Contacts of the strand formed by residues 66 - 71 (chain X) in PDB entry 3JW0
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 THR 66 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4X PHE* 3.5 26.5 - - + +
6X LYS* 4.3 18.6 - - + -
12X THR* 6.0 0.4 - - + -
44X ILE 4.8 0.3 - - - +
45X PHE* 3.8 15.4 - - - -
46X ALA 5.3 1.4 + - - -
64X GLU 3.4 6.7 + - - -
65X SER* 1.3 71.3 - - - +
67X LEU* 1.3 71.4 + - - +
68X HIS* 4.2 18.9 + - + +
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Residues in contact with LEU 67 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3X ILE* 4.0 20.6 - - + -
4X PHE 3.0 23.5 + - - +
5X VAL* 4.4 6.5 - - + -
6X LYS 3.5 9.8 + - - -
23X ILE* 4.7 4.5 - - + -
26X VAL* 4.8 6.5 - - + -
43X LEU* 3.8 30.5 - - + -
44X ILE 3.7 9.4 - - - +
45X PHE* 4.2 14.4 - - + -
50X LEU* 3.7 24.0 - - + -
56X LEU* 5.1 0.9 - - + -
61X ILE* 4.2 16.4 - - + -
65X SER 3.5 13.5 - - - +
66X THR* 1.3 85.8 - - - +
68X HIS* 1.3 74.5 + - - +
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Residues in contact with HIS 68 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5X VAL* 4.6 0.7 - - - -
6X LYS* 3.5 42.9 - - + +
7X THR 5.6 1.6 - - - -
8X LEU* 6.3 3.8 - - + -
42X ARG 2.9 8.0 - - - +
43X LEU* 3.0 6.7 - - - -
44X ILE* 2.9 52.0 + - + +
46X ALA 5.5 3.0 + - - -
66X THR* 4.2 15.7 + - + -
67X LEU* 1.3 87.4 + - - +
69X LEU* 1.3 60.7 + - - +
70X VAL* 3.3 5.2 + - + -
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Residues in contact with LEU 69 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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943C MET* 5.4 0.7 - - + -
947C ASN* 6.0 1.1 - - - +
5X VAL* 3.7 15.5 - - + +
6X LYS 2.9 18.8 + - - +
7X THR* 3.9 31.6 - - + -
8X LEU* 4.2 11.6 + - - +
13X ILE* 4.2 3.8 - - + -
30X ILE* 3.9 18.6 - - + -
34X GLU* 4.9 0.2 - - + -
36X ILE* 3.9 26.0 - - + -
41X GLN* 2.9 38.8 - - + +
42X ARG 3.8 0.4 - - - +
43X LEU* 3.6 14.4 - - + -
68X HIS* 1.3 69.4 - - - +
70X VAL* 1.3 62.7 + - - +
71X LEU* 4.0 14.7 + - + +
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Residues in contact with VAL 70 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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950C GLY* 3.5 30.1 - - - +
8X LEU* 4.8 17.0 - - + -
41X GLN* 3.7 2.3 - - - -
42X ARG* 2.7 60.8 + - + +
44X ILE* 4.1 19.7 - - + -
68X HIS* 3.3 4.9 + - + +
69X LEU* 1.3 75.5 - - - +
71X LEU* 1.3 70.8 + - - +
72X ARG* 3.3 3.2 + - + +
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Residues in contact with LEU 71 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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916C LEU* 4.1 18.8 - - + -
943C MET* 4.3 8.5 - - + +
944C ALA* 4.5 1.1 - - - -
947C ASN* 2.9 46.5 + - + +
948C ALA* 5.3 2.0 - - - -
950C GLY 4.0 19.1 + - - -
8X LEU* 5.0 4.9 - - - +
36X ILE* 4.0 33.0 - - + -
40X GLN 3.7 11.2 - - - +
69X LEU* 4.0 17.4 + - + +
70X VAL* 1.3 75.0 - - - +
72X ARG* 1.3 59.2 + - - +
73X LEU* 3.1 25.8 + - + +
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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