Contacts of the strand formed by residues 82 - 88 (chain F) in PDB entry 3CHB
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 82 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20F LEU* 3.8 3.8 - - + -
21F ASN* 2.9 27.8 + - - -
22F ASP 2.9 19.1 + - - +
24F ILE* 3.9 28.7 - - + -
42F PHE* 4.1 12.6 - - + -
75F ALA* 5.2 2.2 - - + -
80F ALA 4.1 5.8 - - - +
81F LYS* 1.3 71.3 - - - +
83F GLU* 1.3 62.5 + - - +
84F LYS 3.9 15.9 - - - +
85F LEU* 4.2 14.1 - - + -
99F ILE* 4.0 26.2 - - + -
100F SER 3.8 11.9 - - - +
101F MET* 4.4 4.0 - - + -
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Residues in contact with GLU 83 (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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5F ILE* 4.7 1.4 - - - +
19F THR* 3.7 2.3 - - - +
20F LEU* 2.9 26.9 + - - -
21F ASN* 3.1 27.4 + - - +
81F LYS 3.7 3.0 + - - -
82F VAL* 1.3 71.7 - - - +
84F LYS* 1.3 83.7 + - + +
100F SER* 2.7 44.1 + - - +
102F ALA* 4.1 29.6 + - + +
103F ASN* 5.6 1.5 - - - +
26G SER* 5.7 2.0 - - - -
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Residues in contact with LYS 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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5F ILE* 3.7 26.4 - - + +
6F THR* 4.1 15.8 + - - +
17F ILE* 4.1 14.5 - - + +
18F HIS 3.2 7.6 - - - +
19F THR* 3.6 31.4 + - + +
20F LEU* 4.7 0.7 - - - +
82F VAL* 3.9 3.0 - - - +
83F GLU* 1.3 105.6 - - + +
85F LEU* 1.3 66.0 + - - +
99F ILE* 3.6 2.4 - - - -
100F SER* 3.0 34.5 + - - +
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Residues in contact with LEU 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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5F ILE* 4.2 2.7 - - - -
16F GLN 3.8 0.5 - - - +
17F ILE* 3.4 5.3 - - - +
18F HIS* 2.8 37.0 + - + +
20F LEU* 4.0 13.4 - - + +
40F ILE* 4.3 8.1 - - + -
42F PHE* 4.0 9.6 - - + -
48F PHE* 3.5 43.5 - - + -
82F VAL* 4.2 4.5 - - + -
84F LYS* 1.3 73.7 - - - +
86F CYS* 1.3 58.8 + - - +
87F VAL* 3.9 13.3 + - + +
96F ILE* 4.4 16.8 - - + -
98F ALA 3.4 9.2 - - - +
99F ILE* 3.7 35.2 - - + -
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Residues in contact with CYS 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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5F ILE* 3.7 9.2 - - + +
8F LEU* 4.9 3.1 - - - -
9F CYS* 2.1 55.4 - - + -
12F TYR* 5.8 0.9 - - - -
15F THR* 4.0 8.5 - - - -
16F GLN 3.5 4.3 - - - -
17F ILE* 4.1 0.9 - - + -
85F LEU* 1.3 71.0 - - - +
87F VAL* 1.3 62.5 + - - +
96F ILE* 3.7 0.5 - - - -
97F ALA* 2.8 40.4 + - - -
98F ALA* 2.9 29.7 + - + +
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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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15F THR* 3.1 6.1 - - - -
16F GLN* 2.8 39.5 + - + +
18F HIS* 3.6 29.8 - - + +
48F PHE* 3.7 26.5 - - + -
85F LEU* 3.9 18.2 - - + +
86F CYS* 1.3 80.6 - - - +
88F TRP* 1.3 64.0 + - - +
94F ARG* 3.8 21.3 - - + -
95F ALA 3.1 14.8 - - - +
96F ILE* 4.2 6.7 - - + -
97F ALA 4.2 0.7 - - - +
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Residues in contact with TRP 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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3C GAL 3.6 64.2 - - - +
4C SIA 5.1 5.4 + - - -
12F TYR* 4.5 13.1 - + - +
13F HIS 3.7 9.4 + - - -
14F ASN* 3.1 14.6 - - + +
15F THR* 3.4 26.6 - - + +
51F GLU* 4.7 2.5 - - - -
57F HIS* 5.7 0.7 - - - -
61F GLN* 4.4 0.2 - - - -
87F VAL* 1.3 73.4 - - - +
89F ASN* 1.3 61.1 + - - +
90F ASN* 3.4 13.5 + - - +
91F LYS* 4.1 3.5 + - + -
94F ARG* 3.5 9.7 - - - +
95F ALA* 2.8 55.7 + - + +
96F ILE 3.6 7.9 - - - -
97F ALA* 3.3 34.1 - - + -
31G LEU* 3.8 16.6 - - + -
32G ALA* 4.1 18.2 - - + -
33G GLY 5.3 0.2 - - - -
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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