Contacts of the helix formed by residues 51 - 67 (chain N) in PDB entry 1OCR
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 51 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40N GLU* 5.3 1.7 - - - +
46N THR* 4.3 15.3 - - - +
49N GLY 4.5 5.6 - - - +
50N ASP* 1.3 70.5 - - - +
52N GLN* 1.3 64.3 + - - +
53N ILE 3.3 0.2 - - - -
54N TYR* 3.4 8.2 + - - +
55N ASN* 3.1 30.6 + - - +
441N SER* 2.7 34.4 + - - +
202O SER* 3.0 26.5 - - - +
203O ASN* 4.2 4.3 + - - -
205O SER* 5.5 0.7 - - - +
206O PHE* 3.1 25.3 - - - -
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Residues in contact with GLN 52 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50N ASP* 3.1 13.4 + - + +
51N ASP* 1.3 77.9 - - - +
53N ILE* 1.3 61.0 + - + +
55N ASN* 3.1 7.6 + - - +
56N VAL* 2.8 31.9 + - - +
120N ALA* 3.4 39.7 + - + +
121N GLY 3.5 4.8 + - - -
123N GLY* 3.8 12.7 - - - +
138N HIS* 3.3 35.0 + - - -
201O GLY* 4.8 1.9 - - - -
202O SER* 4.2 30.2 + - - +
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Residues in contact with ILE 53 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48N LEU* 4.2 18.6 - - + -
50N ASP* 3.0 35.4 + - - +
52N GLN* 1.3 80.1 - - + +
54N TYR* 1.3 63.2 + - - +
56N VAL* 3.3 9.1 + - + +
57N VAL* 3.0 23.0 + - + +
120N ALA* 4.9 5.8 - - + +
40Y VAL* 4.2 30.7 - - + -
43Y GLN* 3.4 41.3 - - + +
44Y LEU* 3.9 14.6 - - + -
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Residues in contact with TYR 54 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37N ILE* 3.6 26.0 - - + +
40N GLU* 3.7 32.8 - - + +
41N LEU* 3.3 20.9 - - + +
48N LEU* 4.2 16.0 - - + +
50N ASP 3.5 3.5 + - - +
51N ASP* 3.4 16.8 + - - +
52N GLN 3.1 0.2 - - - -
53N ILE* 1.3 79.5 - - - +
55N ASN* 1.3 74.5 + - - +
57N VAL* 2.8 23.2 + - + +
58N VAL* 2.8 29.6 + - + +
439N ARG* 4.1 5.8 - - - -
440N TYR 3.4 20.1 + - - -
441N SER* 3.9 16.6 - - - -
515N HEA 2.5 31.7 + - - -
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Residues in contact with ASN 55 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51N ASP* 3.1 16.1 + - - +
52N GLN* 3.1 10.5 + - - +
54N TYR* 1.3 91.8 - - - +
56N VAL* 1.3 60.5 + - - +
58N VAL* 3.3 6.0 + - - +
59N THR* 3.0 28.2 + - - -
123N GLY* 3.7 22.3 + - - +
125N GLY 5.0 0.2 + - - -
439N ARG* 4.1 10.0 - - - +
441N SER* 5.7 0.2 - - - -
199O ILE* 3.9 22.5 - - + +
201O GLY 3.2 33.3 + - - -
202O SER* 4.1 2.0 + - - +
204O HIS* 5.2 1.4 - - - +
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Residues in contact with VAL 56 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52N GLN* 2.8 19.5 + - - +
53N ILE* 3.5 16.8 - - + +
55N ASN* 1.3 76.3 - - - +
57N VAL* 1.3 66.6 + - + +
59N THR* 3.6 1.9 - - - -
60N ALA* 3.0 24.6 + - + +
116N SER* 4.0 31.2 - - - +
120N ALA 3.3 26.9 - - - +
121N GLY* 3.9 3.6 - - - -
122N ALA 4.0 6.9 - - - +
123N GLY* 3.8 20.4 - - - +
39Y ILE* 5.9 2.5 - - + -
43Y GLN* 5.9 2.9 - - + -
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Residues in contact with VAL 57 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33N LEU* 3.7 43.2 - - + +
36N LEU* 4.3 11.9 - - + -
37N ILE* 3.8 12.8 - - + +
48N LEU* 4.8 5.4 - - + -
53N ILE* 3.0 19.9 + - + +
54N TYR* 2.8 14.0 + - + +
56N VAL* 1.3 79.2 - - + +
58N VAL* 1.3 66.1 + - - +
60N ALA* 3.3 2.3 + - - +
61N HIS* 2.9 23.2 + - - +
40Y VAL* 4.0 26.9 - - + -
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Residues in contact with VAL 58 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37N ILE* 4.0 12.6 - - + -
54N TYR* 2.8 58.4 + - + +
55N ASN* 3.7 8.5 - - - +
57N VAL* 1.3 73.0 - - - +
59N THR* 1.3 65.1 + - - +
61N HIS* 3.4 3.8 - - - +
62N ALA 3.3 12.8 + - - -
125N GLY* 5.7 1.8 - - - -
439N ARG* 4.8 7.0 - - + -
515N HEA 3.8 61.3 - - + +
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Residues in contact with THR 59 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55N ASN 3.0 17.1 + - - -
56N VAL 3.6 2.2 - - - -
58N VAL* 1.3 75.2 - - - +
60N ALA* 1.3 67.3 + - - +
62N ALA* 3.0 15.8 + - - +
63N PHE* 3.2 38.1 + - + -
112N LEU* 6.2 0.7 - - + -
122N ALA* 3.5 24.5 + - + +
124N THR* 3.5 3.7 + - - +
125N GLY* 2.8 38.9 + - - +
126N TRP 4.2 7.4 - - - +
146N THR* 5.8 0.7 - - + -
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Residues in contact with ALA 60 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33N LEU* 3.7 23.3 - - + -
56N VAL* 3.0 20.6 + - + +
57N VAL* 3.8 2.2 - - - +
59N THR* 1.3 76.4 - - - +
61N HIS* 1.3 64.3 + - - +
63N PHE* 3.3 6.4 + - - +
64N VAL* 3.0 32.3 + - + +
112N LEU* 4.9 12.3 - - + -
116N SER* 5.7 6.7 - - - -
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Residues in contact with HIS 61 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30N GLY 3.5 18.7 + - - -
33N LEU* 3.7 16.5 - - + +
34N SER* 3.7 11.4 - - - -
37N ILE* 4.0 14.1 - - + -
57N VAL 2.9 13.8 + - - +
58N VAL 3.4 9.4 - - - +
60N ALA* 1.3 79.3 - - - +
62N ALA* 1.3 62.3 + - - +
64N VAL* 3.9 1.0 - - - +
65N MET* 3.2 28.2 + - + +
515N HEA 1.8 102.9 + + + -
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Residues in contact with ALA 62 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58N VAL 3.3 1.2 + - - -
59N THR 3.0 6.0 + - - +
61N HIS* 1.3 81.3 - - - +
63N PHE* 1.3 61.8 + - - +
65N MET* 4.1 0.3 - - - +
66N ILE* 3.1 30.8 + - - +
126N TRP* 3.4 30.7 - - + -
515N HEA 3.7 43.7 - - + -
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Residues in contact with PHE 63 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59N THR* 3.2 35.8 + - + -
60N ALA 3.3 2.0 + - - +
62N ALA* 1.3 76.8 - - - +
64N VAL* 1.3 58.6 + - - +
67N PHE* 2.9 58.6 + + + +
68N PHE* 3.5 6.5 + - + -
112N LEU* 3.7 33.4 - - + -
124N THR* 5.6 0.2 - - - -
125N GLY 4.8 0.4 - - - -
126N TRP* 3.3 45.8 - + + -
128N VAL* 4.4 7.9 - - + -
146N THR* 3.8 19.7 - - + -
150N LEU* 4.3 28.3 - - + -
235N PHE* 6.0 1.3 - + - -
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Residues in contact with VAL 64 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26N ALA* 3.2 38.1 - - + +
29N VAL* 4.3 6.3 - - + -
30N GLY* 3.7 15.0 - - - +
33N LEU* 4.1 11.2 - - + -
60N ALA* 3.0 20.9 + - + +
61N HIS 3.9 2.0 - - - +
63N PHE* 1.3 74.9 - - - +
65N MET* 1.3 64.0 + - - +
68N PHE* 2.9 30.0 + - - -
69N MET* 2.9 8.5 + - - +
109N PHE* 4.1 17.7 - - + -
112N LEU* 4.1 16.4 - - + -
113N LEU* 6.0 1.3 - - + -
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Residues in contact with MET 65 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27N GLY* 4.8 3.6 - - - +
30N GLY* 3.9 31.0 - - - +
31N THR* 4.3 6.1 - - - +
61N HIS* 3.2 26.5 + - + +
62N ALA 4.2 1.1 - - - +
64N VAL* 1.3 76.3 - - - +
66N ILE* 1.3 58.6 + - - +
69N MET* 3.3 21.0 - - - +
70N VAL* 2.9 35.7 + - - +
515N HEA 3.6 87.7 - - + -
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Residues in contact with ILE 66 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62N ALA 3.1 18.9 + - - +
65N MET* 1.3 81.1 - - - +
67N PHE* 1.3 78.0 + - + +
70N VAL* 4.1 1.7 - - - +
71N MET* 3.4 24.1 + - - +
126N TRP* 3.9 30.7 - - + -
242N GLU* 3.4 27.6 - - + +
246N LEU* 3.9 26.0 - - + -
381N LEU* 5.2 3.6 - - + -
515N HEA 4.0 36.3 - - + -
516N HEA 5.7 1.6 - - + -
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Residues in contact with PHE 67 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63N PHE* 2.9 52.4 + + + +
66N ILE* 1.3 90.9 - - + +
68N PHE* 1.3 77.7 + - + +
69N MET 3.7 0.2 - - - -
71N MET* 4.3 18.4 - - + +
72N PRO* 3.3 18.3 - - - +
105N LEU* 5.3 3.5 - - - +
126N TRP* 4.4 9.4 - + - -
150N LEU* 4.6 20.9 - - + -
153N ALA* 4.3 20.4 - - + +
154N GLY* 6.1 1.1 - - - -
199N LEU* 5.2 5.6 - - + -
202N LEU* 5.0 6.5 - - + -
238N PHE* 4.0 30.1 - + - -
242N GLU* 4.6 6.7 - - - -
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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