Contacts of the helix formed by residues 59 - 75 (chain A) in PDB entry 3ORY
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 THR 59 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A LEU* 2.8 31.4 + - - +
52A MET* 3.5 4.0 + - - -
53A ASP* 3.8 15.0 - - + +
57A ARG 3.6 11.2 - - - +
58A ILE* 1.3 78.8 - - - +
60A SER* 1.3 65.3 + - - +
61A HIS* 3.2 9.4 - - - -
62A LEU* 3.0 16.3 + - + +
63A SER* 3.0 12.0 + - - -
316A HIS* 3.9 35.1 + - + +
318A PHE* 3.8 16.5 - - - -
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Residues in contact with SER 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A PHE* 3.7 17.4 - - - +
40A LEU* 4.1 11.2 - - - -
43A ILE* 2.7 32.8 + - - +
50A PRO* 3.7 5.9 - - - +
51A LEU* 2.9 30.8 + - - +
58A ILE* 3.7 10.3 - - - +
59A THR* 1.3 77.9 + - - +
61A HIS* 1.3 56.4 + - - +
63A SER* 3.4 5.3 + - - -
64A GLY 3.0 24.4 + - - -
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Residues in contact with HIS 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A LEU* 4.0 23.3 - - + +
39A PHE* 3.6 16.3 - - - -
40A LEU* 3.9 20.1 - - + +
58A ILE 3.1 26.6 + - - -
59A THR* 3.6 9.9 - - - -
60A SER* 1.3 78.8 + - - +
62A LEU* 1.3 87.1 + - + +
65A LEU* 3.0 29.1 + - - +
131A LEU* 5.2 0.9 - - + -
135A MET* 3.5 61.5 - - + +
138A ASP* 4.9 2.8 + - - +
139A ALA* 5.2 0.2 - - + -
316A HIS* 6.2 0.9 - + - -
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Residues in contact with LEU 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A THR* 3.0 10.6 + - + +
61A HIS* 1.3 107.0 - - + +
63A SER* 1.3 59.2 + - - +
65A LEU* 4.4 2.9 - - + -
66A PHE* 2.9 31.0 + - - +
138A ASP* 4.0 14.4 - - + +
139A ALA* 4.0 27.4 - - + +
142A LEU* 3.7 15.1 - - + +
311A ILE* 4.9 3.1 - - + -
312A LEU* 4.2 16.7 - - + +
316A HIS* 3.6 43.5 - - + +
318A PHE* 4.2 4.7 - - + -
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Residues in contact with SER 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A ILE* 4.1 8.0 - - - +
51A LEU* 3.6 31.8 - - - +
59A THR 3.0 6.5 + - - -
60A SER 3.7 6.3 - - - -
62A LEU* 1.3 74.7 - - - +
64A GLY* 1.3 65.4 - - - +
66A PHE* 3.7 0.6 - - - +
67A TYR* 3.0 46.3 + - - +
318A PHE* 3.7 23.5 - - - -
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Residues in contact with GLY 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A PHE* 3.6 17.5 - - - -
43A ILE* 2.9 27.6 - - - +
60A SER 3.0 10.9 + - - -
63A SER* 1.3 76.5 - - - +
65A LEU* 1.3 55.8 + - - +
67A TYR* 5.3 0.7 - - - -
68A ARG* 2.9 37.4 + - - +
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Residues in contact with LEU 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A LEU* 4.2 9.0 - - + -
39A PHE* 3.4 16.2 - - + -
61A HIS 3.0 19.8 + - - +
62A LEU* 3.9 4.7 - - + +
63A SER 3.3 0.2 - - - -
64A GLY* 1.3 74.4 - - - +
66A PHE* 1.3 62.9 + - - +
69A THR* 2.6 30.5 + - - -
81A TYR* 3.5 40.8 - - + +
83A PHE* 5.6 1.1 - - + -
139A ALA* 3.6 45.8 - - + +
142A LEU* 4.1 11.9 - - + -
143A LEU* 3.9 20.2 - - + -
146A MET* 4.5 0.9 - - - +
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Residues in contact with PHE 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A LEU 2.9 19.0 + - - +
63A SER* 3.7 3.4 - - - +
64A GLY 3.2 0.2 - - - -
65A LEU* 1.3 78.5 - - - +
67A TYR* 1.3 104.1 + + - +
70A ILE* 3.1 47.3 + - + +
142A LEU* 4.0 6.4 - - + +
146A MET* 3.7 26.6 - - + +
308A VAL* 3.6 21.1 - - + -
312A LEU* 3.5 30.1 - - + -
318A PHE* 5.5 0.2 - + - -
323A VAL* 4.1 16.2 - - + -
326A ALA* 3.8 13.9 - - + -
327A LEU* 4.1 15.5 - - + -
330A TYR* 5.7 0.2 - + - -
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Residues in contact with TYR 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A SER* 3.0 45.1 + - - +
64A GLY* 5.3 1.1 - - - -
66A PHE* 1.3 104.5 - + - +
68A ARG* 1.3 62.8 + - - +
70A ILE* 3.5 8.0 + - + +
71A ASN* 3.0 32.8 + - - +
318A PHE* 4.5 12.1 - + - -
322A ARG* 3.6 37.1 + - + +
323A VAL* 4.0 6.9 + - - +
326A ALA* 3.8 17.7 - - + -
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Residues in contact with ARG 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A LEU* 4.7 7.7 - - - +
39A PHE* 3.8 24.9 - - + -
64A GLY* 2.9 20.5 + - - +
67A TYR* 1.3 74.4 - - - +
69A THR* 1.3 59.8 + - - +
71A ASN* 3.2 18.1 + - - +
72A ILE* 2.9 43.6 + - + +
81A TYR* 5.3 1.1 - - - +
192A LEU 3.2 17.9 + - - -
193A THR* 3.3 22.4 + - + -
194A ILE* 3.7 6.7 + - - +
195A SER* 3.0 48.5 + - - +
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Residues in contact with THR 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A LEU* 2.6 27.3 + - - +
68A ARG* 1.3 75.3 - - - +
70A ILE* 1.3 64.9 + - - +
72A ILE* 3.3 6.8 + - - +
73A VAL* 3.0 24.2 + - + +
79A PRO* 4.2 12.6 - - + -
81A TYR* 2.8 33.7 + - + +
143A LEU* 4.4 1.2 - - + +
146A MET* 3.9 14.6 - - + -
148A ILE* 3.9 34.3 - - + -
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Residues in contact with ILE 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A PHE* 3.1 54.0 + - + +
67A TYR* 3.6 11.2 - - + +
69A THR* 1.3 76.0 - - - +
71A ASN* 1.3 57.7 + - - +
73A VAL* 3.3 3.5 + - - +
74A GLU* 2.8 53.6 + - + +
146A MET* 3.9 6.3 - - + -
326A ALA* 3.8 17.7 - - + +
329A ARG* 5.6 0.2 - - + -
330A TYR* 3.8 41.0 - - + -
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Residues in contact with ASN 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A LEU* 4.2 13.3 - - + +
67A TYR* 3.0 29.6 + - - +
68A ARG* 3.2 23.9 + - - +
70A ILE* 1.3 76.4 - - - +
72A ILE* 1.3 58.7 + - - +
74A GLU* 3.3 19.4 + - - +
75A ALA* 3.0 28.2 + - - +
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Residues in contact with ILE 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A LEU* 4.5 13.5 - - + -
30A ILE* 4.1 14.4 - - + -
68A ARG* 2.9 44.0 + - + +
69A THR* 3.6 9.0 - - - +
71A ASN* 1.3 76.6 - - - +
73A VAL* 1.3 61.1 + - - +
75A ALA* 3.2 10.5 + - - +
76A GLY 3.4 0.2 + - - -
77A ILE* 3.2 50.7 + - + +
79A PRO* 4.0 19.1 - - + -
81A TYR* 4.6 3.1 - - - +
192A LEU* 4.0 32.8 - - + +
193A THR* 5.6 1.8 - - + -
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Residues in contact with VAL 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A THR 3.0 19.7 + - - +
70A ILE 3.6 3.8 - - - +
72A ILE* 1.3 75.8 - - - +
74A GLU* 1.3 50.8 + - - +
76A GLY* 2.8 9.5 + - - -
77A ILE 3.7 6.5 - - - -
79A PRO* 3.8 27.8 - - + -
148A ILE* 4.1 5.6 - - + -
330A TYR* 4.0 29.2 - - + -
333A ALA* 4.2 4.7 - - + +
334A PHE* 4.1 19.3 - - - +
337A ASN* 2.8 29.9 + - + +
338A ILE* 3.8 27.4 - - + -
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Residues in contact with GLU 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A ARG* 5.4 2.3 + - - +
70A ILE* 2.8 41.1 + - + +
71A ASN* 3.3 24.4 + - - +
73A VAL* 1.3 71.8 - - + +
75A ALA* 1.3 58.9 + - - +
76A GLY 3.2 1.0 + - - -
329A ARG* 3.6 27.2 - - - +
330A TYR* 5.4 0.2 - - - -
333A ALA* 3.7 22.2 - - + -
337A ASN* 3.5 11.1 + - - +
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Residues in contact with ALA 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A LEU* 3.4 40.9 - - + +
21A ARG* 3.7 29.9 + - + +
24A HIS* 3.7 11.4 + - - +
71A ASN 3.0 11.1 + - - +
72A ILE 3.4 11.0 - - - +
73A VAL 3.1 0.4 - - - -
74A GLU* 1.3 75.1 - - - +
76A GLY* 1.3 59.6 + - - +
77A ILE* 3.4 2.8 + - + -
337A ASN* 4.3 0.2 - - - -
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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
------------------------------------------------------------
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