Contacts of the strand formed by residues 100 - 105 (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 SER 100 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43E ARG* 3.5 16.0 - - - +
44E GLN 2.8 21.9 + - - -
45E ASP* 2.9 15.4 + - - -
98E GLN 3.2 9.9 + - - -
99E THR* 1.3 76.5 - - - +
101E VAL* 1.4 75.4 + - - +
102E TYR* 3.9 11.6 - - - -
118E THR 3.5 1.4 - - - +
119E ARG* 3.9 0.7 - - - -
120E LEU* 3.0 33.7 + - - +
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Residues in contact with VAL 101 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43E ARG* 3.3 2.6 - - - -
44E GLN* 2.7 49.7 + - + +
100E SER* 1.4 78.4 + - - +
102E TYR* 1.3 62.2 + - - +
103E PHE* 3.5 27.8 + - + -
118E THR 3.3 11.7 - - - +
119E ARG* 3.6 40.2 - - + +
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Residues in contact with TYR 102 (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* 2.6 25.3 + - - -
21E LEU* 3.6 26.9 - - + -
41E TRP* 3.8 6.1 - - + -
42E TYR 3.4 4.7 - - - -
43E ARG* 3.7 14.8 - - + -
53E ILE* 3.7 22.2 - - + -
76E TYR* 2.7 39.0 + + - -
89E LEU* 3.8 9.4 - - + -
91E LEU* 4.3 4.5 - - + +
98E GLN* 2.7 33.4 + - - +
100E SER* 3.9 22.7 - - - -
101E VAL* 1.3 72.7 - - - +
103E PHE* 1.3 55.7 + - - +
117E GLY* 3.3 2.6 - - - -
118E THR* 2.8 24.3 + - - +
120E LEU* 4.0 18.6 - - + -
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Residues in contact with PHE 103 (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* 3.8 8.1 - - - -
48D GLY 3.5 23.1 - - - -
49D GLU* 5.1 0.2 - - - -
50D LEU* 3.8 29.2 - - + -
6E GLN* 3.6 2.9 - - - +
41E TRP* 3.4 4.9 - - - -
42E TYR* 2.8 38.0 + - - +
44E GLN* 3.2 25.8 - - + -
50E LEU* 4.3 12.6 - - + -
101E VAL* 3.5 28.9 - - + -
102E TYR* 1.3 73.9 - - - +
104E CYS* 1.3 60.1 + - - +
114E PHE* 3.9 18.6 - + + -
115E GLY 3.7 13.5 - - - -
116E GLN 3.6 18.6 - - - -
117E GLY* 3.7 12.3 - - - -
119E ARG* 4.0 1.1 - - - -
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Residues in contact with CYS 104 (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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4E VAL* 3.9 2.7 - - + +
6E GLN* 2.9 15.1 + - - +
23E CYS* 2.2 49.8 - - + -
39E MET* 4.4 7.2 - - - -
40E TYR 3.3 16.8 - - - +
41E TRP* 3.8 18.2 - - + -
87E PHE* 4.9 1.3 - - - -
103E PHE* 1.3 76.0 - - - +
105E ALA* 1.4 69.3 + - - +
113E PHE 3.9 0.5 - - - +
114E PHE* 3.4 5.5 - - - -
115E GLY 3.0 26.2 + - - -
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Residues in contact with ALA 105 (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* 5.1 0.7 - - + -
4E VAL* 4.4 0.7 - - - -
39E MET* 3.4 3.8 - - - -
40E TYR* 2.8 36.1 + - + -
42E TYR* 4.0 15.3 - - + -
103E PHE 4.4 0.2 + - - -
104E CYS* 1.4 77.8 - - - +
106E SER* 1.3 59.0 + - - +
107E PRO* 3.8 6.5 - - + -
112E ALA* 3.6 14.8 - - + +
113E PHE 3.5 5.8 - - - -
114E PHE* 3.6 28.9 - - + -
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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