Contacts of the strand formed by residues 105 - 109 (chain K) in PDB entry 1JJ2
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 TYR 105 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6960 C 5.0 7.8 + - - -
59K GLU* 3.7 26.7 - - + -
60K GLU 4.1 0.6 + - - -
61K ALA* 3.3 28.5 - - + +
62K ALA* 2.7 34.7 + - - +
103K ALA* 3.1 4.6 - - - -
104K ASP* 1.3 88.7 - - + +
106K VAL* 1.3 69.5 + - - +
107K LYS* 4.0 19.3 + - + +
123K ASP* 3.6 24.5 - - + +
124K ASP* 4.5 14.9 + - + -
145K LEU* 4.1 13.7 - - + -
148K GLU* 5.7 2.2 - - - -
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Residues in contact with VAL 106 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62K ALA* 3.2 13.7 - - + +
93K VAL* 3.6 34.1 - - + -
94K ARG* 3.7 26.9 - - + +
97K VAL* 3.6 13.7 - - + -
100K ALA* 4.0 29.6 - - + +
103K ALA* 5.6 0.2 - - + -
105K TYR* 1.3 78.5 - - - +
107K LYS* 1.3 62.9 + - - +
122K ALA* 4.0 1.4 - - + +
123K ASP* 2.8 46.3 + - - +
124K ASP 3.3 2.3 + - - -
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Residues in contact with LYS 107 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6960 C 4.4 16.8 + - - -
6970 G 2.9 64.3 + - - +
61K ALA* 4.7 1.3 - - + -
62K ALA 2.7 12.0 + - - +
63K THR* 3.1 12.9 - - + -
64K ILE* 3.1 25.3 + - - +
105K TYR* 4.0 22.8 + - + +
106K VAL* 1.3 75.9 - - - +
108K VAL* 1.3 71.2 + - - +
109K LEU* 3.8 14.4 - - + -
124K ASP* 3.0 35.2 + - + +
125K PHE 4.6 6.7 - - - -
126K SER 4.7 0.2 - - - +
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Residues in contact with VAL 108 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64K ILE* 3.4 9.6 - - + +
66K VAL* 3.8 19.1 - - + -
69K ILE* 4.3 6.1 - - + -
93K VAL* 3.5 44.2 - - + -
107K LYS* 1.3 75.3 - - - +
109K LEU* 1.3 72.2 + - - +
120K LEU* 4.3 8.5 - - + -
122K ALA* 3.9 8.5 - - + -
124K ASP 2.9 7.5 + - - -
125K PHE* 3.4 21.9 - - + -
126K SER 3.3 23.2 + - - -
129K ALA* 3.6 8.7 - - + +
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Residues in contact with LEU 109 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6880 A 3.9 14.1 - - + +
6970 G 3.6 66.4 - - + +
6980 A 3.4 10.5 - - - +
63K THR* 3.8 25.4 - - + +
64K ILE 2.7 9.2 + - - +
65K ASP* 3.1 18.0 - - - +
66K VAL* 2.9 30.5 + - - +
107K LYS* 3.8 18.8 - - + -
108K VAL* 1.3 75.6 - - - +
110K GLY* 1.3 59.4 + - - +
111K ALA 3.6 1.1 - - - -
126K SER* 3.8 3.4 - - - -
129K ALA* 3.7 2.7 - - - -
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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