Contacts of the strand formed by residues 46 - 52 (chain C) in PDB entry 2PJ7
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 ASN 46 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C TRP* 3.6 3.0 - - - +
19C GLU* 5.1 3.4 + - - +
37C ALA* 4.3 12.6 - - + +
39C GLY 3.8 3.2 + - - -
40C THR* 3.5 21.6 - - - +
44C GLY 4.0 3.0 + - - -
45C ASN* 1.3 70.9 - - - +
47C ILE* 1.3 59.4 + - - +
48C TYR* 3.2 50.6 + - + +
113C ILE* 3.1 16.1 - - - +
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Residues in contact with ILE 47 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37C ALA* 3.2 3.2 - - - +
38C ILE* 3.0 48.3 + - + +
39C GLY 3.0 19.9 + - - +
40C THR 3.7 23.1 - - - +
41C THR* 3.9 18.6 - - + -
46C ASN* 1.3 69.1 - - - +
48C TYR* 1.3 61.0 + - - +
108C LEU* 4.0 22.2 - - + -
110C VAL 4.2 4.5 - - - +
111C LEU* 4.2 12.1 - - + +
113C ILE* 3.8 6.5 - - + -
175C GLU* 4.1 27.8 - - + -
178C ALA* 4.1 12.3 - - + -
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Residues in contact with TYR 48 (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 TRP* 3.9 18.5 - + + -
19C GLU* 3.5 34.9 + - + +
22C THR* 4.3 19.1 - - + +
35C ARG* 3.5 47.9 + - + -
36C THR 3.4 13.5 - - - +
37C ALA* 4.4 9.2 - - + -
46C ASN* 3.2 49.6 + - + -
47C ILE* 1.3 74.5 - - - +
49C LEU* 1.3 60.7 + - - +
50C LEU* 6.0 0.4 - - + -
108C LEU* 3.7 12.9 - - - +
109C PRO* 3.3 22.0 - - + +
110C VAL 5.1 1.2 + - - +
113C ILE* 4.7 2.4 - - - +
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Residues in contact with LEU 49 (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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34C SER 3.9 0.3 - - - +
35C ARG* 3.4 5.4 - - - +
36C THR* 2.8 46.3 + - - +
38C ILE* 3.8 21.3 - - + -
48C TYR* 1.3 73.2 - - - +
50C LEU* 1.3 68.4 + - - +
51C LYS* 4.1 0.4 + - + -
63C PHE* 3.7 24.7 - - + -
106C TYR* 3.8 16.4 - - + -
107C VAL 3.8 11.9 - - - +
108C LEU* 3.9 22.4 - - + -
182C PHE* 3.3 40.8 - - + -
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Residues in contact with LEU 50 (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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21C TRP* 3.8 35.0 - - + -
22C THR* 4.0 11.2 - - + +
25C VAL* 4.4 8.5 - - + -
26C THR* 3.4 25.6 - - - +
33C ILE* 3.9 12.3 - - + -
34C SER 3.5 1.1 - - - +
35C ARG* 3.8 22.0 - - + -
48C TYR 5.9 0.4 - - - -
49C LEU* 1.3 76.7 - - - +
51C LYS* 1.3 60.1 + - - +
52C VAL* 3.9 5.8 - - + -
83C VAL* 4.0 15.3 - - + -
105C PHE 3.4 1.9 - - - +
106C TYR* 3.4 2.8 - - - -
107C VAL* 2.8 46.9 + - + +
109C PRO* 4.4 12.3 - - + -
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Residues in contact with LYS 51 (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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32C LEU 3.4 1.7 - - - +
33C ILE* 3.4 5.1 - - - -
34C SER* 2.8 49.0 + - - +
49C LEU* 4.1 1.0 + - + -
50C LEU* 1.3 71.0 - - - +
52C VAL* 1.3 61.7 + - - +
53C GLY 3.9 2.7 + - - +
55C PRO* 5.1 10.5 - - - +
56C GLY 5.5 2.4 + - - +
59C LYS* 5.0 3.2 - - - +
104C ASP* 2.6 46.5 + - + -
105C PHE 3.5 2.5 - - - -
106C TYR* 3.6 37.7 - - + +
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Residues in contact with VAL 52 (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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32C LEU* 3.3 11.0 - - + +
33C ILE* 4.4 17.3 - - + -
50C LEU* 4.5 9.0 - - + -
51C LYS* 1.3 75.7 - - - +
53C GLY* 1.3 61.9 + - - +
82C PHE* 5.4 1.1 - - + -
83C VAL* 4.5 17.3 - - + -
86C ALA* 3.9 27.1 - - + -
87C VAL* 4.8 3.4 - - + -
100C LEU* 3.8 16.3 - - + +
104C ASP* 3.4 4.8 - - - -
105C PHE* 2.7 51.7 + - + +
107C VAL* 4.3 16.2 - - + -
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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