Contacts of the strand formed by residues 39 - 45 (chain E) in PDB entry 4JRX
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 MET 39 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23E CYS* 3.7 33.7 - - - +
25E GLN* 3.7 17.3 - - + +
38E SER* 1.3 78.3 - - - +
40E TYR* 1.3 61.3 + - - +
55E TYR* 3.4 3.6 - - - +
56E SER 2.8 32.7 + - - +
80E ARG* 3.8 20.4 - - - +
84E LYS 3.6 16.2 - - - +
85E ARG 3.3 28.0 - - - +
87E PHE* 3.4 34.3 - - + -
104E CYS* 4.4 1.3 - - - -
105E ALA 3.4 7.2 - - - +
106E SER* 3.6 11.2 - - - +
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Residues in contact with TYR 40 (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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7C GLN* 3.0 18.5 + - - +
112D ASN 3.8 0.5 + - - -
117D ASP 2.6 29.0 + - - -
118D LYS* 3.9 3.6 - - - -
119D LEU* 3.7 12.6 - - + -
38E SER* 3.5 28.7 + - - -
39E MET* 1.3 73.6 - - - +
41E TRP* 1.4 61.4 + - - +
42E TYR* 3.6 29.6 - - + -
52E LEU* 3.6 14.1 - - + -
54E TYR 3.8 4.7 - - - -
55E TYR* 3.3 29.6 - + + -
87E PHE* 4.0 2.5 - - - -
104E CYS* 3.3 10.4 - - - -
105E ALA* 2.8 31.6 + - + +
107E PRO* 3.4 37.5 - - + -
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Residues in contact with TRP 41 (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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6E GLN* 3.6 37.0 - - + -
21E LEU* 3.8 29.2 - - + -
22E GLN 3.9 4.9 - - - -
23E CYS* 3.7 19.9 - - + +
40E TYR* 1.4 71.2 - - - +
42E TYR* 1.3 63.4 + - - +
52E LEU* 3.4 5.7 - - - +
53E ILE* 2.8 36.7 + - + -
54E TYR* 2.9 14.3 + - + +
78E VAL* 4.4 3.6 - - + -
87E PHE* 2.7 53.0 + + + -
89E LEU* 3.6 41.4 - - + +
102E TYR* 3.8 14.1 - - + -
103E PHE 3.4 23.8 - - - -
104E CYS* 3.8 6.5 - - + -
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Residues in contact with TYR 42 (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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119D LEU* 2.6 48.6 + - - +
120D ILE* 5.2 1.3 - - + -
121D PHE* 3.8 15.5 - + - -
40E TYR* 3.6 26.3 - - + +
41E TRP* 1.3 74.2 - - - +
43E ARG* 1.3 60.5 + - - +
50E LEU* 3.9 31.0 - - + -
51E ARG 3.2 9.2 - - - +
52E LEU* 3.6 34.3 - - + -
53E ILE* 3.7 4.8 - - - +
102E TYR* 3.4 11.1 - - - +
103E PHE* 2.8 39.9 + - + +
105E ALA* 4.0 15.0 - - + -
114E PHE* 4.0 15.7 - + - -
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Residues in contact with ARG 43 (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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42E TYR* 1.3 73.1 - - - +
44E GLN* 1.3 60.9 - - - +
45E ASP* 2.8 37.9 + - - +
49E GLY 3.6 1.4 - - - +
50E LEU* 3.5 2.1 - - - -
51E ARG* 2.9 54.9 + - + +
53E ILE* 3.8 8.3 - - + -
71E VAL* 4.2 16.4 - - + -
76E TYR* 2.9 31.8 + - - -
97E SER* 2.6 32.9 + - - -
98E GLN* 3.9 4.4 - - - +
99E THR 3.7 9.1 + - - -
100E SER* 3.5 12.3 + - - +
101E VAL 3.3 5.2 - - - -
102E TYR* 3.7 15.5 - - + -
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Residues in contact with GLN 44 (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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44D GLN* 2.8 44.8 + - - -
102D VAL* 5.3 1.8 - - - +
104D PHE* 3.5 13.9 - - - -
43E ARG* 1.3 71.9 - - - +
45E ASP* 1.3 67.4 + - - +
46E PRO* 4.8 1.0 - - - +
49E GLY* 3.3 14.1 - - - +
50E LEU* 3.8 18.8 - - + +
100E SER* 2.8 14.9 + - - -
101E VAL* 2.7 34.7 + - + +
103E PHE* 3.2 17.6 - - + -
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Residues in contact with ASP 45 (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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43E ARG* 2.8 41.3 + - - +
44E GLN* 1.3 78.8 - - - +
46E PRO* 1.4 78.0 - - + +
47E GLY 3.2 0.7 + - - -
48E MET* 2.9 32.5 + - + +
49E GLY* 3.3 11.1 + - - -
51E ARG* 3.0 15.5 + - - +
99E THR 3.8 5.0 - - - +
100E SER* 2.9 20.5 + - - -
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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
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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