Contacts of the strand formed by residues 92 - 98 (chain E) in PDB entry 4D9R
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 ALA 92 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38E ARG* 3.7 22.9 - - + +
39E GLN 3.5 15.3 - - - +
40E ALA* 3.6 13.9 - - + +
41E PRO* 4.2 4.0 - - - -
90E ASP 3.1 11.1 + - - +
91E THR* 1.3 78.2 - - - +
93E VAL* 1.3 59.9 + - - +
94E TYR* 3.5 11.1 - - + +
116E LEU* 3.8 8.5 - - - +
117E VAL 3.0 26.9 + - - +
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Residues in contact with VAL 93 (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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37E VAL 3.8 0.7 - - - +
38E ARG* 3.4 3.6 - - - -
39E GLN* 2.8 41.6 + - + +
92E ALA* 1.3 73.8 - - - +
94E TYR* 1.3 62.5 + - - +
95E TYR* 3.5 37.2 - - + +
113E GLN 5.1 0.9 - - - +
114E GLY* 3.8 18.6 - - - -
115E THR 3.3 7.2 - - - +
116E LEU* 4.0 23.1 - - + +
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Residues in contact with TYR 94 (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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6E GLN* 2.7 25.7 + - - -
20E VAL* 5.0 4.0 - - + -
36E TRP* 4.9 4.0 - - + -
37E VAL 3.4 2.2 - - - +
38E ARG* 3.6 31.8 + - + -
48E MET* 3.7 21.1 - - + -
68E PHE* 4.5 3.1 - + - -
81E LEU* 3.6 29.4 - - + -
83E ILE* 3.5 28.2 - - + +
90E ASP* 2.6 42.6 + - - +
92E ALA* 3.5 19.5 - - + +
93E VAL* 1.3 72.5 - - - +
95E TYR* 1.3 55.2 - - - +
115E THR* 2.9 28.8 + - - +
117E VAL* 4.1 18.8 - - + -
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Residues in contact with TYR 95 (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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38D GLN* 3.7 19.4 + - - -
42D LYS 4.1 5.5 + - - -
43D VAL* 3.8 23.1 - - + -
44D PRO* 4.4 2.7 - - + -
6E GLN* 3.5 4.5 - - - -
36E TRP* 3.3 13.1 - - - -
37E VAL* 2.7 48.8 + - + +
39E GLN* 3.9 22.3 + - + -
45E LEU* 4.6 6.1 - - + -
93E VAL* 3.5 28.8 - - + +
94E TYR* 1.3 73.7 - - - +
96E CYS* 1.3 60.6 + - - +
111E TRP* 3.6 34.1 - + + -
112E GLY 3.7 13.5 - - - -
113E GLN 3.8 10.7 + - - -
114E GLY* 3.6 13.0 - - - -
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Residues in contact with CYS 96 (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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4E LEU* 4.1 6.0 - - - +
6E GLN* 3.3 21.8 + - - -
22E CYS* 2.0 53.6 - - + -
34E MET* 4.0 7.9 - - + -
35E ASN 3.3 7.6 - - - +
36E TRP* 3.9 12.3 - - + -
95E TYR* 1.3 76.4 - - - +
97E GLU* 1.3 62.0 + - - +
111E TRP* 3.6 2.3 - - - +
112E GLY* 2.9 34.5 + - - -
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Residues in contact with GLU 97 (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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170B ARG* 3.2 11.7 - - - -
36D TYR* 2.6 26.7 + - - -
89D LEU* 5.9 0.3 - - - +
98D PHE* 5.8 0.7 - - - -
34E MET* 3.6 3.5 - - - -
35E ASN* 2.7 69.7 + - + +
37E VAL* 4.8 4.3 - - + +
47E TRP* 4.5 5.4 + - - -
95E TYR 4.2 0.2 - - - -
96E CYS* 1.3 75.7 - - - +
98E ARG* 1.3 66.4 + - - +
109E ASN* 2.9 15.8 - - - +
110E ASN 3.5 8.1 - - - +
111E TRP* 3.2 43.2 + - + +
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Residues in contact with ARG 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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170B ARG* 4.7 0.2 - - - -
2E VAL* 3.3 25.0 - - - +
4E LEU* 3.6 20.5 - - + +
27E TYR* 3.3 53.4 - - + +
32E TYR* 3.6 44.7 + - + -
33E GLY 3.8 1.8 - - - +
34E MET* 3.7 8.1 - - - -
97E GLU* 1.3 81.8 - - - +
99E GLU* 1.3 62.4 + - - +
100E GLY 3.3 26.9 + - - +
101E GLY* 4.3 0.2 - - - -
108E VAL* 3.0 34.6 + - - +
109E ASN* 4.1 7.6 - - - +
110E ASN* 3.0 21.8 + - + +
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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