Contacts of the helix formed by residues 36 - 48 (chain I) in PDB entry 6RAR
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 36 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5I GLU* 4.1 32.1 - - + +
6I LEU* 4.8 7.2 - - + +
8I LYS* 6.1 4.7 - - + +
11I ILE* 3.8 20.4 - - + -
31I ALA* 3.3 36.5 + - + +
34I ASP* 3.6 23.6 - - + +
35I GLY* 1.3 68.9 - - - +
37I ASP* 1.3 67.3 + - - +
38I ASP* 3.3 3.1 - - + +
39I PHE* 3.2 28.5 + - + +
40I PHE* 3.4 17.1 + - + -
138I TYR* 3.5 4.6 + - - -
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Residues in contact with ASP 37 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35I GLY* 3.1 9.1 + - - +
36I ILE* 1.3 72.4 - - - +
38I ASP* 1.3 71.7 + - - +
40I PHE* 3.0 5.0 + - - +
41I GLU* 2.9 24.8 + - - +
137I LYS* 2.9 25.8 + - - -
138I TYR* 2.7 36.4 + - - -
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Residues in contact with ASP 38 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8I LYS* 4.0 17.0 + - - +
36I ILE* 3.3 3.4 - - + +
37I ASP* 1.3 82.7 - - - +
39I PHE* 1.3 61.2 + - - +
41I GLU* 3.6 11.5 + - - +
42I GLY* 3.3 15.6 + - - -
71I TRP* 3.3 56.2 + - + +
75I ARG* 4.9 1.0 + - - -
110I PHE* 4.7 0.5 - - - -
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Residues in contact with PHE 39 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8I LYS* 3.8 37.3 - - + +
11I ILE* 3.5 38.4 - - + -
12I ILE* 4.1 11.2 - - + -
15I LEU* 5.0 4.9 - - + -
28I ILE* 6.2 2.9 - - + -
31I ALA* 4.7 0.4 - - + -
36I ILE* 3.2 23.9 + - + +
37I ASP 3.1 0.6 - - - -
38I ASP* 1.3 79.0 - - - +
40I PHE* 1.3 97.7 + + - +
42I GLY* 3.2 4.2 + - - -
43I ILE* 2.9 49.0 + - + +
110I PHE* 3.6 32.4 - + - -
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Residues in contact with PHE 40 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28I ILE* 3.9 10.8 - - + -
31I ALA* 3.6 25.1 - - + -
32I MET* 3.3 62.8 - - + -
36I ILE* 3.4 19.5 + - + -
37I ASP 3.0 4.0 + - - +
39I PHE* 1.3 95.7 - + - +
41I GLU* 1.3 66.6 + - - +
43I ILE* 3.7 11.4 - - + +
44I ARG* 2.9 25.1 + - - +
128I ILE* 4.5 11.0 - - + -
138I TYR* 3.6 42.0 - + + +
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Residues in contact with GLU 41 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37I ASP* 2.9 16.6 + - - +
38I ASP* 3.7 11.3 - - - +
40I PHE* 1.3 76.6 - - - +
42I GLY* 1.3 61.5 + - - +
44I ARG* 3.4 6.4 + - - +
45I MET* 3.2 35.3 + - + +
71I TRP* 2.9 29.8 + - + -
75I ARG* 3.0 36.9 + - - +
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Residues in contact with GLY 42 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38I ASP 3.3 4.8 + - - -
39I PHE 3.2 7.3 + - - -
41I GLU* 1.3 77.8 - - - +
43I ILE* 1.3 64.6 + - - +
45I MET* 3.2 9.1 + - - +
46I ALA 3.0 18.4 + - - -
71I TRP* 3.7 19.2 - - - -
110I PHE* 4.0 9.9 - - - -
114I VAL* 3.5 18.2 - - - +
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Residues in contact with ILE 43 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12I ILE* 4.1 8.3 - - + -
15I LEU* 6.2 0.7 - - + -
39I PHE* 2.9 54.1 + - + +
40I PHE* 3.7 11.7 - - + +
42I GLY* 1.3 73.5 - - - +
44I ARG* 1.3 64.0 + - - +
46I ALA* 3.1 5.4 + - - +
47I LEU* 3.0 38.9 + - + +
110I PHE* 4.3 4.7 - - + -
119I LEU* 3.4 32.1 - - + -
128I ILE* 3.8 30.5 - - + -
140I ILE* 4.5 4.3 - - + -
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Residues in contact with ARG 44 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40I PHE 2.9 18.4 + - - +
41I GLU* 3.7 6.7 - - - +
42I GLY 3.2 0.2 - - - -
43I ILE* 1.3 73.7 - - - +
45I MET* 1.3 66.5 + - + +
48I ASP* 2.8 37.8 + - + +
51I VAL* 6.2 0.9 - - + -
137I LYS 5.0 7.1 + - - -
138I TYR 5.8 1.1 - - - +
139I ALA 3.4 25.0 + - - -
140I ILE* 4.1 25.1 - - + +
141I PRO* 3.5 30.9 - - - +
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Residues in contact with MET 45 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41I GLU* 3.2 26.7 + - + +
42I GLY* 3.2 7.5 + - - +
44I ARG* 1.3 78.3 - - + +
46I ALA* 1.3 52.1 + - - +
48I ASP 3.8 0.2 + - - -
51I VAL* 3.7 20.2 - - + +
53I PHE* 4.1 10.4 - - + -
71I TRP* 4.3 29.6 - - + -
74I PHE* 4.5 7.0 - - - -
75I ARG* 4.5 11.9 - - + -
78I ALA* 3.9 29.8 - - + -
79I ASN* 4.5 3.8 - - - +
82I MET* 4.3 17.0 - - + -
114I VAL* 4.1 9.2 - - + -
117I LYS* 2.7 31.0 + - - -
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Residues in contact with ALA 46 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42I GLY 3.0 13.1 + - - +
43I ILE 3.1 8.5 + - - +
45I MET* 1.3 76.9 - - - +
47I LEU* 1.3 64.0 + - + +
113I ARG 4.5 2.5 - - - +
114I VAL* 3.9 25.5 - - + +
117I LYS* 3.1 34.4 + - - +
119I LEU* 3.7 31.0 - - + -
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Residues in contact with LEU 47 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43I ILE* 3.0 25.4 + - + +
46I ALA* 1.3 82.8 - - + +
48I ASP* 1.3 63.0 + - - +
49I PRO* 3.5 10.0 - - - +
117I LYS* 4.4 4.7 - - - +
118I ASP* 6.0 0.7 - - - -
119I LEU* 4.0 28.3 - - + +
123I VAL 4.3 1.8 - - - +
124I SER* 3.4 46.2 - - - +
125I GLU* 3.6 18.1 - - + +
128I ILE* 3.8 20.0 - - + -
140I ILE* 3.9 14.1 - - + -
142I ILE* 4.3 0.9 - - - +
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Residues in contact with ASP 48 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44I ARG* 2.8 24.8 + - + +
45I MET 3.8 0.2 + - - -
46I ALA 3.6 0.2 - - - -
47I LEU* 1.3 76.1 - - - +
49I PRO* 1.3 70.6 - - - +
50I LEU* 2.7 41.7 + - - +
51I VAL* 3.2 24.7 + - + +
117I LYS* 2.7 24.4 + - - -
140I ILE* 4.1 10.0 - - + +
141I PRO* 3.8 30.9 - - - +
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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