1.3 69.2 - - - -
70B GLY* 1.3 66.0 + - - +
72B THR* 4.3 6.5 - - - -
73B GLY 2.8 24.9 + - - -
104B GLN* 6.0 0.8 - - - +
108B VAL* 4.9 5.0 - - - +
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Residues in contact with GLY 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B PHE* 4.3 4.5 - - - -
45B SER* 4.5 11.4 - - - -
47B ILE* 6.0 1.8 - - - -
48B GLN* 3.1 27.4 + - - +
68B GLY* 3.1 1.6 - - - -
69B THR* 1.3 86.7 - - - +
71B LYS* 1.3 59.0 + - - +
74B THR* 3.0 19.9 + - - -
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Residues in contact with LYS 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B ILE* 5.4 4.2 - - + +
65B ALA* 3.6 29.2 - - + -
66B GLN 3.3 28.9 + - - +
67B SER* 3.3 19.9 - - - +
68B GLY* 3.2 8.1 + - - +
70B GLY* 1.3 74.4 - - - +
72B THR* 1.3 68.9 + - - +
74B THR* 2.9 23.9 + - - -
75B PHE* 3.4 13.2 + - + -
169B ASP* 3.1 32.5 + - - +
170B GLU* 3.8 19.7 + - - +
199B LEU* 3.9 22.2 - - + -
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Residues in contact with THR 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B GLY 3.1 19.5 + - - -
69B THR* 3.9 7.4 - - - -
71B LYS* 1.3 81.2 + - - +
73B GLY* 1.3 61.9 + - - +
75B PHE* 3.5 22.4 + - + -
76B SER* 2.7 36.3 + - - +
104B GLN* 5.3 6.7 + - + -
105B ILE* 4.3 17.8 - - + +
108B VAL* 3.5 37.2 - - + +
169B ASP* 5.1 1.7 + - - -
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Residues in contact with GLY 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B PHE* 3.9 21.1 - - - -
48B GLN* 3.9 6.5 - - - -
69B THR 2.8 18.5 + - - -
70B GLY 3.9 1.6 - - - -
72B THR* 1.3 77.3 - - - +
74B THR* 1.3 53.3 + - - +
76B SER* 4.2 4.9 - - - -
77B ILE* 2.8 39.0 + - - +
108B VAL* 4.6 1.5 - - - +
112B LEU* 4.4 5.2 - - - -
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Residues in contact with THR 74 (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* 4.0 8.1 - - + +
48B GLN* 3.2 22.5 + - - +
51B ALA* 3.7 29.6 - - + -
52B ILE* 3.9 19.8 - - + +
55B ILE* 4.2 10.8 - - + -
70B GLY 3.0 15.2 + - - -
71B LYS* 2.9 17.5 + - - -
73B GLY* 1.3 78.5 - - - +
75B PHE* 1.3 64.3 + - + +
78B ALA* 3.3 20.6 + - - +
199B LEU* 5.2 7.2 - - + -
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Residues in contact with PHE 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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55B ILE* 4.4 13.9 - - + -
71B LYS* 3.4 25.9 + - + -
72B THR* 3.8 16.2 - - + -
74B THR* 1.3 79.8 - - + +
76B SER* 1.3 71.4 + - - +
77B ILE 3.4 0.2 - - - -
78B ALA* 4.0 1.2 - - - +
79B ALA* 2.9 31.9 + - - +
94B MSE 3.9 27.1 - - + -
105B ILE* 4.1 18.4 - - + -
165B MSE 5.1 0.2 - - - +
167B ILE* 3.7 33.6 - - + +
169B ASP* 3.7 39.9 - - + -
199B LEU* 3.6 22.9 - - + -
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Residues in contact with SER 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B THR* 2.7 35.4 + - - +
75B PHE* 1.3 85.6 - - - +
77B ILE* 1.3 59.8 + - - +
79B ALA* 3.8 3.3 - - - +
80B LEU* 2.9 38.0 + - - +
94B MSE 5.0 3.4 - - - -
105B ILE* 4.9 2.3 - - - +
108B VAL* 3.8 4.1 - - - +
109B VAL* 4.3 17.6 + - - +
112B LEU* 3.5 22.7 - - - -
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Residues in contact with ILE 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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23B PHE* 3.8 23.1 - - + -
28B LEU* 4.2 19.3 - - + -
32B LEU* 3.3 27.4 - - + +
36B VAL* 3.7 26.7 - - + -
41B PHE* 4.6 7.9 - - + -
48B GLN* 4.3 6.1 - - - +
52B ILE* 4.3 19.3 - - + -
73B GLY* 2.8 36.5 + - - +
74B THR 4.2 1.8 - - - +
76B SER* 1.3 73.2 - - - +
78B ALA* 1.3 62.4 + - - +
80B LEU* 3.3 0.6 + - - -
81B GLN* 3.1 17.9 + - + +
112B LEU* 4.1 13.5 - - + -
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Residues in contact with ALA 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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52B ILE* 4.0 8.0 - - + +
55B ILE* 3.3 36.6 - - + -
56B ILE* 3.1 28.1 - - + +
74B THR 3.3 18.0 + - - +
75B PHE 4.1 1.8 - - - +
77B ILE* 1.3 79.9 - - - +
79B ALA* 1.3 62.8 + - - +
81B GLN 3.1 10.4 + - - -
82B ARG* 3.2 8.5 + - - +
165B MSE 4.7 2.2 - - - -
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Residues in contact with ALA 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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75B PHE 2.9 21.0 + - - +
76B SER* 3.8 4.5 - - - +
78B ALA* 1.3 77.2 - - - +
80B LEU* 1.3 61.8 + - - +
82B ARG* 3.1 12.5 + - - +
83B ILE* 3.2 18.8 + - - +
92B ALA* 4.6 14.9 - - + +
94B MSE 5.4 7.2 - - - -
141B ILE* 4.9 7.2 - - + -
165B MSE 3.8 26.4 - - - -
167B ILE* 5.3 4.5 - - + -
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Residues in contact with LEU 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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32B LEU* 3.8 20.9 - - + -
76B SER 2.9 21.4 + - - +
77B ILE 3.8 3.8 - - - +
79B ALA* 1.3 76.5 - - - +
81B GLN* 1.3 60.3 + - - +
82B ARG 3.5 0.3 + - - -
83B ILE* 3.5 14.4 + - + +
109B VAL* 3.7 17.5 - - + +
112B LEU* 3.5 32.1 - - + -
113B ALA* 3.8 11.0 - - + +
116B MSE 3.6 25.1 - - + +
118B ILE* 3.7 33.2 - - + -
141B ILE* 3.8 17.9 - - + -
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Residues in contact with GLN 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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26B MSE 5.8 0.4 - - - +
27B GLU 4.0 8.5 + - - +
28B LEU* 3.1 17.5 - - + -
29B ASP* 2.7 41.3 + - - +
32B LEU* 3.7 11.9 - - + +
56B ILE* 3.2 42.2 - - + -
77B ILE 3.1 10.3 + - - +
78B ALA 3.1 1.7 + - - +
80B LEU* 1.3 78.1 - - - +
82B ARG* 1.3 59.0 + - - +
83B ILE 3.4 3.3 + - - +
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Residues in contact with ARG 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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55B ILE 3.6 7.0 + - - -
56B ILE* 2.6 34.5 + - + +
57B GLU 3.7 5.7 + - - -
58B GLY* 3.3 19.8 - - - +
78B ALA 3.2 7.8 + - - +
79B ALA* 3.1 9.6 + - - +
81B GLN* 1.3 77.6 - - - +
83B ILE* 1.3 63.9 + - - +
84B ASP* 3.6 3.1 + - - +
91B GLN* 4.2 2.9 - - - +
164B LYS* 5.8 8.8 - - - +
165B MSE 3.4 30.3 - - + -
195B GLN* 3.6 7.9 - - - +
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Residues in contact with ILE 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 ALA 3.2 15.2 + - - +
80B LEU* 3.8 14.2 - - + +
81B GLN 3.4 4.7 - - - +
82B ARG* 1.3 79.1 - - - +
84B ASP* 1.3 70.6 + - - +
85B THR* 3.4 9.4 + - - +
91B GLN* 3.5 35.0 - - + +
92B ALA* 4.3 7.2 - - + -
116B MSE 5.4 1.7 - - + +
118B ILE* 3.7 28.0 - - + -
140B GLN* 3.6 20.2 - - + +
141B ILE* 3.8 25.1 - - + -
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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
------------------------------------------------------------
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