Contacts of the helix formed by residues 36 - 46 (chain I) in PDB entry 6O81
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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7I VAL* 4.0 18.6 - - + -
8I MET 5.1 0.2 - - - +
9I ALA* 5.9 1.3 - - + -
29I PRO* 4.9 4.9 - - + +
34I PRO* 3.2 9.3 - - + -
35I LEU* 1.3 77.9 - - - +
37I TRP* 1.3 65.4 + - + +
38I TYR 3.4 0.4 - - - -
39I PRO* 3.5 4.9 - - + +
40I LEU* 3.3 37.2 + - + +
53I VAL* 4.7 16.8 - - + -
67I PHE* 5.1 19.7 - - + -
105I SER 4.8 0.4 - - - +
106I CYS* 3.8 39.5 - - + +
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Residues in contact with TRP 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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33I LYS* 5.1 7.0 - - + -
34I PRO* 3.2 24.4 + - + +
36I ILE* 1.3 84.4 - - + +
38I TYR* 1.3 87.7 + + - +
40I LEU* 3.2 12.5 + - + +
41I ASN* 2.6 63.6 + - + +
70I LYS* 5.5 11.0 - - + -
71I MET 6.2 0.7 - - - -
72I LYS* 6.5 0.9 - - + -
292I ASP* 5.5 5.4 - - + -
295I ARG* 5.8 4.9 - - + -
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Residues in contact with TYR 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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32I ASN* 5.4 0.9 - - - +
33I LYS* 3.4 29.0 + - + +
34I PRO 3.5 20.4 - - - -
35I LEU* 4.7 3.6 - - - -
37I TRP* 1.3 94.0 - + - +
39I PRO* 1.3 67.5 - - + +
41I ASN* 3.8 8.4 - - - +
42I LEU* 2.9 28.4 + - - +
45I ARG* 4.7 5.1 + - - +
108I LEU 4.6 3.6 - - - +
109I ILE* 4.0 33.2 - - + -
110I THR 6.1 0.2 - - - +
288I ASP* 3.7 26.6 + - + +
292I ASP* 3.7 28.7 - - + +
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Residues in contact with PRO 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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7I VAL* 4.6 14.1 - - + -
35I LEU 3.3 17.9 - - - +
36I ILE* 3.5 9.2 - - - +
38I TYR* 1.3 89.6 - - + +
40I LEU* 1.3 57.8 + - - +
42I LEU* 3.3 8.5 + - + +
43I LEU* 2.9 35.1 + - - +
104I LEU* 4.6 16.0 - - + +
105I SER 3.4 26.0 - - - +
106I CYS* 3.7 9.6 - - - +
108I LEU* 3.8 17.5 - - + +
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Residues in contact with LEU 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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7I VAL* 4.7 3.6 - - + -
36I ILE* 3.3 31.9 + - + +
37I TRP* 3.2 16.2 + - + +
39I PRO* 1.3 80.5 - - + +
41I ASN* 1.3 57.3 + - - +
43I LEU* 3.4 6.4 + - + +
44I GLU* 2.9 38.8 + - + +
51I VAL* 3.8 30.3 - - + -
53I VAL* 3.9 15.0 - - + -
67I PHE* 5.6 2.2 - - + +
70I LYS* 5.1 8.7 - - + -
72I LYS* 4.9 8.5 - - + -
75I ILE* 4.3 30.7 - - + -
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Residues in contact with ASN 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 TRP* 2.6 54.8 + - + +
38I TYR* 3.9 10.8 - - - +
40I LEU* 1.3 72.2 - - - +
42I LEU* 1.3 58.8 + - - +
44I GLU* 4.5 3.9 - - - +
45I ARG* 2.9 60.3 + - - +
295I ARG* 3.7 24.5 - - - +
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Residues in contact with LEU 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 TYR 2.9 18.1 + - - +
39I PRO* 3.3 8.9 + - + +
41I ASN* 1.3 77.4 - - - +
43I LEU* 1.3 64.3 + - + +
45I ARG* 3.4 28.6 + - + +
46I VAL* 3.8 21.6 + - + +
48I PHE* 5.1 0.7 - - - -
104I LEU* 5.7 7.0 - - + -
108I LEU 5.7 2.2 - - - +
110I THR* 3.7 42.0 - - + +
111I ASP 6.2 0.2 - - - -
112I VAL 4.6 7.0 - - - +
113I ALA* 5.5 3.1 - - - -
114I LEU* 3.7 33.6 - - + +
204I LEU* 6.2 0.2 - - + -
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Residues in contact with LEU 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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5I ALA* 3.7 26.7 - - + -
7I VAL* 3.9 18.4 - - + -
39I PRO 2.9 20.2 + - - +
40I LEU* 3.8 6.3 - - + +
42I LEU* 1.3 80.0 - - + +
44I GLU* 1.3 59.5 + - - +
45I ARG 3.3 0.2 + - - -
46I VAL 3.0 25.1 - - - +
47I GLY 3.0 6.9 - - - +
48I PHE* 3.3 38.6 - - + +
51I VAL* 3.8 28.0 - - + -
102I LEU* 4.9 2.5 - - + -
104I LEU* 3.9 20.6 - - + -
114I LEU* 5.3 6.5 - - + -
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Residues in contact with GLU 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 LEU* 2.9 24.6 + - + +
41I ASN* 4.5 4.0 - - - +
43I LEU* 1.3 73.5 - - + +
45I ARG* 1.3 63.8 + - - +
47I GLY 3.8 8.7 + - - +
48I PHE 3.1 21.9 - - - +
49I GLU* 4.7 3.2 - - - -
51I VAL* 3.5 17.7 - - + +
72I LYS* 4.6 15.4 - - + +
73I PRO* 3.4 29.3 - - - +
74I ASP 3.9 15.2 + - - +
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Residues in contact with ARG 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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38I TYR* 4.7 4.6 + - - -
41I ASN* 2.9 45.5 + - - +
42I LEU* 3.4 40.3 - - + +
43I LEU 3.2 0.6 - - - -
44I GLU* 1.3 79.9 - - - +
46I VAL* 1.3 63.3 + - + +
47I GLY 3.9 1.3 + - - -
110I THR 5.0 4.8 + - - -
295I ARG* 3.4 36.2 - - - +
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Residues in contact with VAL 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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196E MET 3.4 27.4 - - - +
197E SER* 3.8 9.2 - - - -
198E ILE* 3.8 20.7 + - + +
42I LEU* 3.8 18.8 - - + +
43I LEU 3.0 13.9 + - - +
45I ARG* 1.3 78.4 - - + +
47I GLY* 1.3 61.9 + - - +
48I PHE* 3.3 12.3 - - + -
114I LEU* 5.3 9.0 - - + +
115I HIS* 6.2 1.1 - - + -
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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