Contacts of the strand formed by residues 72 - 81 (chain E) in PDB entry 4BEI
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 VAL 72 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39E VAL* 5.7 7.0 - - + -
40E ILE* 3.8 29.4 - - + -
66E ASN* 3.4 34.0 - - + +
68E SER* 4.5 5.4 - - - +
71E THR* 1.3 75.0 + - - +
73E LYS* 1.3 72.2 + - - +
74E PHE* 3.9 5.6 - - + -
105E ALA* 3.3 5.1 - - - +
106E LEU* 2.9 40.7 + - + +
137E ALA* 4.7 10.5 - - + -
138E GLU* 5.3 2.5 - - + +
139E ASN* 6.3 1.3 - - - +
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Residues in contact with LYS 73 (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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71E THR 4.3 0.4 + - - -
72E VAL* 1.3 80.4 - - - +
74E PHE* 1.3 63.9 + - - +
103E SER* 4.2 18.2 - - - +
104E ASP 3.1 19.3 - - - +
105E ALA* 4.3 7.9 - - + +
138E GLU* 2.9 52.7 + - + +
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Residues in contact with PHE 74 (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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40E ILE* 4.0 13.2 - - + -
64E ILE* 3.9 24.2 - - + -
72E VAL* 3.9 7.2 - - + -
73E LYS* 1.3 80.7 - - - +
75E LYS* 1.3 66.6 + - - +
76E TYR* 3.7 24.2 - + - -
103E SER* 4.2 2.9 + - - -
104E ASP* 2.7 53.7 + - + +
105E ALA* 3.9 13.0 - - - -
106E LEU* 3.9 31.0 - - + -
112E LEU* 4.3 9.0 - - + -
135E VAL* 3.8 22.2 - - + -
136E VAL 3.4 13.0 - - - +
137E ALA* 3.8 10.3 - - + +
138E GLU* 4.2 2.0 - - - +
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Residues in contact with LYS 75 (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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74E PHE* 1.3 74.3 - - - +
76E TYR* 1.3 61.0 + - - +
77E TRP* 4.1 14.3 - - + -
101E GLN* 2.8 31.0 + - + +
102E GLU* 3.9 13.4 - - - +
103E SER* 3.4 31.1 + - - +
104E ASP* 5.6 0.2 - - - -
135E VAL* 3.5 1.7 - - - +
136E VAL* 2.7 44.2 + - + +
237F ASN* 5.8 1.7 - - - +
239F ASP* 3.4 36.2 + - - -
241F SER* 4.9 4.3 - - - +
242F TYR* 4.0 24.9 - - + +
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Residues in contact with TYR 76 (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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62E LEU* 3.9 21.8 - - + -
64E ILE* 3.7 23.8 - - + -
74E PHE* 3.7 18.8 - + + -
75E LYS* 1.3 77.4 - - - +
77E TRP* 1.3 75.9 + - - +
101E GLN* 3.3 14.4 + - - -
102E GLU 4.9 2.9 + - - +
104E ASP* 3.7 25.9 + - + -
112E LEU* 4.0 12.4 - - + +
114E VAL* 3.7 22.1 - - + +
116E ARG* 4.2 17.3 + - - -
133E LEU* 3.9 10.1 - - + -
134E GLN 3.2 13.5 - - - +
135E VAL* 4.1 5.6 - - + -
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Residues in contact with TRP 77 (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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75E LYS* 4.1 15.9 - - + -
76E TYR* 1.3 96.8 - - - +
78E LEU* 1.3 60.2 + - - +
79E SER* 3.6 9.6 - - - -
101E GLN* 3.5 37.9 - - + +
116E ARG* 4.7 7.4 - - - +
132E SER 3.8 0.2 - - - +
133E LEU* 3.8 4.3 - - - +
134E GLN* 3.0 59.2 + - + +
136E VAL* 3.7 29.8 - - + -
212F LEU* 4.1 9.2 - - + -
213F ILE 3.2 18.4 + - - -
214F ILE* 3.6 27.6 - - + -
215F PRO* 3.5 23.1 - - + -
242F TYR* 3.9 17.0 - + - -
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Residues in contact with LEU 78 (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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44E LEU* 4.2 2.7 - - + -
60E SER* 3.8 20.6 - - - +
62E LEU* 4.1 20.4 - - + -
77E TRP* 1.3 76.1 - - - +
79E SER* 1.3 64.0 + - - +
89E PRO* 3.9 3.5 - - - +
90E ALA* 2.9 42.8 + - + +
91E LYS* 4.4 1.7 + - - +
116E ARG* 3.8 32.7 + - + +
118E PHE* 4.3 13.0 - - + -
131E VAL* 3.8 15.3 - - + -
132E SER 3.7 15.5 - - - +
133E LEU* 3.7 22.4 - - + +
215F PRO* 4.7 2.1 - - - +
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Residues in contact with SER 79 (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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77E TRP* 3.6 8.7 - - - -
78E LEU* 1.3 76.5 + - - +
80E ILE* 1.3 64.2 + - - +
88E PHE 3.8 5.6 - - - -
89E PRO* 4.6 1.4 - - - +
90E ALA 4.3 0.4 - - - +
130E THR 3.9 0.5 - - - +
131E VAL* 3.6 1.7 - - - -
132E SER* 2.8 44.2 + - - +
134E GLN* 5.0 3.4 - - - -
205F THR* 5.7 0.2 - - - +
213F ILE* 2.7 51.7 + - - +
215F PRO* 3.8 9.0 - - - +
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Residues in contact with ILE 80 (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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79E SER* 1.3 82.5 - - - +
81E LYS* 1.3 63.7 + - - +
82E GLY 4.3 0.2 - - - -
87E TYR* 3.5 4.3 - - - +
88E PHE* 2.8 84.6 + - + +
90E ALA* 4.2 14.4 - - + -
118E PHE* 3.8 18.6 - - + -
129E TYR* 3.8 18.8 - - + -
130E THR 3.5 7.0 - - - +
131E VAL* 3.7 28.9 - - + -
149E PHE* 4.2 11.0 - - + -
213F ILE* 4.6 4.7 - - - +
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Residues in contact with LYS 81 (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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80E ILE* 1.3 76.0 - - - +
82E GLY* 1.3 66.5 + - - +
86E ILE 3.5 10.5 - - - +
87E TYR* 3.6 21.8 - - + -
128E LYS 4.4 0.3 - - - +
129E TYR* 3.4 4.1 - - - -
130E THR* 2.7 49.1 + - + +
248E THR* 4.5 0.2 - - - +
1272E O4B 2.6 113.8 + - - +
213F ILE* 3.9 13.0 - - + -
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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