Contacts of the strand formed by residues 53 - 59 (chain E) in PDB entry 4JCQ
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 ILE 53 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22E ARG* 3.5 31.9 - - + +
24E VAL* 4.2 10.8 - - + -
42E LEU* 4.3 12.8 - - + +
45E LEU* 3.8 40.2 - - + -
51E ASP 4.0 0.7 - - - +
52E PRO* 1.3 75.1 - - - +
54E THR* 1.3 67.4 + - - +
55E ILE* 4.4 4.3 - - + -
77E ILE* 3.8 27.1 - - + -
79E PRO* 3.8 16.2 - - + -
80E THR 2.9 9.2 + - - +
81E VAL* 3.4 7.9 - - + +
82E LYS* 2.8 33.5 + - - +
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Residues in contact with THR 54 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21E THR 5.5 0.9 + - - -
22E ARG 3.0 10.8 + - - -
23E THR* 3.3 13.4 - - - +
24E VAL 2.9 24.8 + - - +
52E PRO* 4.5 1.8 + - - +
53E ILE* 1.3 73.6 + - - +
55E ILE* 1.3 64.1 + - - +
56E PHE* 3.9 22.7 - - + -
82E LYS* 3.4 16.8 - - + +
84E VAL* 4.0 22.4 - - + -
186E ARG* 5.6 1.9 + - - +
189E LEU* 4.2 20.6 - - + +
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Residues in contact with ILE 55 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24E VAL* 3.2 22.7 - - + +
26E ILE* 3.6 31.6 - - + -
38E VAL* 5.5 0.2 - - + -
42E LEU* 4.2 16.6 - - + -
53E ILE* 4.4 5.4 - - + -
54E THR* 1.3 78.1 - - - +
56E PHE* 1.3 58.5 + - - +
57E ILE* 3.7 15.9 + - + +
74E ILE* 3.9 25.1 - - + -
81E VAL* 3.6 26.5 - - + -
82E LYS 2.8 12.9 + - - +
83E VAL* 3.3 8.1 - - + +
84E VAL 2.7 31.8 + - - -
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Residues in contact with PHE 56 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43D LEU* 4.3 12.3 - - + -
73D MET* 3.9 30.5 - - + -
76D PHE* 4.0 26.2 - + - -
23E THR* 3.6 31.4 - - + -
24E VAL 3.0 6.9 + - - -
25E LEU* 3.6 18.8 - - + -
26E ILE* 2.8 27.7 + - - -
27E TYR* 3.6 15.3 - - + +
54E THR* 3.9 18.4 - - + -
55E ILE* 1.3 73.9 - - - +
57E ILE* 1.3 60.2 + - - +
84E VAL* 3.3 37.2 - - + -
86E THR* 4.5 5.4 - - + -
108E LEU* 4.5 6.3 - - + -
186E ARG* 5.3 2.5 - - - -
189E LEU* 5.3 1.1 - - + -
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Residues in contact with ILE 57 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26E ILE* 3.4 19.7 - - + +
55E ILE* 3.7 15.9 - - + +
56E PHE* 1.3 77.4 - - - +
58E ASN* 1.3 62.4 + - - +
59E SER* 4.2 17.0 - - - +
83E VAL* 4.0 20.9 - - + -
84E VAL 2.9 11.7 + - - +
85E GLY* 3.7 1.2 - - - -
86E THR* 2.9 29.4 + - - +
89E VAL* 3.6 19.1 - - + +
93E GLY* 4.4 13.7 - - - +
96E ILE* 4.0 14.8 - - + -
97E TYR* 3.8 35.2 - - + -
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Residues in contact with ASN 58 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32D GLN* 3.1 16.4 + - - +
35D ALA* 5.4 0.6 - - - +
65D GLU* 3.2 21.0 + - - +
66D ALA* 4.3 4.0 - - - +
69D THR* 2.7 30.4 + - - +
26E ILE 2.9 8.4 + - - -
27E TYR* 3.2 23.0 - - + -
28E GLY 2.9 24.4 + - - -
57E ILE* 1.3 70.8 - - - +
59E SER* 1.3 59.4 + - - +
86E THR* 3.2 18.5 + - + +
87E GLY* 3.9 0.2 - - - -
88E TRP* 3.1 22.6 + - - -
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Residues in contact with SER 59 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26E ILE 4.4 3.1 - - - -
28E GLY 2.7 22.9 + - - -
30E ILE* 3.3 23.2 - - - +
57E ILE* 4.0 15.9 - - - +
58E ASN* 1.3 75.4 + - - +
60E GLN* 1.3 61.0 + - - +
61E GLY 3.1 15.0 + - - -
88E TRP* 2.8 20.0 + - - +
89E VAL* 3.4 0.9 - - - -
90E ALA 2.9 25.3 + - - +
93E GLY* 4.5 4.2 - - - -
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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