Contacts of the helix formed by residues 36 - 46 (chain J) 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 J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7J VAL* 4.0 19.3 - - + -
9J ALA* 5.9 1.3 - - + -
29J PRO* 4.9 4.7 - - + +
34J PRO* 3.2 8.9 - - + -
35J LEU* 1.3 77.1 - - - +
37J TRP* 1.3 66.1 + - + +
38J TYR 3.4 0.4 - - - -
39J PRO* 3.5 5.1 - - + +
40J LEU* 3.3 37.7 + - + +
53J VAL* 4.7 16.6 - - + -
67J PHE* 5.1 19.7 - - + +
105J SER 4.8 0.2 - - - +
106J CYS* 3.8 38.8 - - + -
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Residues in contact with TRP 37 (chain J).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33J LYS* 5.1 7.2 - - + -
34J PRO* 3.2 25.7 + - + +
36J ILE* 1.3 82.1 - - + +
38J TYR* 1.3 86.8 + + - +
40J LEU* 3.2 11.7 + - + +
41J ASN* 2.6 62.8 + - + +
70J LYS* 5.5 11.2 - - + -
71J MET 6.2 0.4 - - - -
72J LYS* 6.5 0.9 - - + -
292J ASP* 5.5 5.4 - - + -
295J ARG* 5.8 4.7 - - + -
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Residues in contact with TYR 38 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32J ASN* 5.4 0.9 - - - +
33J LYS* 3.4 28.5 + - + +
34J PRO 3.5 21.8 - - - -
35J LEU* 4.7 3.1 - - - -
37J TRP* 1.3 94.0 - + - +
39J PRO* 1.3 67.2 - - + +
41J ASN* 3.8 8.4 - - - +
42J LEU* 2.9 28.6 + - - +
45J ARG* 4.7 4.6 + - - -
108J LEU 4.6 4.0 - - - +
109J ILE* 4.0 33.0 - - + -
110J THR 6.1 0.4 - - - +
288J ASP* 3.7 25.0 + - + +
292J ASP* 3.7 28.8 - - + +
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Residues in contact with PRO 39 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7J VAL* 4.6 13.5 - - + -
35J LEU 3.3 17.9 - - - +
36J ILE* 3.5 9.2 - - - +
38J TYR* 1.3 90.6 - - + +
40J LEU* 1.3 57.1 + - + +
42J LEU* 3.3 8.4 + - + +
43J LEU* 2.9 35.5 + - - +
104J LEU* 4.6 16.9 - - + +
105J SER 3.4 25.8 - - - +
106J CYS* 3.7 10.1 - - - +
108J LEU* 3.8 16.2 - - + +
109J ILE* 5.5 0.2 - - + -
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Residues in contact with LEU 40 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7J VAL* 4.7 4.0 - - + -
36J ILE* 3.3 30.6 + - + +
37J TRP* 3.2 16.4 + - + +
39J PRO* 1.3 78.6 - - + +
41J ASN* 1.3 57.6 + - - +
43J LEU* 3.4 4.8 + - + +
44J GLU* 2.9 39.7 + - + +
51J VAL* 3.8 31.6 - - + -
53J VAL* 3.9 14.8 - - + -
67J PHE* 5.6 2.5 - - + +
70J LYS* 5.1 7.6 - - + -
72J LYS* 4.9 9.4 - - + -
75J ILE* 4.3 31.0 - - + -
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Residues in contact with ASN 41 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37J TRP* 2.6 57.5 + - + +
38J TYR* 3.9 10.8 - - - +
40J LEU* 1.3 71.3 - - - +
42J LEU* 1.3 59.7 + - - +
44J GLU* 4.8 3.9 - - - +
45J ARG* 2.9 60.1 + - - +
295J ARG* 3.7 24.9 - - - +
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Residues in contact with LEU 42 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38J TYR 2.9 18.1 + - - +
39J PRO* 3.3 8.7 + - + +
41J ASN* 1.3 76.7 - - - +
43J LEU* 1.3 63.9 + - + +
45J ARG* 3.4 28.4 + - + +
46J VAL* 3.8 20.6 - - + +
48J PHE* 5.1 0.5 - - - -
104J LEU* 5.7 6.7 - - + -
108J LEU 5.7 2.2 - - - +
110J THR* 3.7 42.4 - - + +
111J ASP 6.2 0.2 - - - -
112J VAL 4.6 7.9 - - - +
113J ALA* 5.5 3.4 - - - -
114J LEU* 3.7 33.6 - - + +
204J LEU* 6.2 0.2 - - + -
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Residues in contact with LEU 43 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5J ALA* 3.7 26.7 - - + -
7J VAL* 3.9 18.8 - - + -
39J PRO 2.9 19.9 + - - +
40J LEU* 3.8 6.1 - - + +
42J LEU* 1.3 79.5 - - + +
44J GLU* 1.3 59.3 + - - +
45J ARG 3.4 0.3 + - - -
46J VAL 3.0 24.9 - - - +
47J GLY 3.0 7.1 - - - +
48J PHE* 3.3 39.1 - - + +
51J VAL* 3.8 28.3 - - + -
102J LEU* 4.9 1.8 - - + -
104J LEU* 3.9 20.0 - - + -
114J LEU* 5.3 6.5 - - + -
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Residues in contact with GLU 44 (chain J).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40J LEU* 2.9 23.1 + - + +
41J ASN* 4.5 4.5 - - - +
43J LEU* 1.3 75.5 - - + +
45J ARG* 1.3 65.1 + - - +
47J GLY 3.8 9.0 + - - +
48J PHE 3.1 22.9 - - - +
49J GLU* 4.7 2.8 - - - -
51J VAL* 3.5 17.0 - - + +
72J LYS* 4.6 14.8 - - + +
73J PRO* 3.4 28.5 - - - +
74J ASP 3.9 15.8 + - - +
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Residues in contact with ARG 45 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38J TYR* 4.7 4.6 + - - +
41J ASN* 2.9 44.9 + - - +
42J LEU* 3.4 41.9 - - + +
43J LEU 3.2 0.2 - - - -
44J GLU* 1.3 79.3 - - - +
46J VAL* 1.3 62.0 + - + +
47J GLY 3.9 2.1 + - - -
110J THR 5.0 4.4 + - - -
294J SER 5.5 0.2 - - - -
295J ARG* 3.4 34.9 - - - +
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Residues in contact with VAL 46 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196F MET 3.5 24.9 - - - +
197F SER* 3.7 3.4 - - - -
198F ILE* 3.7 30.1 - - + +
199F PRO* 4.5 1.4 - - - +
42J LEU* 3.8 18.6 - - + +
43J LEU 3.0 13.0 + - - +
45J ARG* 1.3 76.8 - - + +
47J GLY* 1.3 62.9 + - - +
48J PHE* 3.3 13.1 - - + -
114J LEU* 5.3 9.0 - - + +
115J HIS* 6.2 0.7 - - + -
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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