Contacts of the strand formed by residues 84 - 92 (chain F) in PDB entry 5GAG
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 PRO 84 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43F ALA* 4.5 10.6 - - - +
44F ILE* 4.7 4.2 + - + +
47F LYS* 4.1 30.7 - - + +
50F LEU* 3.6 14.3 - - + +
67F ILE* 3.4 32.1 - - + -
68F THR 3.4 7.9 - - - +
69F LYS* 4.3 9.9 - - + -
82F GLY 3.5 3.3 - - - +
83F TYR* 1.3 85.0 - - + +
85F ILE* 1.3 65.8 + - - +
86F GLY 3.5 0.4 - - - -
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Residues in contact with ILE 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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2311A A 3.9 32.1 - - + +
2312A U 3.1 42.6 - - - +
39F GLY* 5.5 0.4 - - - -
40F VAL* 3.1 22.7 + - - +
41F GLY* 3.4 14.6 + - - +
43F ALA* 5.5 1.3 - - - -
44F ILE* 3.8 13.2 - - + -
50F LEU* 4.8 0.4 - - - -
68F THR* 2.9 9.1 + - - +
70F ALA* 4.3 13.2 - - + +
79F ILE* 3.6 31.0 - - + -
83F TYR* 3.1 14.9 + - + +
84F PRO* 1.3 81.8 - - - +
86F GLY* 1.3 59.8 + - - +
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Residues in contact with GLY 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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2312A U 4.5 0.4 - - - -
38F MET 3.4 12.8 - - - -
39F GLY* 4.7 0.9 - - - -
40F VAL* 3.9 2.0 - - - -
50F LEU* 3.7 18.7 - - - +
67F ILE* 3.3 6.4 - - - +
68F THR* 2.5 38.9 + - - +
84F PRO 3.5 2.0 - - - -
85F ILE* 1.3 82.8 - - - +
87F CYS* 1.3 55.5 + - - -
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Residues in contact with CYS 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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2312A U 4.6 0.6 + - - -
37F ASN* 3.3 5.8 - - - +
38F MET* 2.9 50.2 + - - -
50F LEU* 3.7 17.7 - - + -
53F ALA* 4.6 0.7 - - - -
54F ALA* 4.3 21.3 - - - -
57F LEU* 3.8 17.3 - - - +
65F PRO* 4.1 7.6 - - + -
66F LEU 3.2 14.6 - - - +
67F ILE* 3.9 14.4 - - + +
68F THR* 3.8 2.7 + - - +
86F GLY* 1.3 74.6 - - - +
88F LYS* 1.3 59.9 + - - +
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Residues in contact with LYS 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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2313A C 3.6 33.3 + - - +
2314A A 3.0 29.6 + - - +
42B C 4.0 21.2 - - - +
35F THR* 4.6 4.5 - - + -
36F LEU 3.1 11.0 - - - +
37F ASN* 3.8 10.1 - - - +
57F LEU* 4.1 2.2 - - - -
65F PRO* 3.8 0.2 - - - +
66F LEU* 2.9 57.6 + - + +
68F THR* 3.9 12.8 - - + +
87F CYS* 1.3 75.5 - - - +
89F VAL* 1.3 63.6 + - - +
90F THR* 4.1 9.4 - - - +
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Residues in contact with VAL 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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42B C 3.5 2.7 - - - +
34F ILE 3.7 2.1 - - - +
35F THR* 3.4 2.9 - - - -
36F LEU* 2.9 38.5 + - + +
57F LEU* 4.1 10.9 - - + +
61F SER* 3.6 35.7 - - - +
63F GLN* 3.3 31.2 - - + +
64F LYS 4.0 4.0 - - - +
65F PRO* 3.5 32.5 - - + -
88F LYS* 1.3 79.0 - - - +
90F THR* 1.3 60.5 + - - +
91F LEU* 3.9 8.3 - - + -
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Residues in contact with THR 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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2314A A 4.5 2.9 + - - +
42B C 2.6 36.0 + - - +
43B C 3.2 31.6 + - - +
33F LYS* 3.9 26.7 - - + +
34F ILE 3.8 2.7 - - - +
35F THR* 3.4 29.6 - - + +
63F GLN* 3.4 5.5 + - - -
88F LYS* 4.1 9.4 - - - -
89F VAL* 1.3 71.0 - - - +
91F LEU* 1.3 59.5 + - - +
92F ARG* 4.2 14.4 - - - +
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Residues in contact with LEU 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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43B C 5.8 0.2 - - - -
33F LYS* 3.6 1.9 - - - +
34F ILE* 2.8 43.6 + - + +
36F LEU* 4.2 11.0 - - + -
61F SER* 3.9 28.3 - - - +
63F GLN* 3.4 31.6 - - - +
89F VAL* 3.9 9.2 - - + -
90F THR* 1.3 72.3 - - - +
92F ARG* 1.3 66.1 + - - +
95F ARG* 3.8 23.3 - - + +
96F MET* 3.8 15.1 - - + +
99F PHE* 4.1 34.5 - - + -
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Residues in contact with ARG 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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43B C 2.1 51.7 + - - +
44B G 6.0 0.4 - - - -
45B A 2.7 68.1 + - - +
32F GLU* 4.1 17.0 + - - +
33F LYS* 3.8 36.6 - - + +
90F THR* 4.2 8.1 - - - +
91F LEU* 1.3 78.6 - - - +
93F GLY* 1.3 70.0 + - - +
94F GLU 3.4 1.7 + - - -
95F ARG* 3.5 8.0 + - - +
96F MET* 3.4 15.7 + - - -
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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