Contacts of the strand formed by residues 100 - 106 (chain E) in PDB entry 5JVI
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 100 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38E GLY 3.0 7.5 + - - +
39E ILE* 3.4 20.3 - - + +
40E PHE* 2.8 28.8 + - - +
77E ALA* 4.4 13.5 - - + +
81E TYR* 3.9 27.4 - - + -
92E SER* 3.4 27.8 - - - +
93E TYR* 4.0 12.6 - - + +
98E ALA 3.8 2.0 - - - +
99E ALA* 1.3 71.9 - - - +
101E ARG* 1.3 61.1 - - - +
102E SER* 4.8 0.2 - - - +
115E TRP* 6.0 0.4 - - + -
120E MET* 3.4 31.9 - - + -
144E LEU* 4.0 23.1 - - + -
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Residues in contact with ARG 101 (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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40E PHE* 3.3 30.5 - - + -
42E TYR* 2.9 45.2 + - + -
51E PRO* 5.9 3.6 - - + -
93E TYR* 5.4 0.8 - - - -
99E ALA* 3.5 30.6 + - - +
100E ILE* 1.3 78.0 - - - +
102E SER* 1.3 63.3 + - - +
115E TRP* 4.8 2.1 - - - -
118E SER 4.9 5.9 + - - +
119E GLN* 3.3 21.1 - - + +
120E MET* 2.9 26.0 + - - +
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Residues in contact with SER 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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39E ILE* 5.7 1.0 - - - +
40E PHE 3.0 9.2 + - - -
41E THR* 3.3 9.5 + - - +
42E TYR* 2.8 34.7 + - - -
73E ALA* 4.4 20.2 + - - -
77E ALA* 4.8 2.4 - - - +
100E ILE* 4.8 0.9 + - - +
101E ARG* 1.3 72.1 - - - +
103E SER* 1.3 56.7 + - - +
119E GLN* 4.0 1.1 - - - +
120E MET* 3.2 34.3 - - - +
122E TYR* 4.0 20.1 - - - -
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Residues in contact with SER 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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42E TYR* 3.4 9.0 - - - +
44E ALA* 4.3 7.6 - - - -
50E LEU* 3.8 14.6 - - - -
51E PRO* 2.6 31.5 + - - +
102E SER* 1.3 73.2 - - - +
104E VAL* 1.3 61.9 + - - +
106E TYR 5.3 0.2 - - - -
119E GLN* 2.8 25.5 + - - -
120E MET 2.9 8.0 + - - -
121E VAL* 3.5 4.0 - - - +
122E TYR* 2.9 30.0 + - - +
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Residues in contact with VAL 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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41E THR* 4.6 3.1 - - + -
42E TYR 3.0 16.8 + - - +
43E ASP 3.9 0.2 - - - -
44E ALA* 2.9 27.5 + - - +
55E TRP* 3.7 24.5 - - + -
69E PRO* 3.6 28.9 - - + +
70E ALA* 3.9 16.6 - - + +
73E ALA* 3.6 20.4 - - + -
103E SER* 1.3 76.8 - - - +
105E HIS* 1.3 72.3 + - + +
106E TYR 3.2 2.4 + - - -
122E TYR* 3.8 17.0 - - + +
134E SER* 4.4 2.0 - - - +
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Residues in contact with HIS 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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43E ASP* 3.8 7.9 - - - +
44E ALA* 3.7 1.1 - - - -
45E LYS 3.6 4.7 + - - +
46E TYR* 2.8 37.4 + + + +
55E TRP* 3.9 10.8 - + - -
65E SER 5.2 0.2 - - - -
66E TYR* 2.7 79.9 + + - +
69E PRO* 3.9 16.7 - - + +
104E VAL* 1.3 80.7 - - + +
106E TYR* 1.3 59.5 + - - +
107E SER 4.2 2.9 - - - -
122E TYR 3.5 3.8 + - - -
124E ASP* 2.8 44.5 + - - +
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Residues in contact with TYR 106 (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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44E ALA* 4.0 6.1 - - + -
47E ARG 3.7 10.8 - - - -
48E THR* 3.6 39.3 + - + +
50E LEU* 3.9 20.5 - - + +
103E SER 5.0 0.9 - - - +
104E VAL 3.2 2.1 - - - -
105E HIS* 1.3 73.9 - - - +
107E SER* 1.3 76.5 + - - +
110E TYR* 3.5 57.9 + + - +
114E PHE* 3.8 17.5 - + - -
121E VAL* 3.3 28.5 - - + -
122E TYR 3.2 17.7 + - - +
123E GLY* 3.7 5.6 - - - -
124E ASP 4.3 2.1 + - - -
410E DMS 5.6 0.9 - - - +
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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