Contacts of the strand formed by residues 91 - 97 (chain E) in PDB entry 4MJI
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 91 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39E ARG* 4.7 8.3 - - + +
40E GLN 3.0 23.1 - - - +
41E SER* 4.0 6.3 - - - -
89E ASP 3.2 5.6 + - - +
90E SER* 1.3 75.9 - - - +
92E VAL* 1.3 64.6 + - - +
93E TYR* 3.4 24.2 - - + -
112E ARG* 4.1 12.3 - - - +
113E LEU 3.0 27.9 + - - +
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Residues in contact with VAL 92 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41D ARG 5.3 9.6 - - - +
39E ARG* 3.2 2.4 - - - +
40E GLN* 2.7 57.0 + - + +
41E SER* 5.5 1.3 - - - -
42E LEU 6.2 0.2 - - - +
91E ALA* 1.3 71.5 - - - +
93E TYR* 1.3 63.7 + - - +
94E LEU* 3.9 11.7 + - + +
109E GLU 4.9 2.5 - - - +
110E GLY* 4.3 10.1 - - - -
111E SER 3.4 26.0 - - - +
112E ARG* 3.8 27.8 - - + +
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Residues in contact with TYR 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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9E GLN* 2.3 30.4 + - - -
24E LEU* 3.5 28.0 - - + -
37E TRP* 4.0 7.4 - - + -
38E TYR 3.4 4.3 - - - +
39E ARG* 3.3 45.6 + - + -
49E LEU* 4.0 8.5 - - + -
68E PHE* 3.8 24.0 - + - -
80E LEU* 3.6 18.6 - - + -
82E ILE* 4.3 7.1 - - + +
89E ASP* 2.7 31.7 + - - +
91E ALA* 3.4 21.8 - - + -
92E VAL* 1.3 73.6 - - - +
94E LEU* 1.3 52.6 - - - +
110E GLY* 3.8 0.3 - - - -
111E SER* 3.1 18.2 + - - +
113E LEU* 3.7 11.9 - - + -
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Residues in contact with LEU 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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42D GLY 4.5 13.7 - - - +
43D LEU* 4.7 0.7 - - - -
44D VAL* 3.9 24.0 - - + -
9E GLN* 3.5 1.3 - - - +
37E TRP* 3.2 7.8 - - - -
38E TYR* 2.6 49.8 + - + +
40E GLN* 4.0 19.3 - - + +
46E PRO* 3.7 37.0 - - + -
92E VAL* 4.6 16.4 - - + +
93E TYR* 1.3 71.4 - - - +
95E CYS* 1.3 61.0 + - - +
96E ALA 4.1 0.3 + - - -
107E PHE* 4.0 13.7 - - + -
108E GLY 4.2 17.0 - - - +
109E GLU 4.6 4.7 - - - +
110E GLY* 4.7 0.9 - - - -
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Residues in contact with CYS 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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7E VAL* 3.6 7.5 - - + +
9E GLN* 3.1 27.2 + - + +
26E CYS* 2.1 49.1 - - + -
35E LEU* 3.8 19.1 - - - -
36E TYR 3.6 3.6 - - - -
37E TRP* 4.3 7.0 - - + -
94E LEU* 1.3 73.6 - - - +
96E ALA* 1.3 61.8 + - - +
107E PHE* 3.3 3.0 - - - -
108E GLY 2.7 31.7 + - - -
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Residues in contact with ALA 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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7E VAL* 4.9 0.2 - - - -
35E LEU* 3.4 12.3 - - - +
36E TYR* 3.0 36.6 + - + +
38E TYR* 5.5 0.2 - - - -
94E LEU 4.1 1.2 + - - -
95E CYS* 1.3 76.5 - - - +
97E SER* 1.3 61.5 + - - +
105E LEU* 3.7 32.8 - - + -
106E PHE 3.2 12.8 - - - +
107E PHE* 3.8 18.6 - - + -
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Residues in contact with SER 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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7E VAL* 3.3 19.2 - - - +
28E PRO* 2.8 33.3 - - - +
29E ILE 3.4 1.9 + - - -
32E HIS* 3.0 33.9 + - - -
34E ALA 3.3 7.0 - - - -
36E TYR* 4.7 1.6 - - - -
96E ALA* 1.3 73.0 - - - +
98E SER* 1.3 58.8 + - - +
104E GLU 3.7 2.1 - - - +
105E LEU* 4.7 2.0 - - - -
106E PHE* 3.0 25.9 + - - -
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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