Contacts of the strand formed by residues 50 - 58 (chain A) 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 ALA 50 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21A LEU* 4.5 1.8 - - - -
46A ARG* 3.2 6.0 - - - +
47A ARG 2.7 40.2 + - - +
48A ASN* 3.1 5.8 - - + +
49A GLY* 1.3 79.1 - - - +
51A VAL* 1.3 65.8 + - - +
52A THR* 4.2 1.1 - - - +
85B SER* 6.5 0.4 - - - -
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Residues in contact with VAL 51 (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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17A GLU* 3.9 27.8 - - + +
20A LEU* 3.8 25.8 - - + -
21A LEU* 3.8 30.3 - - + +
44A SER* 4.2 0.9 - - - -
45A VAL 3.3 10.1 - - - +
46A ARG* 4.5 1.6 - - - -
50A ALA* 1.3 83.9 - - - +
52A THR* 1.3 65.2 + - - +
53A HIS* 3.6 34.5 + - + +
74B TYR* 5.5 1.6 - - - -
85B SER* 3.8 14.8 - - - -
86B SER 5.2 0.2 + - - -
87B PRO* 5.7 2.6 - - - +
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Residues in contact with THR 52 (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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43A LEU 3.5 2.8 - - - +
44A SER* 3.5 0.7 - - - -
45A VAL* 2.8 42.3 + - - +
47A ARG* 4.5 13.2 + - - +
50A ALA* 4.2 1.6 + - - +
51A VAL* 1.3 74.3 - - - +
53A HIS* 1.3 65.1 + - - +
54A ILE* 4.1 7.0 - - + -
90A GLU* 3.6 19.7 + - - +
96A ILE* 4.6 12.6 - - + -
83B TYR* 3.6 37.5 - - + -
84B TYR 4.0 3.6 - - - +
85B SER* 4.1 7.9 - - - -
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Residues in contact with HIS 53 (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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13A GLY* 4.0 8.5 - - - -
16A ALA* 5.2 0.2 - - + -
17A GLU* 2.8 35.7 + - + +
32A ARG* 3.2 13.1 + - - -
42A THR* 3.8 5.6 - - + -
43A LEU 3.7 2.9 - - - -
44A SER* 2.9 27.5 + - - -
51A VAL* 3.6 23.8 + - + +
52A THR* 1.3 71.9 - - - +
54A ILE* 1.3 63.0 + - - +
74B TYR* 4.0 10.2 + + - -
83B TYR* 3.1 4.9 - - - +
84B TYR* 2.9 83.6 + + + +
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Residues in contact with ILE 54 (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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42A THR* 3.2 9.2 - - - +
43A LEU* 2.8 56.0 + - + +
45A VAL* 4.1 11.9 - - + -
52A THR* 4.5 5.6 - - + +
53A HIS* 1.3 77.9 - - - +
55A LYS* 1.3 72.6 + - - +
56A ILE* 3.6 0.5 + - - +
65A LEU* 4.3 11.9 - - + -
88A LEU* 4.6 10.5 - - + -
96A ILE* 3.8 40.6 - - + -
81B PRO* 3.6 30.3 - - + -
82B THR 3.6 4.7 - - - +
83B TYR* 4.3 9.6 - - + -
84B TYR* 5.7 0.2 - - - -
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Residues in contact with LYS 55 (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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37A ASN* 2.9 21.7 + - - +
40A ASP* 6.5 0.7 - - + -
41A PHE 3.8 3.4 - - - -
42A THR* 4.9 2.9 - - - +
54A ILE* 1.3 74.1 - - - +
56A ILE* 1.3 59.5 + - - +
57A GLN 4.1 0.2 - - - -
65A LEU* 3.4 26.5 - - - +
66A TYR* 4.1 23.4 + - + +
31B TYR* 3.7 27.6 - - - +
50B GLU* 2.8 35.4 + - - -
78B TYR* 5.0 5.1 + - - -
82B THR* 2.9 36.4 + - + +
84B TYR* 4.9 14.6 - - + -
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Residues in contact with ILE 56 (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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31A ALA* 5.4 1.6 - - + -
40A ASP* 3.2 9.7 - - - +
41A PHE* 2.7 50.2 + - + +
42A THR 4.5 0.9 - - - -
43A LEU* 4.2 28.9 - - + +
54A ILE 4.2 5.2 - - - +
55A LYS* 1.3 75.4 - - - +
57A GLN* 1.3 70.2 + - - +
63A TYR* 4.2 16.6 - - + -
64A ASP 3.5 9.9 - - - +
65A LEU* 3.7 14.4 - - + -
66A TYR* 4.7 1.3 - - - -
74A LEU* 3.7 22.2 - - + -
77A LEU* 3.9 25.4 - - + -
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Residues in contact with GLN 57 (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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40A ASP* 3.8 6.7 - - - +
55A LYS 4.1 1.2 - - - -
56A ILE* 1.3 73.5 - - - +
58A ASN* 1.3 62.9 + - - +
59A THR* 3.6 27.5 - - + +
62A TYR* 3.6 7.6 + - - +
63A TYR* 3.3 9.7 - - - +
64A ASP* 2.8 56.0 + - - +
66A TYR* 3.4 49.5 - - + +
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Residues in contact with ASN 58 (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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39A GLY 3.3 27.9 + - - +
40A ASP* 2.9 16.4 + - - +
41A PHE* 3.9 16.7 - - + -
56A ILE 3.6 0.6 + - - -
57A GLN* 1.3 74.4 - - - +
59A THR* 1.3 60.7 + - - +
60A GLY* 3.2 19.4 + - - +
62A TYR 3.8 5.2 + - - +
63A TYR* 3.7 30.8 + - + -
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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