Contacts of the strand formed by residues 84 - 95 (chain E) in PDB entry 5IXM
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 ARG 84 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42E ARG* 3.1 20.0 - - - +
45E GLN* 5.3 0.3 + - - -
64E ASP 3.7 0.5 - - - +
65E TRP* 3.6 1.2 + - - -
66E LEU* 2.8 57.2 + - + -
69E ASP* 2.8 22.5 + - + +
72E TYR* 3.2 26.7 - - - +
82E ALA* 4.8 4.3 - - + +
83E THR* 1.3 76.1 - - - +
85E TRP* 1.3 60.8 + - - +
109E SER* 3.4 3.6 - - - +
110E ASP* 2.5 42.5 + - - -
112E ALA 3.7 7.7 + - - -
113E TYR* 3.9 9.1 - - + +
116E ASP* 2.4 37.3 + - - +
117E LEU* 3.6 24.6 - - + +
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Residues in contact with TRP 85 (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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63E LEU* 4.9 8.7 - - + -
64E ASP 3.0 11.9 - - - +
65E TRP* 4.7 3.8 - - + -
83E THR* 3.4 30.6 + - + -
84E ARG* 1.3 76.1 - - - +
86E LEU* 1.3 65.0 + - - +
87E TYR* 4.4 9.6 - - + -
107E ARG* 3.6 61.2 - - + -
108E VAL* 3.4 11.1 - - - -
109E SER* 2.9 55.0 + - - -
113E TYR* 3.7 7.8 - - - -
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Residues in contact with LEU 86 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62E ALA* 3.5 4.8 - - + +
63E LEU* 3.2 11.4 - - - +
64E ASP* 2.9 43.2 + - + +
85E TRP* 1.3 76.7 - - - +
87E TYR* 1.3 73.5 + - - +
88E TYR* 4.2 13.9 - - + +
106E THR* 4.7 5.4 - - + -
107E ARG 3.3 10.1 - - - +
108E VAL* 3.6 5.6 - - + -
113E TYR* 3.5 28.0 + - + +
114E PHE* 3.5 38.4 - - + -
119E SER* 4.2 6.5 - - - +
121E TYR* 4.2 17.5 - - + +
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Residues in contact with TYR 87 (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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61E MET* 3.1 35.0 - - + +
62E ALA 3.2 15.0 - - - -
63E LEU* 4.5 16.4 - - + -
85E TRP* 4.4 8.0 - - + -
86E LEU* 1.3 76.5 - - - +
88E TYR* 1.3 68.4 + - - +
89E TRP* 3.9 24.6 - + + +
105E TYR* 3.5 33.7 - + - -
106E THR* 3.4 4.5 - - - +
107E ARG* 2.9 40.4 + - + +
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Residues in contact with TYR 88 (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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60E THR* 3.4 29.2 - - - -
61E MET* 3.2 5.4 - - - +
62E ALA* 2.9 43.7 + - + +
86E LEU* 4.2 4.7 - - + -
87E TYR* 1.3 81.2 - - - +
89E TRP* 1.3 64.6 + - - +
90E GLY* 3.6 18.9 - - - -
104E ASN* 4.1 17.0 + - - -
105E TYR 3.3 13.5 - - - -
106E THR* 3.2 24.7 - - - +
121E TYR* 3.3 57.1 - + + -
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Residues in contact with TRP 89 (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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52E TYR* 2.7 30.0 + + - -
60E THR 3.5 2.2 - - - -
61E MET* 3.4 29.0 - - + +
87E TYR* 3.9 24.7 - + + +
88E TYR* 1.3 79.9 - - - +
90E GLY* 1.3 78.0 + - - +
91E HIS* 4.2 3.1 - + + +
103E ILE* 3.5 37.7 - - + +
104E ASN* 3.7 0.3 - - - -
105E TYR* 2.9 48.2 + - + +
133E PHE* 4.1 18.6 - + - -
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Residues in contact with GLY 90 (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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59E GLY* 3.0 4.1 - - - -
60E THR* 2.9 36.5 + - - -
88E TYR* 3.6 20.2 - - - -
89E TRP* 1.3 79.0 - - - +
91E HIS* 1.3 61.8 + - - +
103E ILE 3.2 7.4 - - - -
104E ASN* 4.8 0.7 - - - -
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Residues in contact with HIS 91 (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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52E TYR* 3.0 32.2 + + - +
56E PRO* 2.8 32.0 + - + +
57E GLY* 3.3 33.2 - - - -
58E SER 3.4 6.4 + - - -
89E TRP* 4.2 3.1 - + - +
90E GLY* 1.3 75.1 - - - +
92E SER* 1.3 73.1 + - - +
101E PHE* 3.7 27.5 - - + +
102E ASN* 3.3 5.7 - - - +
103E ILE* 2.9 50.8 + - + +
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Residues in contact with SER 92 (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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57E GLY* 3.3 0.2 - - - -
58E SER* 2.9 37.4 + - - +
91E HIS* 1.3 80.8 - - - +
93E GLY* 1.3 59.6 + - - +
101E PHE 3.4 6.1 - - - -
102E ASN* 3.4 11.4 + - - -
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Residues in contact with GLY 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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56E PRO 3.5 18.5 + - - +
57E GLY* 3.6 6.1 - - - -
92E SER* 1.3 78.2 + - - +
94E VAL* 1.3 66.7 + - - +
95E MET 4.0 0.6 + - - -
99E TRP 3.9 0.2 - - - +
100E ARG* 3.6 2.3 - - - -
101E PHE* 2.9 34.6 + - - +
102E ASN* 4.1 1.7 + - - +
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Residues in contact with VAL 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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55E ALA 4.8 4.0 + - - +
57E GLY* 5.1 0.2 - - - -
93E GLY* 1.3 76.3 - - - +
95E MET* 1.3 58.0 + - - +
96E ASP 3.8 1.6 + - - -
97E GLN* 3.9 32.2 + - - +
99E TRP 3.1 13.5 - - - +
100E ARG* 3.8 19.7 - - + +
22F SER 5.9 1.3 - - - +
23F ASP* 3.5 33.4 - - - +
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Residues in contact with MET 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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55E ALA* 3.6 29.1 + - + +
56E PRO* 4.2 24.9 - - + -
93E GLY 4.0 2.0 + - - -
94E VAL* 1.3 68.3 - - - +
96E ASP* 1.3 84.0 + - - +
97E GLN 3.1 2.5 - - - -
99E TRP* 2.9 61.2 + - + +
101E PHE* 3.9 24.0 - - + -
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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