Contacts of the strand formed by residues 37 - 51 (chain F) in PDB entry 5X6E
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 TYR 37 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28F ILE* 5.1 7.6 - - + -
29F PHE* 4.7 14.4 - - + -
33F ASP* 5.4 3.6 - - - -
35F GLN* 2.3 56.9 + - + -
36F GLU* 1.3 82.0 - - - +
38F CYS* 1.3 59.4 + - - +
39F ILE* 3.9 21.0 - - + +
69F ILE 3.7 1.6 - - - +
70F MET* 3.6 3.1 - - - -
71F SER* 2.5 39.4 + - - +
96F VAL* 4.0 21.8 - - + -
97F ILE 3.4 16.4 - - - +
98F LYS* 4.2 12.8 - - + -
99F ILE* 3.5 7.7 - - - +
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Residues in contact with CYS 38 (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 PHE* 5.9 4.9 - - - -
37F TYR* 1.3 71.0 - - - +
39F ILE* 1.3 63.0 + - - +
40F PHE* 5.1 1.8 - - - -
68F VAL* 4.2 12.3 - - - -
69F ILE 3.8 2.7 - - - -
70F MET* 3.7 19.7 - - + -
97F ILE* 2.7 58.0 + - + +
99F ILE* 3.5 5.5 - - + +
102F LEU* 3.5 43.1 - - + -
116F VAL* 6.3 1.6 - - - -
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Residues in contact with ILE 39 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28F ILE* 3.6 26.2 - - + +
29F PHE* 3.3 37.9 - - + -
37F TYR* 3.9 21.5 - - + +
38F CYS* 1.3 79.5 - - - +
40F PHE* 1.3 59.2 + - - +
41F LEU* 3.5 12.1 + - + +
68F VAL* 3.4 4.4 - - - -
69F ILE* 2.7 52.3 + - + +
85F LEU* 4.4 12.1 - - + -
94F ALA* 4.4 13.5 - - + -
95F TYR 3.8 7.0 - - - +
96F VAL* 4.8 8.7 - - + -
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Residues in contact with PHE 40 (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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5F ALA 3.7 21.3 - - - -
8F PHE* 3.8 28.3 - + + -
9F LYS* 3.9 22.4 - - + -
12F LEU* 3.9 21.1 - - + -
38F CYS* 4.0 3.2 + - - -
39F ILE* 1.3 69.2 - - - +
41F LEU* 1.3 65.4 + - - +
42F TYR* 3.1 23.9 + + + -
66F ALA* 4.5 4.3 - - + -
67F PHE 3.4 18.4 - - - -
68F VAL* 3.8 15.5 - - + +
94F ALA* 4.3 0.9 - - - -
95F TYR* 2.9 45.6 + + - +
97F ILE* 4.6 4.2 - - + +
115F TYR* 4.0 21.5 - + - -
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Residues in contact with LEU 41 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28F ILE* 5.1 7.9 - - + -
39F ILE* 3.5 6.8 + - + +
40F PHE* 1.3 71.4 - - - +
42F TYR* 1.3 54.6 + - - +
43F ASP 4.4 10.3 - - - +
44F GLY* 3.7 22.0 - - - +
46F THR* 4.0 22.4 - - + -
63F TYR* 3.8 24.9 - - + +
64F LYS 4.2 0.4 - - - -
65F GLY 2.7 37.0 - - - +
66F ALA* 3.2 1.2 - - - -
67F PHE* 2.9 25.7 + - + +
69F ILE* 4.6 11.7 - - + -
85F LEU* 6.2 0.7 - - + -
92F ALA* 5.0 8.1 - - + -
93F THR 4.1 13.5 - - - +
94F ALA* 3.8 16.6 - - + -
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Residues in contact with TYR 42 (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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76A THR* 5.6 1.2 - - - +
5F ALA* 5.3 1.3 - - + -
6F GLU* 2.7 45.0 + - - -
9F LYS* 3.4 39.5 + - + -
40F PHE* 3.1 24.5 + + + -
41F LEU* 1.3 70.6 - - - +
43F ASP* 1.3 76.1 + - + +
65F GLY* 3.0 18.8 - - - -
66F ALA* 3.1 11.7 + - + +
93F THR* 2.9 26.5 + - + +
95F TYR* 4.1 20.2 - + + -
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Residues in contact with ASP 43 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41F LEU* 4.4 5.1 - - - +
42F TYR* 1.3 100.3 - - + +
44F GLY* 1.3 58.3 + - - +
64F LYS* 5.9 2.5 + - - -
65F GLY* 4.3 7.6 - - - -
91F GLN* 2.1 39.0 + - + +
92F ALA* 3.5 1.9 + - - -
93F THR* 2.7 40.3 + - - +
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Residues in contact with GLY 44 (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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41F LEU* 3.7 9.3 - - - +
43F ASP* 1.3 85.4 + - - +
45F ILE* 1.3 70.4 + - - +
64F LYS* 3.4 5.5 + - - +
65F GLY* 3.0 25.3 + - - +
89F SER* 4.0 2.0 - - - -
91F GLN* 3.6 18.6 - - - -
92F ALA* 4.2 2.2 - - - -
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Residues in contact with ILE 45 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41F LEU* 5.2 1.3 - - - +
44F GLY* 1.3 82.9 - - - +
46F THR* 1.3 64.8 + - - +
62F TYR* 5.1 2.9 - - + -
63F TYR 3.3 6.7 - - - +
64F LYS* 4.3 33.0 - - + +
87F VAL* 3.6 9.3 - - - +
88F ILE* 3.0 47.7 + - + -
89F SER* 3.1 30.0 + - - +
91F GLN* 3.9 3.7 + - - +
92F ALA* 5.3 0.6 - - - +
154F TYR* 4.3 18.6 - - + +
166F LEU* 5.1 19.7 - - + -
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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
----------------------------------------------------------
28F ILE* 5.3 1.3 - - - -
41F LEU* 4.0 20.2 - - + -
45F ILE* 1.3 75.4 - - - +
47F LYS* 1.3 58.1 + - - +
62F TYR* 3.2 4.5 - - - +
63F TYR* 2.5 61.1 + - + +
69F ILE* 5.1 2.2 - - + -
85F LEU* 3.2 39.0 + - + +
86F GLU 2.8 23.3 + - - -
87F VAL* 3.8 10.1 + - - +
88F ILE* 3.4 7.0 - - - -
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Residues in contact with LYS 47 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46F THR* 1.3 72.8 - - - +
48F LEU* 1.3 61.3 + - - +
49F THR* 3.5 27.1 - - + -
57F ILE* 6.1 1.2 - - - +
59F ASN* 3.7 11.3 + - + +
61F GLN 3.4 5.4 - - - +
62F TYR* 3.4 22.0 - - + -
63F TYR* 4.9 0.9 - - - -
85F LEU* 3.2 13.2 - - - +
86F GLU* 2.8 65.6 + - + +
88F ILE* 3.6 23.4 - - + +
173F GLU* 2.2 36.9 + - - -
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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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128E LEU* 4.0 29.2 - - + -
29F PHE* 4.0 19.1 - - + -
47F LYS* 1.3 74.6 - - - +
49F THR* 1.3 62.6 + - - +
59F ASN* 3.9 0.3 - - - -
60F LEU* 3.0 43.1 + - + +
61F GLN* 2.7 18.7 + - + +
63F TYR* 4.0 25.1 - - + +
69F ILE* 5.3 4.5 - - + -
83F TYR* 3.6 26.5 - - + -
84F ASN 3.3 17.9 - - - +
85F LEU* 4.1 7.2 - - + -
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Residues in contact with THR 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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47F LYS* 3.5 25.0 - - + +
48F LEU* 1.3 74.6 - - - +
50F SER* 1.3 61.6 + - - +
51F ILE* 5.2 3.5 - - - +
57F ILE* 4.6 10.3 - - + -
58F MET 3.2 10.1 - - - +
59F ASN* 3.2 27.8 - - - +
60F LEU* 4.8 0.7 - - - -
83F TYR* 3.3 5.9 - - - -
84F ASN* 2.4 68.2 + - - +
86F GLU* 5.1 5.2 + - - +
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Residues in contact with SER 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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132E ASN* 3.6 25.8 + - - -
220E LYS* 3.9 15.4 - - - +
31F GLN* 4.7 1.4 + - - -
49F THR* 1.3 73.5 - - - +
51F ILE* 1.3 70.2 + - - +
52F SER 4.2 0.9 + - - -
56F THR 4.3 0.5 - - - +
57F ILE* 3.5 2.3 - - - +
58F MET* 3.0 32.2 + - - +
60F LEU* 4.8 1.6 - - - +
82F TYR 3.8 12.2 + - - -
83F TYR* 3.7 22.4 - - - -
84F ASN* 4.5 1.1 - - - +
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Residues in contact with ILE 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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31F GLN* 3.0 33.6 + - - +
32F TRP* 4.5 17.7 - - + -
49F THR* 5.2 4.3 - - - +
50F SER* 1.3 84.9 + - - +
52F SER* 1.3 75.6 + - - +
53F GLU 4.0 0.2 + - - -
55F GLY* 4.3 9.4 - - - +
56F THR 4.1 2.0 - - - -
57F ILE* 3.7 33.0 - - + -
84F ASN* 3.8 20.0 - - - +
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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