Contacts of the strand formed by residues 14 - 18 (chain A) in PDB entry 2JB2
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 SER 14 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13A HIS* 1.3 74.9 - - - +
15A VAL* 1.3 67.8 + - - +
37A LYS* 3.3 22.7 - - - -
285A THR 4.7 1.0 + - - -
286A ALA* 3.4 11.6 - - - -
287A ASP* 3.0 49.9 + - - +
288A TYR* 3.2 9.5 + - - +
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Residues in contact with VAL 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A SER* 1.3 80.6 - - - +
16A VAL* 1.3 72.3 + - - +
17A VAL* 4.2 2.9 - - + -
31A LEU* 3.8 35.4 - - + -
36A TYR* 4.2 20.0 - - + -
37A LYS* 2.9 10.5 + - - +
38A VAL* 3.4 7.0 - - + +
39A THR* 3.2 23.7 + - - -
286A ALA* 3.8 5.0 - - - +
288A TYR* 3.3 26.2 - - + +
290A ILE* 4.1 18.4 - - + -
482A ILE* 4.7 7.2 - - + -
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Residues in contact with VAL 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A VAL* 1.3 74.6 - - - +
17A VAL* 1.3 65.5 + - - +
18A LEU* 4.0 2.5 - - + +
39A THR* 3.4 9.9 - - - +
41A LEU* 4.0 20.0 - - + -
271A VAL 4.7 7.2 - - - +
273A VAL* 4.0 18.6 - - + -
284A ILE* 4.0 31.9 - - + -
286A ALA* 3.5 15.4 - - + +
288A TYR 3.0 13.0 + - - +
289A ALA* 3.2 15.8 - - + +
290A ILE 2.9 24.6 + - - +
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Residues in contact with VAL 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A VAL* 4.2 9.6 - - + -
16A VAL* 1.3 75.6 - - - +
18A LEU* 1.3 62.2 + - - +
19A GLY 3.5 9.3 + - - +
24A GLY* 3.4 42.8 - - - +
27A SER* 4.5 10.5 - - - -
28A ALA 4.5 0.7 - - - +
31A LEU* 4.8 0.7 - - + -
38A VAL* 3.8 24.9 - - + -
39A THR 2.8 9.9 + - - +
40A VAL* 3.4 9.4 - - + -
41A LEU* 2.9 29.8 + - - +
290A ILE* 3.4 16.8 - - + +
292A THR* 4.6 1.8 - - + -
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Residues in contact with LEU 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A VAL* 4.0 13.5 - - + +
17A VAL* 1.3 71.7 - - - +
19A GLY* 1.3 52.9 + - - +
41A LEU* 4.0 5.2 - - + -
261A VAL* 3.8 34.5 - - + -
264A MET* 3.7 30.1 - - + -
273A VAL* 4.1 22.7 - - + -
289A ALA* 4.1 11.2 - - + -
290A ILE 2.9 22.2 + - - +
291A CYS* 4.1 10.5 - - - -
292A THR* 2.7 35.2 + - - +
293A ILE* 3.7 23.2 + - + -
301A LEU* 4.7 1.3 - - + -
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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