Contacts of the strand formed by residues 18 - 25 (chain E) in PDB entry 4PJE
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 18 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263C VAL* 4.0 14.1 - - + -
10E MET* 3.6 29.8 - - + -
12E ALA* 3.9 11.4 - - + -
17E ILE* 1.3 75.3 - - - +
19E GLN* 1.3 62.8 + - - +
20E ILE* 4.7 2.9 - - + -
73E LEU 3.7 1.2 - - - +
74E LEU* 3.5 6.0 - - - +
75E LEU* 2.9 44.1 + - + -
78E LEU* 3.8 23.6 - - + -
105E LEU* 3.9 35.0 - - + -
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Residues in contact with GLN 19 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181C PRO* 3.6 43.8 + - + +
183C LEU* 4.6 4.2 - - - +
263C VAL* 5.8 0.2 - - - +
10E MET* 3.4 20.3 - - - +
18E VAL* 1.3 76.6 - - - +
20E ILE* 1.3 59.7 + - - +
21E ASN* 2.9 30.9 + - - +
70E TYR* 3.1 12.1 + - - -
72E TYR* 3.6 44.7 - - + -
73E LEU 3.5 2.7 - - - -
74E LEU* 3.9 13.0 - - + +
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Residues in contact with ILE 20 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7E PRO* 4.6 1.3 - - + -
10E MET* 4.0 16.4 - - - -
18E VAL* 4.7 6.3 - - + -
19E GLN* 1.3 72.2 - - - +
21E ASN* 1.3 66.9 + - - +
34E TRP* 3.4 24.1 - - + -
72E TYR* 3.1 3.4 - - - -
73E LEU* 2.7 44.3 + - + +
75E LEU* 4.0 17.5 - - + -
86E TYR* 3.7 39.0 - - + -
103E THR* 3.5 37.9 - - + +
105E LEU* 4.7 10.1 - - + -
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Residues in contact with ASN 21 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181C PRO* 5.3 1.4 - - - +
182C PRO 3.2 25.9 + - - -
183C LEU* 3.6 15.1 - - + +
184C VAL 5.0 1.6 - - - +
265C MET* 5.4 6.4 - - - +
5E ASP 4.6 0.2 - - - -
6E GLN* 3.4 8.7 - - - +
7E PRO* 3.3 29.7 - - + +
19E GLN* 2.9 23.1 + - - +
20E ILE* 1.3 76.0 - - - +
22E CYS* 1.3 61.4 + - - +
23E THR* 5.8 2.9 - - + -
34E TRP* 4.3 0.2 - - - -
70E TYR* 2.6 35.3 + - + -
71E SER 3.6 3.8 - - - -
72E TYR* 3.5 3.3 - - - +
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Residues in contact with CYS 22 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4E ILE* 3.6 18.4 - - - -
5E ASP 3.3 6.3 - - - +
6E GLN* 4.5 1.3 - - + -
21E ASN* 1.3 77.7 - - - +
23E THR* 1.3 68.8 + - - +
24E TYR* 4.2 1.4 + - - -
32E LEU* 4.5 5.4 - - - -
34E TRP* 3.5 14.8 - - + -
70E TYR* 3.6 2.8 - - - -
71E SER* 2.8 40.7 + - - +
88E CYS* 2.0 52.0 - - + -
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Residues in contact with THR 23 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183C LEU* 5.9 4.9 - - + -
4E ILE* 3.5 1.7 - - - -
5E ASP* 2.8 50.2 + - - +
21E ASN* 5.8 2.5 - - + -
22E CYS* 1.3 79.2 - - - +
24E TYR* 1.3 61.7 + - - +
25E GLN* 3.8 18.4 + - - +
68E LYS 5.5 1.8 - - - +
69E GLY 3.5 8.5 - - - +
70E TYR* 4.1 19.5 - - + -
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Residues in contact with TYR 24 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3E ASN 3.6 3.6 - - - -
4E ILE* 3.4 24.2 - - + -
22E CYS* 4.7 2.9 - - - -
23E THR* 1.3 75.4 - - - +
25E GLN* 1.3 67.9 + - - +
26E THR* 3.7 21.8 - - + -
29E PHE* 3.5 33.7 - + + -
32E LEU* 3.7 23.1 - - + -
64E LEU* 3.6 29.4 - - + +
66E ARG* 3.7 17.3 + - - +
69E GLY* 3.1 48.9 + - - +
70E TYR* 3.6 6.1 - - - -
90E GLY* 5.3 0.4 - - - -
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Residues in contact with GLN 25 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2E GLN* 3.2 7.6 - - - -
3E ASN* 2.8 72.9 + - + +
5E ASP* 3.2 7.8 + - - +
23E THR* 3.8 24.0 + - - +
24E TYR* 1.3 81.2 + - - +
26E THR* 1.3 59.8 + - - +
69E GLY 5.2 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