Contacts of the strand formed by residues 83 - 89 (chain F) in PDB entry 4B3E
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 ASP 83 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46F HIS* 4.4 3.4 - - - -
63F HIS* 3.0 28.4 + - - -
71F HIS* 3.0 17.0 + - + -
72F GLY 3.0 36.0 + - - +
73F GLY 4.8 0.2 - - - -
74F PRO* 3.3 21.1 - - - +
79F ARG* 3.4 13.4 + - + -
80F HIS* 2.9 42.2 + - - +
81F VAL 3.1 1.4 + - - -
82F GLY* 1.3 74.0 - - - +
84F LEU* 1.3 61.1 + - - +
85F GLY 3.3 3.4 - - - +
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Residues in contact with LEU 84 (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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20F PHE* 5.0 2.7 - - + -
31F VAL* 4.7 8.7 - - + -
45F PHE* 3.3 40.0 + - + +
47F VAL* 4.1 22.9 - - + +
74F PRO* 3.8 13.8 - - + +
79F ARG* 4.2 0.4 - - - +
82F GLY 3.1 11.2 + - - +
83F ASP* 1.3 75.7 - - - +
85F GLY* 1.3 60.1 + - - +
86F ASN 3.7 2.1 + - - +
99F ILE* 3.9 26.2 - - + +
101F ASP* 3.7 38.4 - - + +
104F ILE* 4.0 24.9 - - + -
117F LEU* 4.5 6.1 - - + -
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Residues in contact with GLY 85 (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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44F GLY* 3.5 4.9 - - - -
45F PHE* 2.9 27.7 + - - +
46F HIS* 4.5 1.8 - - - -
72F GLY 5.6 0.4 - - - -
73F GLY* 5.2 0.2 - - - -
74F PRO* 3.6 19.0 - - - +
83F ASP* 3.3 6.7 + - - +
84F LEU* 1.3 77.0 - - - +
86F ASN* 1.3 63.4 + - - -
124F ASP* 3.9 10.3 + - - +
126F LEU* 3.8 13.5 - - - -
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Residues in contact with ASN 86 (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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42F LEU* 3.7 38.7 - - + +
43F HIS 3.3 3.9 - - - +
44F GLY 3.4 10.7 + - - -
45F PHE* 4.5 1.1 - - - -
84F LEU 3.7 4.2 + - - +
85F GLY* 1.3 74.5 - - - -
87F VAL* 1.3 64.5 + - - +
99F ILE* 4.4 1.2 - - - +
123F ALA* 3.6 1.4 - - - +
124F ASP* 2.7 51.3 + - - +
126F LEU* 4.0 13.5 - - - +
128G LYS 4.2 13.2 + - - +
129G GLY 3.4 3.1 - - - +
130G GLY* 3.3 21.1 + - - -
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Residues in contact with VAL 87 (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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35F ILE* 4.6 3.4 - - + -
38F LEU* 5.0 2.0 - - + -
41F GLY 3.7 0.9 - - - +
42F LEU* 3.5 1.7 - - - -
43F HIS* 2.8 45.7 + - + +
45F PHE* 3.6 30.0 - - + +
86F ASN* 1.3 77.0 - - - +
88F THR* 1.3 60.2 + - - +
89F ALA 4.1 0.2 + - - -
95F ALA* 4.4 13.5 - - + -
97F VAL* 3.6 33.7 - - + -
99F ILE* 4.1 1.8 - - + -
119F VAL* 4.1 22.4 - - + -
129G GLY 3.3 6.5 - - - -
130G GLY* 4.0 6.5 - - - +
131G ASN* 6.0 0.2 - - + -
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Residues in contact with THR 88 (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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41F GLY* 3.4 13.2 - - - +
42F LEU* 3.3 19.3 - - + +
87F VAL* 1.3 72.5 - - - +
89F ALA* 1.3 72.9 + - - +
90F ASP* 5.5 0.9 - - - -
94F VAL 3.9 0.9 - - - +
95F ALA* 3.3 18.7 - - - -
125G ASP* 4.3 2.4 + - - -
129G GLY* 2.8 27.5 + - - -
131G ASN* 3.6 34.7 + - - +
139G ASN* 4.3 15.0 - - + +
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Residues in contact with ALA 89 (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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38F LEU* 3.7 26.0 - - + -
39F THR 3.4 23.3 - - - +
40F GLU* 3.6 2.9 - - - +
41F GLY 2.9 28.4 + - - +
43F HIS* 4.3 1.3 - - + -
87F VAL 4.1 1.0 + - - -
88F THR* 1.3 82.2 - - - +
90F ASP* 1.3 62.1 + - - +
93F GLY 4.0 13.0 - - - -
94F VAL 3.4 8.3 - - - -
95F ALA* 4.0 0.8 - - - +
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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