Contacts of the strand formed by residues 97 - 103 (chain E) in PDB entry 6AHU
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 PHE 97 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11E CYS* 3.6 31.2 - - + -
12E GLU 3.6 3.8 - - - -
13E LEU* 3.7 30.7 - - + -
24E LEU* 6.3 0.9 - - + -
29E LEU* 3.9 22.4 - - + -
32E LEU* 4.1 11.9 - - + -
33E VAL* 5.4 3.1 - - + -
65E VAL* 3.6 28.7 - - + -
81E LEU* 4.4 25.9 + - + +
82E PRO* 5.6 0.3 - - - +
84E ILE* 3.6 47.0 + - + -
95E PRO* 6.2 2.0 - - + -
96E CYS* 1.3 76.2 - - - +
98E PHE* 1.3 72.5 + - - +
198I ARG* 5.1 5.7 - - - -
202I ASP* 5.6 2.8 - - - +
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Residues in contact with PHE 98 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11E CYS* 3.4 4.4 - - - -
12E GLU* 2.8 49.6 + - + +
14E VAL* 3.7 31.9 - - + -
81E LEU* 6.2 0.2 - - - -
96E CYS* 3.4 43.5 - - - -
97E PHE* 1.3 79.2 - - - +
99E ASN* 1.3 67.3 + - - +
24I THR* 5.0 5.2 - - + -
28I LEU* 3.6 37.5 - - + -
195I LEU* 5.3 1.8 - - + -
197I ILE* 3.2 31.6 - - + -
198I ARG* 3.6 7.6 - - - -
199I GLY* 3.5 18.6 - - - +
202I ASP* 6.0 1.8 - - + -
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Residues in contact with ASN 99 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9E LEU* 6.4 0.4 - - + -
10E LEU 3.4 16.4 - - - +
11E CYS* 4.5 1.5 - - - +
78E TRP* 3.0 35.3 - - + +
81E LEU* 4.8 8.1 - - + +
98E PHE* 1.3 78.0 - - - +
100E THR* 1.3 64.4 + - - +
101E LEU* 5.0 2.5 - - - +
102E HIS 6.0 0.4 - - - +
28I LEU* 5.8 0.7 - - - +
199I GLY* 4.2 4.9 - - - -
200I PRO* 4.6 10.6 - - - +
201I TYR* 3.3 17.9 + - - +
202I ASP* 3.2 46.9 + - - +
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Residues in contact with THR 100 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10E LEU* 3.3 35.7 + - + +
11E CYS 5.3 1.1 - - - -
12E GLU* 4.1 24.2 - - + +
64E ILE* 5.9 3.1 - - + -
98E PHE 4.4 4.7 - - - +
99E ASN* 1.3 79.8 - - - +
101E LEU* 1.3 71.2 + - - +
113E PHE* 3.7 21.9 - - + -
117E TYR* 4.8 17.3 - - + -
200I PRO* 6.0 1.2 - - - +
201I TYR* 3.3 23.2 - - - -
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Residues in contact with LEU 101 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A U 3.8 17.3 - - - +
26A G 5.6 4.7 - - - +
10E LEU* 4.1 16.1 + - - +
99E ASN* 5.0 2.4 - - - +
100E THR* 1.3 86.8 + - - +
102E HIS* 1.3 79.7 + - - +
103E VAL* 3.3 29.7 + - + +
113E PHE* 3.7 42.8 - - + -
201I TYR* 4.4 18.2 - - + +
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Residues in contact with HIS 102 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A G 4.9 1.8 - - - +
25A U 3.6 22.8 + - - +
7E ARG* 4.0 34.9 - - + +
8E TYR 4.4 1.6 - - - -
9E LEU* 3.6 35.5 - - + +
69E CYS* 4.6 0.2 - - - -
74E TYR* 3.6 39.3 - + + -
78E TRP* 4.8 32.0 - + + +
99E ASN* 6.0 1.2 - - - +
101E LEU* 1.3 71.2 - - - +
103E VAL* 1.3 66.5 + - - +
104E GLY* 3.8 2.3 + - - -
201I TYR* 5.3 2.6 - - - -
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Residues in contact with VAL 103 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A U 5.5 1.3 - - - -
26A G 4.8 4.7 - - - +
7E ARG* 3.9 2.6 - - - +
8E TYR 2.9 40.9 + - - +
10E LEU* 5.0 4.3 - - + -
101E LEU* 3.6 30.3 - - + +
102E HIS* 1.3 74.6 + - - +
104E GLY* 1.3 60.7 + - - +
105E GLY 3.1 20.9 + - - +
106E THR* 3.8 16.4 - - + +
109E THR* 4.3 6.5 - - + +
110E CYS* 3.8 40.2 - - + +
113E PHE* 5.5 3.4 - - + -
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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