Contacts of the helix formed by residues 41 - 51 (chain I) in PDB entry 3J7Y
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 HIS 41 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2101A C 3.6 21.3 + - - -
2102A A 3.8 30.1 + - - +
2136A C 2.9 30.9 + - - -
2137A C 3.3 20.0 + - - -
39I VAL 4.0 0.8 + - - -
40I MET* 1.3 72.1 - - - +
42I PHE* 1.3 57.0 + - - +
43I GLN* 3.1 24.0 + - + -
44I ARG* 2.8 30.3 + - - +
45I GLN* 3.1 4.7 + - - +
229N VAL* 3.5 39.2 - - + +
242N TRP* 5.5 0.2 - - - -
22o ARG* 6.1 1.8 - - - +
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Residues in contact with PHE 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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2136A C 4.6 12.6 + - - +
2137A C 5.7 8.5 - - - -
2153A A 3.4 24.7 - - - -
2154A A 4.9 1.3 - - - -
40I MET 3.6 3.3 + - - -
41I HIS* 1.3 74.8 + - - +
43I GLN* 1.3 57.6 + - + +
45I GLN* 3.2 17.2 + - + +
46I LYS* 2.9 50.5 + - + +
25o ARG* 3.2 57.4 - - + -
26o PHE 4.6 0.9 - - - -
27o VAL* 4.0 20.9 - - + -
31o ALA* 4.5 7.9 - - + -
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Residues in contact with GLN 43 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2137A C 3.3 42.7 + - - -
2138A U 4.0 2.8 + - - -
41I HIS* 3.1 19.2 + - + +
42I PHE* 1.3 78.2 - - + +
44I ARG* 1.3 56.4 + - - +
46I LYS* 3.2 24.1 + - - +
47I LEU* 2.9 29.0 + - - +
225N GLY 4.7 4.9 - - - +
226N ILE* 4.2 16.1 - - + +
229N VAL* 3.2 24.3 - - + +
73Z LYS* 5.9 0.6 - - - +
78Z ARG* 3.9 23.2 + - - +
35o MET* 4.8 1.9 - - - +
38o ARG* 5.4 6.7 - - - +
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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 MET* 3.4 39.3 - - + +
41I HIS* 2.8 20.6 + - + +
43I GLN* 1.3 74.5 - - - +
45I GLN* 1.3 54.5 + - - +
47I LEU* 3.2 9.0 + - - +
48I MET* 2.9 57.2 + - - +
215N PHE* 4.6 6.3 - - - -
226N ILE* 5.3 1.6 - - - -
229N VAL* 3.5 27.4 - - + +
230N LEU* 3.6 22.0 - - + +
234N ASP* 2.9 36.4 + - - +
238N LYS 5.1 1.4 + - - -
239N GLY* 5.6 2.6 + - - -
241N TYR 4.5 9.5 + - - -
242N TRP* 3.4 32.7 + - + +
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Residues in contact with GLN 45 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39I VAL* 4.8 9.9 - - - +
40I MET* 3.7 39.1 + - + +
41I HIS 3.1 7.5 + - - +
42I PHE* 3.3 15.3 - - + +
44I ARG* 1.3 78.4 - - - +
46I LYS* 1.3 58.8 + - - +
48I MET* 3.2 10.6 + - - +
49I ALA* 2.9 28.6 + - - +
24o PRO* 5.8 0.4 - - - +
25o ARG* 3.5 34.6 + - - +
26o PHE* 5.3 1.7 - - - -
27o VAL* 3.7 18.1 - - + +
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Residues in contact with LYS 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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2137A C 5.0 6.2 + - - -
2152A A 4.1 2.8 + - - -
2153A A 3.2 30.0 + - - +
42I PHE* 2.9 38.5 + - + +
43I GLN* 3.4 29.9 - - - +
45I GLN* 1.3 76.3 - - - +
47I LEU* 1.3 57.5 + - - +
49I ALA* 3.2 4.2 + - - +
50I VAL* 2.9 32.6 + - - +
27o VAL* 3.9 16.0 - - + +
31o ALA* 3.9 12.3 - - + +
32o LYS* 5.3 0.8 - - - +
35o MET* 4.1 27.8 - - + +
38o ARG* 3.8 26.7 - - - +
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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 GLN 2.9 11.9 + - - +
44I ARG* 3.3 10.5 - - - +
46I LYS* 1.3 75.8 - - - +
48I MET* 1.3 53.2 + - - +
50I VAL* 3.2 3.0 + - + +
51I THR* 2.8 59.9 + - + +
215N PHE* 3.6 31.2 - - + +
218N ILE* 3.6 27.1 - - + -
219N ALA* 6.4 0.2 - - + -
226N ILE* 3.3 38.4 - - + -
230N LEU* 4.3 10.3 - - + -
35o MET* 3.7 12.3 - - + +
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Residues in contact with MET 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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40I MET* 4.0 25.4 - - + -
44I ARG* 2.9 46.5 + - - +
45I GLN* 3.4 8.1 - - - +
47I LEU* 1.3 76.7 - - - +
49I ALA* 1.3 62.0 + - - +
51I THR 3.2 5.5 + - - -
52I GLU* 3.5 10.9 + - - +
215N PHE* 3.8 23.3 - - + -
239N GLY* 4.9 5.6 - - - -
240N LYS 5.2 0.4 - - - +
247N MET* 4.4 8.7 - - - -
250N ARG* 3.1 59.9 + - - +
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Residues in contact with ALA 49 (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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45I GLN 2.9 13.0 + - - +
46I LYS 3.3 8.7 - - - +
48I MET* 1.3 78.9 - - - +
50I VAL* 1.3 62.6 + - - +
52I GLU* 3.5 26.0 + - - +
27o VAL* 3.7 22.4 - - + -
32o LYS* 3.5 34.4 + - + +
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Residues in contact with VAL 50 (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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46I LYS 2.9 17.7 + - - +
47I LEU* 3.2 9.8 + - - +
49I ALA* 1.3 79.2 - - - +
51I THR* 1.3 69.4 + - + +
52I GLU* 3.3 4.4 + - - +
211N ASN* 3.1 24.9 + - - +
213N TRP* 4.2 13.5 - - + -
218N ILE* 4.6 0.7 - - + -
32o LYS* 4.3 18.2 - - + +
35o MET* 3.7 33.4 - - + -
36o ILE* 4.4 12.9 - - + +
39o LEU* 3.7 26.0 - - + -
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Residues in contact with THR 51 (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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47I LEU* 2.8 42.2 + - + +
48I MET* 3.2 1.1 + - - -
50I VAL* 1.3 79.6 - - + +
52I GLU* 1.3 63.0 + - - +
53I TYR 4.0 0.2 + - - -
211N ASN* 4.4 0.2 - - - -
213N TRP 3.5 23.9 - - - +
214N THR* 3.7 8.3 - - - +
215N PHE* 3.9 13.9 - - - +
218N ILE* 3.6 18.2 - - + -
250N ARG* 2.8 41.6 + - - -
251N VAL 4.0 8.1 - - - +
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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