Contacts of the strand formed by residues 72 - 81 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39F VAL* 5.6 7.0 - - + -
40F ILE* 3.8 29.4 - - + -
66F ASN* 3.4 33.5 - - + +
68F SER* 5.4 3.4 - - - -
70F GLU 4.9 0.9 - - - +
71F THR* 1.3 75.0 + - - +
73F LYS* 1.3 72.2 + - - +
74F PHE* 3.9 5.4 - - + -
105F ALA* 3.3 4.5 - - - +
106F LEU* 2.9 41.0 + - + +
137F ALA* 4.7 10.5 - - + -
138F GLU* 5.3 2.0 - - + +
139F ASN* 6.3 1.8 - - - +
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Residues in contact with LYS 73 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71F THR 4.4 0.2 + - - -
72F VAL* 1.3 81.4 - - - +
74F PHE* 1.3 64.4 + - - +
103F SER* 5.3 6.7 - - - +
104F ASP 3.3 10.1 - - - +
105F ALA* 4.3 5.8 - - + +
138F GLU* 2.9 40.8 + - + +
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Residues in contact with PHE 74 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40F ILE* 4.0 13.7 - - + -
64F ILE* 3.9 24.9 - - + -
72F VAL* 3.9 7.0 - - + -
73F LYS* 1.3 78.5 - - - +
75F LYS* 1.3 67.7 + - - +
76F TYR* 3.7 23.8 - + + -
103F SER* 4.3 4.3 + - - -
104F ASP* 2.7 52.2 + - + +
105F ALA* 4.0 11.9 - - - -
106F LEU* 3.8 33.2 - - + -
112F LEU* 4.3 8.3 - - + -
135F VAL* 3.8 22.2 - - + -
136F VAL 3.4 13.0 - - - +
137F ALA* 3.8 10.1 - - + +
138F GLU* 4.2 1.8 - - - +
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Residues in contact with LYS 75 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237E ASN* 5.5 4.3 - - - +
239E ASP* 2.9 40.1 + - - -
241E SER* 4.9 3.4 - - - +
242E TYR* 3.9 25.6 - - + +
74F PHE* 1.3 74.3 - - - +
76F TYR* 1.3 62.0 + - - +
77F TRP* 4.0 14.8 - - + -
101F GLN* 2.8 31.6 + - + +
102F GLU* 3.9 12.8 - - - +
103F SER* 3.4 30.2 + - - +
135F VAL* 3.5 1.9 - - - +
136F VAL* 2.7 42.5 + - - +
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Residues in contact with TYR 76 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62F LEU* 3.9 22.0 - - + -
64F ILE* 3.6 24.7 - - + -
74F PHE* 3.7 18.2 - + + -
75F LYS* 1.3 78.0 - - - +
77F TRP* 1.3 74.7 + - - +
101F GLN* 3.3 15.2 + - - -
102F GLU 4.8 3.8 + - - +
104F ASP* 3.7 23.1 - - + -
112F LEU* 4.0 15.2 - - + +
114F VAL* 3.7 23.0 - - + +
116F ARG* 4.0 19.3 + - - -
133F LEU* 3.9 9.0 - - + -
134F GLN 3.2 13.2 - - - +
135F VAL* 4.1 6.5 - - + -
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Residues in contact with TRP 77 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212E LEU* 4.2 8.1 - - + -
213E ILE 3.2 10.3 + - - -
214E ILE* 3.5 28.3 - - + -
215E PRO* 3.4 31.4 - - + -
242E TYR* 3.6 33.4 - + - -
75F LYS* 4.0 13.9 - - + -
76F TYR* 1.3 98.1 - - - +
78F LEU* 1.3 60.6 + - - +
79F SER* 3.6 5.8 - - - -
101F GLN* 3.6 28.7 - - + +
116F ARG* 4.5 8.1 - - - +
132F SER 3.8 0.2 - - - +
133F LEU* 3.8 4.8 - - - +
134F GLN* 3.0 58.8 + - + +
136F VAL* 3.6 29.4 - - + -
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Residues in contact with LEU 78 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215E PRO* 4.5 2.1 - - - +
44F LEU* 4.2 2.5 - - + -
60F SER* 3.8 20.9 - - - +
62F LEU* 4.0 19.5 - - + -
77F TRP* 1.3 76.1 - - - +
79F SER* 1.3 64.6 + - - +
89F PRO* 3.9 3.8 - - - +
90F ALA* 2.9 41.8 + - + +
91F LYS 4.4 1.7 + - - -
116F ARG* 3.8 32.4 + - + +
118F PHE* 4.4 13.2 - - + -
131F VAL* 3.8 15.9 - - + -
132F SER 3.6 15.3 - - - +
133F LEU* 3.7 22.9 - - + +
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Residues in contact with SER 79 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205E THR* 5.7 0.2 - - - +
213E ILE* 2.6 50.5 + - - +
215E PRO* 3.6 9.0 - - - +
77F TRP* 3.6 8.4 - - - -
78F LEU* 1.3 76.1 + - - +
80F ILE* 1.3 64.3 + - - +
88F PHE 3.8 5.6 - - - -
89F PRO* 4.6 1.4 - - - +
90F ALA 4.2 0.9 - - - +
130F THR 3.9 0.3 - - - +
131F VAL* 3.6 1.7 - - - -
132F SER* 2.8 45.4 + - - -
134F GLN* 4.9 3.1 - - - -
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Residues in contact with ILE 80 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213E ILE* 4.6 6.1 - - - +
79F SER* 1.3 82.1 - - - +
81F LYS* 1.3 63.3 + - - +
82F GLY 4.3 0.2 - - - -
87F TYR* 3.5 4.2 - - - +
88F PHE* 2.8 84.4 + - + +
90F ALA* 4.2 13.9 - - + +
118F PHE* 3.9 17.9 - - + -
129F TYR* 3.8 19.3 - - + -
130F THR 3.4 6.7 - - - +
131F VAL* 3.6 30.1 - - + -
149F PHE* 4.2 10.5 - - + -
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Residues in contact with LYS 81 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213E ILE* 3.9 13.4 - - + +
80F ILE* 1.3 74.1 - - - +
82F GLY* 1.3 65.5 + - - +
86F ILE 3.5 10.1 - - - +
87F TYR* 3.6 30.7 - - + +
128F LYS 4.4 0.2 - - - +
129F TYR* 3.4 4.3 - - - +
130F THR* 2.7 49.0 + - + +
248F THR* 4.2 1.2 - - - +
1272F O4B 2.6 106.7 + - - +
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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