Contacts of the strand formed by residues 84 - 98 (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 ASN 84 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27F LEU* 4.0 21.7 - - + +
29F PHE 3.5 3.1 - - - -
30F ASN* 3.1 7.0 - - - +
31F GLN* 2.4 46.5 + - - +
32F TRP* 3.8 7.1 - - - -
47F LYS 3.5 0.5 - - - +
48F LEU* 3.2 7.7 - - - +
49F THR* 2.4 72.2 + - - +
51F ILE* 3.8 30.9 - - - +
83F TYR* 1.3 69.6 - - - +
85F LEU* 1.3 58.9 + - - +
86F GLU* 3.8 1.1 - - + +
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Residues in contact with LEU 85 (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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26F GLU 3.7 0.9 - - - +
27F LEU* 3.5 4.1 - - - +
28F ILE* 3.2 51.1 + - + +
29F PHE* 3.0 45.5 + - + +
39F ILE* 4.4 11.7 - - + -
41F LEU* 6.2 0.4 - - + -
46F THR* 3.2 27.7 + - + +
47F LYS 3.2 25.6 - - - +
48F LEU* 4.1 12.1 - - + -
63F TYR* 4.2 12.6 - - + -
69F ILE* 4.7 10.1 - - + -
83F TYR 4.3 0.2 + - - -
84F ASN* 1.3 72.2 - - - +
86F GLU* 1.3 60.3 + - - +
87F VAL 3.9 0.3 + - - -
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Residues in contact with GLU 86 (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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25F LYS* 4.3 23.9 - - - +
26F GLU 3.6 5.6 - - - +
27F LEU* 4.2 20.2 - - + +
46F THR* 2.8 18.8 + - - -
47F LYS* 2.8 57.1 + - + +
49F THR* 5.1 5.7 + - - +
84F ASN* 3.8 2.5 - - + -
85F LEU* 1.3 70.6 - - - +
87F VAL* 1.3 73.9 + - - +
88F ILE* 3.8 0.5 + - - +
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Residues in contact with VAL 87 (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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22F PHE* 4.3 16.4 - - + -
23F HIS 3.8 22.2 - - - +
24F LYS* 4.5 0.5 - - - +
25F LYS* 3.2 20.7 + - - +
26F GLU 3.1 19.0 + - - +
28F ILE* 4.4 17.5 - - + -
45F ILE 3.6 11.4 - - - +
46F THR* 3.9 4.7 - - - +
86F GLU* 1.3 84.2 - - - +
88F ILE* 1.3 60.4 + - - +
89F SER 3.1 24.5 - - - +
92F ALA* 3.5 23.8 - - + -
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Residues in contact with ILE 88 (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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24F LYS* 3.2 28.7 - - - +
45F ILE* 3.0 27.7 + - + +
46F THR 3.4 32.8 - - - +
47F LYS* 3.5 36.3 - - + +
62F TYR* 4.1 15.9 - - + +
86F GLU* 5.7 0.2 - - - +
87F VAL* 1.3 73.2 - - - +
89F SER* 1.3 69.5 + - - +
166F LEU* 5.4 11.0 - - + -
167F ASP 5.0 11.2 - - - +
168F ASN* 5.1 10.8 - - + +
173F GLU* 5.5 0.7 - - - +
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Residues in contact with SER 89 (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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24F LYS* 3.8 2.1 - - - -
44F GLY* 4.0 0.5 - - - -
45F ILE* 3.1 36.8 + - - +
87F VAL* 3.1 23.6 - - - +
88F ILE* 1.3 82.7 - - - +
90F GLU* 1.3 63.7 + - - +
91F GLN* 2.3 38.7 + - - -
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Residues in contact with GLU 90 (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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21F GLN* 5.7 1.0 + - - -
22F PHE 4.0 0.5 - - - +
23F HIS* 3.2 29.0 - - + +
24F LYS* 3.7 27.6 - - + +
88F ILE 3.6 1.8 + - - -
89F SER* 1.3 71.7 - - - +
91F GLN* 1.3 62.3 + - + +
92F ALA 3.9 0.3 + - - -
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Residues in contact with GLN 91 (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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21F GLN* 5.3 8.3 - - - +
43F ASP* 2.1 38.0 + - + +
44F GLY* 3.6 9.3 - - - +
45F ILE* 5.8 3.0 - - - +
89F SER* 2.3 36.4 + - - +
90F GLU* 1.3 84.1 - - + +
92F ALA* 1.3 68.9 + - - +
93F THR* 5.4 2.7 - - - +
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Residues in contact with ALA 92 (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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21F GLN* 3.3 11.1 - - - +
22F PHE* 2.9 53.1 + - + +
28F ILE* 6.0 1.1 - - + -
41F LEU* 5.0 9.6 - - + -
43F ASP 3.5 6.3 - - - -
44F GLY* 4.2 2.9 - - - -
45F ILE 5.3 0.7 - - - +
46F THR* 6.5 0.4 - - - -
87F VAL* 3.5 25.4 - - + -
91F GLN* 1.3 79.7 - - - +
93F THR* 1.3 62.6 + - - +
94F ALA* 5.5 0.2 - - - -
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Residues in contact with THR 93 (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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19F PRO* 4.1 22.0 - - + -
20F LYS 4.3 3.6 - - - +
21F GLN* 3.7 25.0 + - + +
41F LEU* 3.8 2.2 - - - +
42F TYR* 2.9 35.8 + - + +
43F ASP* 2.7 29.5 + - - +
91F GLN* 5.5 2.8 - - - +
92F ALA* 1.3 75.2 + - - +
94F ALA* 1.3 64.7 + - - +
95F TYR* 4.9 2.2 - - + -
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Residues in contact with ALA 94 (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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19F PRO* 3.7 0.7 - - - +
20F LYS* 3.1 38.2 + - - +
22F PHE* 4.6 14.8 - - + -
28F ILE* 4.8 3.6 - - + -
39F ILE* 4.4 13.5 - - + -
40F PHE 3.5 12.3 - - - +
41F LEU* 3.8 19.7 - - + +
42F TYR 4.0 1.1 - - - +
92F ALA* 4.2 0.9 - - + -
93F THR* 1.3 77.3 - - - +
95F TYR* 1.3 66.5 + - - +
96F VAL* 4.0 3.4 + - + +
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Residues in contact with TYR 95 (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 LYS* 3.4 38.8 - - + +
12F LEU* 3.6 26.5 - - + -
13F GLU* 3.6 26.9 + - + -
17F ILE* 3.7 23.3 - - + -
18F LYS* 4.1 3.8 - - - -
19F PRO* 3.5 43.7 - - + +
39F ILE* 3.8 2.6 - - - +
40F PHE* 2.9 49.5 + + + +
42F TYR* 4.1 20.4 - + + -
93F THR* 4.9 3.0 - - + +
94F ALA* 1.3 77.0 - - - +
96F VAL* 1.3 61.5 + - - +
97F ILE* 3.5 6.1 - - - +
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Residues in contact with VAL 96 (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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17F ILE* 4.6 9.9 - - - +
18F LYS 4.8 6.1 + - - +
20F LYS* 4.8 7.6 - - + -
22F PHE* 4.1 30.7 - - + -
28F ILE* 4.7 9.4 - - + -
37F TYR* 4.0 35.7 - - + -
38F CYS 4.1 1.8 - - - -
39F ILE* 4.8 9.6 - - + +
94F ALA 4.0 4.7 + - - +
95F TYR* 1.3 74.5 - - - +
97F ILE* 1.3 67.3 + - - +
101F GLU* 5.2 0.5 - - - +
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Residues in contact with ILE 97 (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* 5.8 2.7 - - + -
12F LEU* 4.2 33.2 - - + -
17F ILE* 4.5 7.4 - - + -
37F TYR* 3.4 10.4 - - - -
38F CYS* 2.7 64.4 + - + +
40F PHE* 4.6 5.4 - - + +
95F TYR 3.5 17.3 - - - +
96F VAL* 1.3 80.0 - - - +
98F LYS* 1.3 70.2 + - - +
101F GLU* 3.3 26.0 - - + +
102F LEU* 4.7 10.1 - - + +
105F LEU* 4.4 14.6 - - + -
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Residues in contact with LYS 98 (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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35F GLN* 5.9 2.7 - - - +
36F GLU* 3.8 20.6 + - - +
37F TYR* 4.2 16.3 - - + -
38F CYS* 5.4 0.2 - - - -
77F GLU* 2.7 33.7 + - - +
97F ILE* 1.3 85.1 - - - +
99F ILE* 1.3 93.9 + - - +
100F ASN* 3.0 37.2 + - + +
101F GLU* 3.1 26.1 + - + +
102F LEU* 3.6 1.6 + - - -
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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