Contacts of the strand formed by residues 68 - 77 (chain B) in PDB entry 4JE4
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 ASP 68 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38B GLU* 3.5 6.9 - - - +
39B THR* 2.9 37.6 + - + +
67B VAL* 1.3 78.2 - - - +
69B TYR* 1.3 59.6 + - - +
91B ASN* 6.2 2.2 - - + -
92B TYR 3.9 3.3 - - - -
93B ARG* 3.1 38.9 + - - +
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Residues in contact with TYR 69 (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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18B LEU* 5.5 4.5 - - + -
36B TYR* 5.0 3.1 - + + -
37B GLY* 3.6 24.2 - - - -
38B GLU* 3.7 23.2 + - + +
39B THR* 3.3 6.7 + - - -
62B GLY 5.0 0.2 + - - -
63B LEU* 3.6 29.6 - - + -
64B LYS* 2.8 59.2 + - - +
67B VAL* 3.2 30.1 - - + -
68B ASP* 1.3 72.3 - - - +
70B THR* 1.3 62.1 + - - +
71B ILE* 4.3 10.9 + - + +
91B ASN* 3.2 5.0 - - - +
92B TYR* 2.8 41.4 + - + +
94B THR* 4.1 11.7 - - + -
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Residues in contact with THR 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B TYR* 3.2 7.1 - - - +
37B GLY 2.9 28.5 + - - -
39B THR* 2.5 29.9 + - - +
46B TRP* 3.7 27.6 - - + -
69B TYR* 1.3 72.7 - - - +
71B ILE* 1.3 64.6 + - - +
72B THR* 4.0 13.9 - - - +
89B SER* 4.5 9.6 - - - +
90B ILE 3.4 10.8 - - - +
91B ASN* 2.8 11.5 + - - +
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Residues in contact with ILE 71 (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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8B LEU* 3.5 14.6 - - + +
10B VAL* 4.4 5.6 - - + -
18B LEU* 3.7 30.5 - - + -
20B ILE* 3.9 33.7 - - + -
34B ILE* 4.6 4.3 - - + -
35B THR 3.6 7.2 - - - +
36B TYR* 4.0 11.9 - - + -
60B ILE* 4.3 9.4 - - + -
69B TYR* 4.8 8.7 - - + +
70B THR* 1.3 79.6 - - - +
72B THR* 1.3 65.1 + - - +
73B VAL* 5.0 0.2 - - + -
89B SER* 3.2 3.8 - - - -
90B ILE* 3.0 52.0 + - + -
92B TYR* 4.4 8.5 - - + -
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Residues in contact with THR 72 (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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14A VAL* 5.5 1.1 - - + +
33B VAL 3.7 0.7 - - - +
34B ILE* 3.3 5.5 - - - +
35B THR* 2.8 51.5 + - - +
46B TRP* 4.6 4.5 - - - -
70B THR* 4.0 9.4 - - - +
71B ILE* 1.3 75.4 - - - +
73B VAL* 1.3 66.6 + - - +
74B TYR* 4.0 17.0 - - + +
87B PRO* 3.5 27.6 - - + -
88B ILE 3.2 3.6 - - - +
89B SER* 2.8 26.1 + - - +
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Residues in contact with VAL 73 (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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5B PRO* 4.0 11.5 - - + +
8B LEU* 3.9 29.2 - - + -
20B ILE* 4.8 2.2 - - + -
22B TRP* 4.2 19.1 - - + +
32B TYR* 3.8 24.2 - - + -
33B VAL 3.4 5.4 - - - +
34B ILE* 3.9 18.6 - - + -
71B ILE* 5.0 0.4 - - + -
72B THR* 1.3 77.8 - - - +
74B TYR* 1.3 72.0 + - - +
87B PRO* 3.2 2.0 - - - +
88B ILE* 2.9 44.8 + - + +
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Residues in contact with TYR 74 (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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13A GLY* 5.0 1.6 - - - -
14A VAL* 4.2 13.3 + - - +
17A GLU* 2.6 38.3 + - - -
51A VAL 5.5 1.1 - - - -
53A HIS* 4.0 12.1 + + - -
5B PRO* 4.4 1.1 - - - -
32B TYR* 3.4 16.6 - - - -
33B VAL* 2.8 50.8 + - + +
35B THR* 3.9 22.0 - - + +
48B GLU* 6.1 0.7 - - - -
72B THR* 4.0 12.0 - - + +
73B VAL* 1.3 77.5 - - - +
75B ALA* 1.3 60.3 + - - +
84B TYR* 3.7 27.6 - + + -
85B SER* 3.5 22.2 - - - +
87B PRO* 3.6 25.1 - - + +
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Residues in contact with ALA 75 (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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3B SER 3.1 28.3 - - - +
5B PRO* 4.2 7.2 - - + -
29B VAL* 3.6 22.9 - - + -
31B TYR 4.2 0.4 - - - -
32B TYR* 4.5 1.3 - - - -
74B TYR* 1.3 72.1 - - - +
76B GLY* 1.3 59.7 + - - +
77B TYR* 4.0 14.6 - - + +
84B TYR* 3.2 3.1 - - - -
85B SER* 2.9 31.2 + - - +
86B SER* 3.6 8.1 + - - +
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Residues in contact with GLY 76 (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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29B VAL* 4.0 2.0 - - - +
30B ASP 3.1 24.4 + - - -
31B TYR* 2.9 38.1 + - - -
74B TYR 4.0 0.4 + - - -
75B ALA* 1.3 73.8 - - - +
77B TYR* 1.3 67.1 + - - -
83B TYR 3.3 10.8 - - - -
84B TYR* 3.6 5.1 - - - +
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Residues in contact with TYR 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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91A LYS* 3.6 37.2 - - + +
3B SER* 3.2 35.1 + - - -
27B VAL* 3.3 21.6 + - + +
28B THR 3.1 26.2 - - - -
29B VAL* 3.6 16.6 - - + +
30B ASP* 3.4 8.1 - - - +
31B TYR* 3.4 1.0 - - - -
75B ALA* 4.1 17.5 - - + -
76B GLY* 1.3 78.7 - - - -
78B TYR* 1.3 67.6 + - - +
82B THR* 3.3 7.3 - - - +
83B TYR* 2.8 66.8 + + + -
85B SER* 6.0 0.7 - - - -
86B SER* 5.7 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