Contacts of the strand formed by residues 86 - 93 (chain W) 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 LEU 86 (chain W).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21W ARG* 4.5 2.3 + - - -
26W PHE* 3.7 41.8 - - + +
44W HIS* 3.0 12.0 + - + +
47W VAL* 4.0 24.5 - - + +
48W MET* 3.7 23.3 - - + -
51W GLN* 3.9 25.6 - - + -
77W VAL* 4.3 15.9 - - + -
78W GLN 4.1 2.2 - - - +
79W ARG* 3.9 24.5 - - + +
85W LYS* 1.3 79.7 - - - +
87W GLN* 1.3 69.3 + - - +
88W HIS 4.8 0.7 - - - +
89W ILE* 4.5 7.6 - - + -
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Residues in contact with GLN 87 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76B G 4.9 0.2 - - - +
77B U 5.0 9.8 - - - -
21W ARG* 3.0 55.5 + - - +
26W PHE* 4.1 1.6 - - - -
27W PRO* 3.9 9.5 - - - +
78W GLN* 2.8 30.5 + - + +
79W ARG 3.6 3.8 - - - +
80W HIS* 3.3 56.1 - - - +
81W PRO* 5.3 1.1 - - + +
85W LYS* 4.0 9.1 + - - +
86W LEU* 1.3 79.4 - - - +
88W HIS* 1.3 62.9 + - - +
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Residues in contact with HIS 88 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75B G 2.7 44.2 + - - -
76B G 3.1 39.6 + - - +
26W PHE* 4.2 3.5 - - - -
27W PRO* 3.5 25.8 - - + -
28W ALA* 4.0 5.3 - - - -
29W ILE* 4.1 4.0 - - + -
77W VAL* 3.4 2.1 - - - +
78W GLN* 2.9 38.8 + - - +
86W LEU* 3.5 2.0 - - - +
87W GLN* 1.3 81.7 - - - +
89W ILE* 1.3 89.4 + - - +
90W ASP* 3.1 26.3 + - - -
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Residues in contact with ILE 89 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26W PHE* 3.5 31.2 - - + -
27W PRO 3.8 4.2 + - - -
28W ALA* 3.3 4.4 - - + +
29W ILE 3.0 27.5 + - - +
42W LEU* 4.5 0.4 - - + -
47W VAL* 4.0 16.8 - - + -
56W PHE* 4.7 10.3 - - + -
74W ALA* 5.5 2.2 - - + -
75W GLN 5.4 1.1 - - - +
76W ASP 3.3 13.2 - - - +
77W VAL* 4.8 11.4 - - + -
86W LEU* 4.5 8.1 - - + -
88W HIS* 1.3 90.6 + - - +
90W ASP* 1.3 74.2 + - - +
91W PHE* 3.6 35.9 - - + -
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Residues in contact with ASP 90 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74B U 5.2 1.2 + - - -
75B G 3.6 15.2 + - - +
102B G 4.4 12.3 + - - -
103B U 4.6 4.2 - - - +
29W ILE* 3.4 8.5 - - - +
31W TYR* 3.3 36.5 + - + +
75W GLN* 3.0 26.6 + - + -
76W ASP* 2.9 29.5 + - + +
88W HIS* 3.1 23.6 + - - -
89W ILE* 1.3 76.7 - - - +
91W PHE* 1.3 61.2 + - - +
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Residues in contact with PHE 91 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4W ILE* 4.2 19.3 - - + -
28W ALA* 4.0 19.1 - - + -
29W ILE 2.9 19.6 + - - +
30W ILE* 3.4 8.6 - - + -
31W TYR* 2.9 32.8 + - - +
40W ILE* 4.7 1.3 - - + -
42W LEU* 4.1 9.6 - - + -
56W PHE* 4.3 16.8 - + - -
61W LEU* 4.6 3.1 - - + -
63W ILE* 3.8 16.4 - - + -
72W VAL* 3.7 37.5 - - + -
73W LYS 3.6 9.0 - - - -
74W ALA* 4.0 8.7 - - - -
75W GLN* 4.7 0.7 - - - -
89W ILE* 3.6 34.3 - - + -
90W ASP* 1.3 79.2 - - - +
92W VAL* 1.3 59.6 + - - +
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Residues in contact with VAL 92 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104B A 5.2 12.1 - - - +
31W TYR* 3.2 16.8 - - + +
32W GLY* 4.7 8.5 - - - -
72W VAL* 3.4 3.1 - - - -
73W LYS* 3.1 42.3 + - + +
75W GLN* 3.2 34.1 - - + +
91W PHE* 1.3 73.4 - - - +
93W ARG* 1.3 76.4 + - - +
94W ALA* 3.1 1.8 + - + +
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Residues in contact with ARG 93 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30W ILE* 3.5 26.7 + - + +
31W TYR* 2.9 16.1 + - - +
32W GLY 2.8 43.7 + - - +
33W GLY* 5.1 3.2 + - - +
35W GLU* 3.5 45.3 + - - +
36W ALA 2.7 24.2 + - - -
38W LEU* 4.0 11.1 - - - +
70W ILE* 3.8 32.3 - - + +
71W LYS 3.7 5.8 - - - +
72W VAL* 4.4 1.6 - - - +
91W PHE 4.1 0.4 + - - -
92W VAL* 1.3 80.5 - - - +
94W ALA* 1.3 60.3 + - - +
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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