Contacts of the helix formed by residues 34 - 44 (chain A) in PDB entry 5FJV
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 ASP 34 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35A ARG* 1.3 107.6 + - - +
36A LEU* 3.0 35.9 + - - +
37A PHE* 2.8 40.9 + - + +
38A LYS* 3.4 7.4 + - - +
101A PHE* 3.3 31.6 - - + +
102A GLY* 4.3 16.2 - - - +
104A ILE* 4.5 4.0 - - - -
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Residues in contact with ARG 35 (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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34A ASP* 1.3 105.6 + - - +
36A LEU* 1.3 77.6 + - + +
37A PHE 3.1 0.7 + - - -
38A LYS* 3.4 11.5 + - - +
39A HIS* 3.5 20.5 + - + -
104A ILE* 4.0 21.5 - - + +
107A LEU* 4.8 2.6 - - + +
50E PRO* 3.8 19.1 - - + -
51E VAL 5.3 2.7 - - - -
53E ASN* 3.7 24.7 + - - -
54E THR* 4.0 17.1 + - - +
92E TYR* 6.3 1.4 - - - -
93E LYS* 3.6 17.8 - - - +
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Residues in contact with LEU 36 (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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34A ASP* 3.0 19.0 + - - +
35A ARG* 1.3 84.7 - - + +
37A PHE* 1.3 62.3 + - - +
38A LYS 3.3 0.2 - - - -
39A HIS* 3.9 7.7 - - - +
40A LEU* 3.3 33.1 + - + +
45E ASN 3.5 24.5 - - - +
46E ARG* 4.9 0.2 - - - -
47E TRP* 3.6 44.7 - - + +
50E PRO* 4.2 0.7 - - + -
93E LYS* 3.1 30.1 - - + +
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Residues in contact with PHE 37 (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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34A ASP* 2.8 27.0 + - + +
36A LEU* 1.3 79.4 - - - +
38A LYS* 1.3 84.8 + - - +
40A LEU* 4.3 3.9 - - - +
41A PHE* 3.3 20.8 + + + +
100A ASP* 5.9 0.4 - - + -
101A PHE* 3.1 59.5 - + - -
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Residues in contact with LYS 38 (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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34A ASP 3.4 6.2 + - - +
35A ARG 3.4 8.5 + - - +
36A LEU 3.3 0.4 - - - -
37A PHE* 1.3 102.6 - - - +
39A HIS* 1.3 65.2 + - - +
41A PHE* 3.3 30.8 + - + +
42A ARG* 3.2 31.3 + - - +
96A TRP* 4.2 27.7 - - + +
97A ASN 5.5 0.2 + - - -
100A ASP* 4.6 8.8 - - - +
101A PHE* 3.1 50.5 - - - +
104A ILE* 4.4 15.7 - - + -
107A LEU* 4.1 16.8 - - + -
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Residues in contact with HIS 39 (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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35A ARG* 3.5 15.6 + - + +
36A LEU 3.9 4.7 - - - +
37A PHE 3.4 0.4 - - - -
38A LYS* 1.3 75.1 - - - +
40A LEU* 1.3 60.8 + - - +
42A ARG* 3.2 10.5 + - - +
43A GLY* 2.8 31.0 + - - -
107A LEU* 3.7 28.5 - - + +
108A ARG 4.6 4.2 + - - -
109A VAL* 4.0 30.6 - - + +
110A PRO* 4.6 0.4 - - + -
113A MET* 6.2 2.6 - - + +
47E TRP* 3.3 36.3 + + + +
49E ARG* 3.6 29.6 - - + +
50E PRO* 4.9 5.9 - - + +
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Residues in contact with LEU 40 (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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36A LEU* 3.3 17.9 + - + +
37A PHE* 4.5 4.3 - - - +
39A HIS* 1.3 78.0 - - - +
41A PHE* 1.3 59.8 + - - +
43A GLY* 5.2 0.4 - - - -
44A TYR* 2.7 83.4 + - + +
47E TRP* 3.4 37.0 - - + -
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Residues in contact with PHE 41 (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 PHE* 3.3 17.9 + + + +
38A LYS* 3.3 30.9 + - + +
39A HIS 3.1 0.6 - - - -
40A LEU* 1.3 79.6 - - - +
42A ARG* 1.3 71.6 + - + +
44A TYR* 4.1 11.8 - - - +
45A ASN* 4.9 8.1 + - - +
95A ARG 4.2 17.5 - - - -
96A TRP* 4.2 13.7 - - + -
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Residues in contact with ARG 42 (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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38A LYS* 3.2 9.9 + - - +
39A HIS* 3.2 23.4 + - - +
41A PHE* 1.3 94.7 - - + +
43A GLY* 1.3 67.5 + - - +
44A TYR 3.1 1.8 - - - -
45A ASN* 3.1 17.2 + - - +
46A ARG* 3.9 10.4 - - - +
93A LYS 4.9 7.5 - - - +
94A LEU* 3.6 52.9 - - + +
95A ARG 4.9 1.3 - - - +
96A TRP* 3.7 21.2 - - - -
107A LEU* 3.2 38.5 - - - +
109A VAL* 4.9 8.3 - - - +
114A ILE* 5.6 1.4 - - - +
139A LEU* 3.6 14.6 - - - +
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Residues in contact with GLY 43 (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 HIS 2.8 18.2 + - - -
40A LEU* 5.2 0.2 - - - -
42A ARG* 1.3 76.7 - - - +
44A TYR* 1.3 65.9 + - - +
45A ASN 3.3 8.5 + - - -
46A ARG* 3.6 12.8 + - - +
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Residues in contact with TYR 44 (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 LEU* 2.7 69.6 + - + +
41A PHE* 4.1 9.6 - - - +
42A ARG 3.1 1.2 - - - -
43A GLY* 1.3 76.7 - - - +
45A ASN* 1.3 61.0 + - - +
46A ARG 3.9 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