Contacts of the strand formed by residues 65 - 69 (chain C) 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 ILE 65 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17C ILE* 4.0 17.9 - - + -
18C GLU 3.9 3.1 - - - -
19C LEU* 4.5 0.9 - - + +
20C LYS* 3.0 18.2 + - - -
36C MET* 3.6 35.0 - - + +
38C THR* 3.7 12.6 - - - +
60C ILE* 4.1 16.2 - - + -
62C GLY* 3.0 15.4 + - - +
63C ASN 3.2 0.4 - - - -
64C ASN* 1.3 78.8 - - - +
66C ARG* 1.3 64.1 + - - +
67C TYR* 3.7 20.4 - - - +
68C PHE* 3.7 33.9 - - + -
100D PHE* 6.1 0.2 - - + -
102D ARG* 3.3 13.4 - - + -
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Residues in contact with ARG 66 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1321 G 2.4 34.4 + - - -
1351 A 3.2 14.5 + - - -
1361 G 2.6 70.1 + - - +
18C GLU 2.8 13.4 + - - +
19C LEU 4.1 5.4 - - - -
20C LYS* 3.5 15.1 - - - +
64C ASN 3.7 0.8 + - - -
65C ILE* 1.3 73.6 - - - +
67C TYR* 1.3 81.9 + - + +
46D CYS* 4.1 9.0 - - - -
47D ARG 3.9 1.4 + - - -
48D ASN* 3.1 22.6 - - - +
101D LEU* 3.3 7.0 - - - +
102D ARG* 3.1 26.3 + - - +
105D SER* 3.0 38.8 + - - -
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Residues in contact with TYR 67 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1361 G 4.8 0.2 + - - -
17C ILE* 3.3 4.0 - - - +
18C GLU* 2.9 64.1 + - + +
65C ILE* 3.9 6.3 - - - -
66C ARG* 1.3 100.0 - - + +
68C PHE* 1.3 64.9 + - - +
69C ILE* 4.0 23.3 - - + -
46D CYS* 5.3 0.9 - - - -
48D ASN* 3.9 12.5 + - - -
52D LEU* 4.5 12.3 - - + -
72D GLU* 2.4 30.3 + - - -
94D ARG* 3.1 13.3 + - - -
96D ILE* 4.5 6.3 - - + -
99D MET* 4.3 14.6 - - - -
100D PHE 3.1 15.9 - - - +
101D LEU* 4.0 14.8 - - + -
102D ARG 4.7 0.4 - - - +
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Residues in contact with PHE 68 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7C LEU* 3.7 40.8 - - + -
15C VAL* 4.2 13.2 - - + -
16C THR 3.6 4.5 - - - +
17C ILE* 3.7 25.6 - - + +
29C ILE* 3.9 22.0 - - + -
32C VAL* 4.6 4.3 - - + -
36C MET* 4.3 2.0 - - + -
38C THR* 3.6 24.9 - - + -
65C ILE* 3.7 31.0 - - + -
67C TYR* 1.3 76.4 - - - +
69C ILE* 1.3 61.6 + - - +
70C LEU* 3.9 16.7 + - + +
99D MET* 3.2 6.7 - - - +
100D PHE* 2.8 43.5 + + + -
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Residues in contact with ILE 69 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C VAL* 3.6 7.3 - - - +
16C THR* 2.7 51.2 + - + +
18C GLU* 4.2 4.3 - - + +
67C TYR* 4.0 19.5 - - + -
68C PHE* 1.3 73.2 - - - +
70C LEU* 1.3 70.8 + - - +
94D ARG* 3.7 26.9 - - - +
96D ILE* 3.9 36.6 - - + -
97D SER 5.9 0.4 - - - +
98D LYS 3.7 3.1 - - - +
99D MET* 4.5 0.7 - - + +
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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