Contacts of the strand formed by residues 79 - 84 (chain F) in PDB entry 5M73
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 79 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20F PRO* 4.0 3.2 - - - +
45F THR* 5.3 0.3 - - - -
46F ALA* 3.9 10.7 + - - +
64F LYS 3.9 18.7 + - - +
65F ASN* 5.2 14.0 + - - +
66F LYS 4.2 2.9 - - - +
67F MET* 3.2 53.8 - - + +
74F ARG* 4.6 16.4 + - - +
75F ASP 3.3 10.3 + - - -
76F VAL* 3.0 50.6 - - + +
77F GLN 4.0 4.3 - - - +
78F TYR* 1.3 82.3 - - - +
80F GLY* 1.3 61.2 + - - +
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Residues in contact with GLY 80 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19F TYR* 3.9 7.4 - - - -
20F PRO* 3.2 20.1 - - - +
46F ALA* 3.5 18.6 - - - -
63F GLU 3.5 8.7 - - - -
64F LYS* 4.1 6.0 + - - -
66F LYS 2.8 21.4 + - - +
67F MET* 4.6 1.1 - - - +
68F TYR 5.2 0.5 + - - -
78F TYR 3.9 0.7 + - - +
79F ARG* 1.3 75.9 - - - +
81F ARG* 1.3 60.6 + - - +
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Residues in contact with ARG 81 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149E A 4.2 4.4 + - - -
197E G 2.7 33.7 + - - -
198E G 2.8 18.9 + - - -
17F CYS* 4.1 17.8 - - + -
18F ILE 3.7 11.2 - - - +
19F TYR* 3.6 35.5 + - + -
46F ALA* 4.1 1.8 - - - +
61F PHE 4.2 0.2 - - - +
62F LEU* 3.5 3.6 - - - +
63F GLU* 2.4 78.9 + - + +
66F LYS* 3.9 16.6 - - + +
80F GLY* 1.3 75.9 - - - +
82F VAL* 1.3 74.4 + - - +
83F ARG* 4.0 12.2 - - - +
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Residues in contact with VAL 82 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16F ILE 3.4 0.5 - - - +
17F CYS* 3.3 6.1 - - - -
18F ILE* 2.9 47.7 + - + +
46F ALA* 4.2 20.0 - - + +
49F ILE* 3.8 30.1 - - + -
50F GLN* 4.7 3.4 - - + +
53F CYS* 4.8 3.4 - - - -
60F VAL* 3.5 28.5 - - + -
61F PHE 3.8 4.3 - - - +
62F LEU* 4.5 9.6 - - + -
81F ARG* 1.3 80.5 - - - +
83F ARG* 1.3 64.8 + - - +
84F VAL* 4.1 10.3 - - + +
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Residues in contact with ARG 83 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148E G 3.8 11.0 + - - -
198E G 5.4 0.6 + - - -
14F ARG* 4.5 6.9 - - - +
15F PHE* 3.1 44.1 + - + +
16F ILE 2.9 9.6 - - - -
17F CYS* 3.7 18.3 - - - -
60F VAL* 2.8 26.7 - - - +
61F PHE* 2.9 47.9 + - + +
63F GLU* 2.8 49.4 + - + +
81F ARG* 4.0 13.9 - - - +
82F VAL* 1.3 73.9 - - - +
84F VAL* 1.3 62.2 + - - +
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Residues in contact with VAL 84 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15F PHE* 3.6 5.7 - - - +
16F ILE* 2.9 56.0 + - + +
18F ILE* 4.5 11.7 - - + -
53F CYS* 6.0 1.3 - - + -
59F ASN* 3.7 1.8 - - - +
60F VAL* 3.5 29.8 - - + -
82F VAL* 4.1 12.3 - - + +
83F ARG* 1.3 78.6 - - - +
85F GLN* 1.3 73.7 + - - +
86F LEU* 3.6 20.7 + - + -
104F VAL* 5.4 9.4 - - + -
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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