Contacts of the strand formed by residues 74 - 78 (chain B) in PDB entry 2JI8
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 GLY 74 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B TYR* 5.2 1.1 - - - -
63B ALA* 3.1 30.9 + - - -
66B ALA* 4.4 7.2 - - - -
67B GLY* 3.8 4.8 - - - -
72B LYS 3.1 5.8 + - - -
73B PRO* 1.3 70.9 - - - +
75B VAL* 1.3 53.4 + - - -
100B PRO 3.3 10.3 + - - -
101B MET* 3.2 6.4 - - - +
102B ILE 2.8 30.1 + - - -
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Residues in contact with VAL 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B LEU* 4.9 6.7 - - + -
25B ILE* 3.9 26.7 - - + -
27B THR 4.1 14.1 + - - +
28B MET* 3.3 33.3 - - + +
29B TYR* 3.1 28.3 + - - -
63B ALA* 4.0 3.6 - - - +
73B PRO 3.5 11.2 + - - +
74B GLY* 1.3 76.0 - - - +
76B CYS* 1.3 61.1 + - - +
102B ILE* 3.4 21.3 - - + +
104B LEU* 4.0 24.0 - - + -
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Residues in contact with CYS 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B TYR 3.2 11.9 - - - +
56B GLU 4.3 2.9 - - - -
59B ALA* 4.0 5.4 - - - -
60B GLY* 3.7 25.4 - - - -
63B ALA* 4.0 8.6 - - + +
75B VAL* 1.3 73.6 - - - +
77B LEU* 1.3 62.3 + - - +
78B THR* 3.9 21.8 - - - -
87B GLY* 5.0 1.3 - - - -
101B MET* 3.9 22.7 - - + -
102B ILE 2.9 7.9 + - - +
103B LEU* 3.6 9.3 - - + +
104B LEU* 2.8 32.2 + - - +
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Residues in contact with LEU 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B MET* 4.3 15.3 - - + -
29B TYR 3.0 7.3 + - - -
30B GLY* 3.2 20.8 - - - -
31B VAL 3.4 7.2 + - - +
36B ILE* 3.9 34.3 - - + -
39B LEU* 3.5 33.9 - - + -
40B ALA* 4.3 10.1 - - + +
50B PHE* 3.6 33.7 - - + -
75B VAL 4.2 0.4 + - - -
76B CYS* 1.3 73.2 - - - +
78B THR* 1.3 67.1 + - - +
104B LEU* 3.3 23.6 - - + +
168B LEU* 4.9 2.2 - - + -
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Residues in contact with THR 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B GLY* 5.7 0.2 - - - -
31B VAL 4.1 6.3 - - - -
36B ILE* 3.3 16.7 - - - +
56B GLU* 3.8 24.7 - - + -
76B CYS* 3.9 10.3 - - - -
77B LEU* 1.3 78.8 - - - +
79B VAL* 1.3 70.3 + - - +
83B GLY 3.9 12.6 - - - +
84B PHE* 3.4 6.2 - - - -
87B GLY* 4.5 1.8 - - - -
103B LEU* 3.7 21.1 - - + -
104B LEU 2.9 7.3 + - - +
105B SER* 2.8 19.6 + - - -
106B GLY 3.1 21.5 + - - -
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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
------------------------------------------------------------
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