Contacts of the strand formed by residues 69 - 74 (chain F) in PDB entry 4PJO
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 69 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80E LYS* 3.8 30.5 - - + +
82E ASP* 4.6 0.9 - - - +
83E ASN* 4.0 0.2 + - - -
21F VAL* 3.5 24.9 - - + -
22F LYS 3.9 3.4 - - - -
23F LEU* 4.3 1.6 - - + +
24F LYS* 3.7 14.9 - - - -
40F MET 5.2 0.2 - - - +
42F MET* 4.0 22.7 - - + -
64F ILE* 4.0 20.0 - - + -
65F ARG 4.7 0.7 - - - +
66F CYS* 3.2 17.6 + - - +
68F ASN* 1.3 77.4 - - - +
70F LEU* 1.3 72.5 + - - +
71F TYR 3.8 13.0 - - - +
72F ILE* 4.7 0.7 - - + +
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Residues in contact with LEU 70 (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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1331 G 6.0 1.6 - - - +
35E LEU* 4.3 9.6 - - + -
38E GLN* 5.6 0.9 - - - +
41E MET* 4.1 22.2 - - + -
43E ILE* 4.7 3.1 - - + -
79E LEU* 3.6 17.4 - - + -
80E LYS 3.0 24.4 + - - -
83E ASN* 3.4 36.3 + - + +
22F LYS* 2.7 36.0 + - + +
23F LEU 4.0 2.9 - - - +
24F LYS* 3.9 18.4 - - + +
68F ASN 3.7 1.0 + - - -
69F VAL* 1.3 73.9 - - - +
71F TYR* 1.3 79.9 + - + +
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Residues in contact with TYR 71 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43E ILE* 3.7 25.4 - - + -
63E GLU* 2.5 30.6 + - - -
72E LYS* 5.0 2.3 + - - -
74E LEU* 3.1 27.0 - - + +
77E ILE* 4.1 15.9 - - + -
78E MET 3.0 16.2 - - - +
79E LEU* 4.0 8.1 - - + -
80E LYS 4.8 0.2 - - - +
20F MET* 5.0 3.1 - - + -
21F VAL* 3.6 1.7 - - - +
22F LYS* 2.8 59.3 + - + +
28F GLU* 4.8 3.1 + - - -
69F VAL* 4.1 6.7 - - - -
70F LEU* 1.3 93.7 - - + +
72F ILE* 1.3 71.2 + - - +
73F ARG* 4.1 21.5 + - + -
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Residues in contact with ILE 72 (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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77E ILE* 3.3 3.5 - - - -
78E MET* 2.9 56.2 + - + +
10F PHE* 4.2 5.4 - - + -
11F LEU* 4.0 20.0 - - + -
14F LEU* 4.5 4.3 - - + -
19F VAL* 4.2 13.9 - - + -
20F MET 3.6 10.5 - - - +
21F VAL* 4.2 9.0 - - + +
33F LEU* 3.7 30.1 - - + -
42F MET* 3.9 30.7 - - + -
69F VAL* 5.4 1.1 - - + -
71F TYR* 1.3 76.2 - - - +
73F ARG* 1.3 70.4 + - - +
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Residues in contact with ARG 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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72E LYS* 4.2 18.2 - - - +
73E GLN 5.0 2.0 + - - -
74E LEU* 3.3 60.1 + - - +
76E ARG 3.6 13.7 - - - +
77E ILE* 3.8 7.0 - - + -
10F PHE* 5.0 0.2 - - - -
14F LEU* 4.3 7.0 - - - -
19F VAL* 3.3 5.4 - - - +
20F MET* 2.9 64.8 + - - +
28F GLU* 4.6 1.6 + - - -
71F TYR* 4.1 17.2 + - + -
72F ILE* 1.3 78.9 - - - +
74F GLY* 1.3 71.0 + - - +
75F VAL* 4.9 8.5 + - - -
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Residues in contact with GLY 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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74E LEU 5.1 0.5 - - - +
76E ARG 3.8 7.9 + - - -
10F PHE* 4.9 0.2 - - - -
14F LEU* 3.8 28.1 - - - +
18F PRO 4.1 2.2 - - - -
19F VAL* 4.4 0.2 - - - -
73F ARG* 1.3 92.0 + - - +
75F VAL* 1.3 76.9 + - - +
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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