Contacts of the helix formed by residues 32 - 58 (chain A) in PDB entry 1OPT
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 LEU 32 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A ALA 4.0 1.6 + - - -
31A ARG* 1.4 77.5 - - - +
33A LEU* 1.3 65.4 + - - +
35A PRO* 3.5 14.5 - - + +
36A LEU* 3.4 27.7 - - + +
94A TRP* 3.6 30.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 33 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A LEU* 1.3 74.1 - - - +
34A PRO* 1.4 67.1 - - + +
36A LEU* 3.3 11.7 + - + +
37A TYR* 2.9 37.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 34 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A ARG* 3.6 39.0 - - + +
32A LEU 4.1 0.4 - - - -
33A LEU* 1.4 94.7 - - + +
35A PRO* 1.4 57.5 - - + +
37A TYR* 3.5 12.0 - - + +
38A SER 3.2 21.0 + - - -
88A HIS* 3.2 30.7 - - + +
280A GLN* 5.6 5.8 - - + +
283A GLU* 5.9 2.5 - - + +
284A THR* 4.8 14.6 - - + +
287A MET* 5.8 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 35 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A ARG* 3.3 28.0 - - + +
32A LEU* 3.5 23.8 - - + +
34A PRO* 1.4 85.9 - - + +
36A LEU* 1.3 57.4 + - + -
38A SER* 3.5 8.8 - - - -
39A LEU 3.1 21.5 + - - -
88A HIS* 3.7 27.8 - - + +
89A TYR* 3.4 29.9 - - + +
94A TRP* 5.0 8.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 36 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A LEU* 3.4 23.3 - - + +
33A LEU* 3.3 13.3 + - + +
35A PRO* 1.3 73.8 - - + +
37A TYR* 1.3 64.3 + - - +
39A LEU* 3.3 10.8 + - + +
40A VAL* 3.1 29.6 + - - +
89A TYR* 5.1 11.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 37 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A LEU* 2.9 30.2 + - + +
34A PRO* 3.5 12.3 - - + +
36A LEU* 1.3 70.9 - - - +
38A SER* 1.3 60.9 + - - +
40A VAL* 3.5 12.5 - - + +
41A PHE* 3.2 61.1 + + - +
284A THR* 2.6 55.4 + - + +
287A MET* 4.3 19.3 - - + -
288A THR* 3.2 20.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 38 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A PRO 3.2 8.7 + - - -
35A PRO* 3.5 11.4 - - - -
36A LEU 3.5 0.4 - - - -
37A TYR* 1.3 76.2 - - - +
39A LEU* 1.3 55.4 + - - +
41A PHE* 3.4 7.5 + - - +
42A ILE* 2.9 34.8 + - - +
85A PHE* 2.7 49.3 + - - +
88A HIS* 3.8 23.1 - - - -
89A TYR* 4.4 2.2 - - - -
287A MET* 5.6 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 39 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A PRO 3.1 16.4 + - - +
36A LEU* 3.3 16.3 + - + +
38A SER* 1.3 70.8 - - - +
40A VAL* 1.3 63.1 + - + +
42A ILE* 3.4 12.4 + - + +
43A PHE* 3.1 59.3 + - + +
86A TRP* 5.0 2.7 - - + -
89A TYR* 3.7 45.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 40 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A LEU 3.1 16.2 + - - +
37A TYR* 3.5 23.1 - - + +
39A LEU* 1.3 79.5 - - + +
41A PHE* 1.3 63.7 + - + +
43A PHE* 5.3 2.0 - - - -
44A GLY* 3.0 28.3 + - - +
45A PHE* 5.6 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 41 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A TYR* 3.2 68.8 + + - +
38A SER* 3.4 5.6 + - - +
40A VAL* 1.3 79.7 - - + +
42A ILE* 1.3 64.1 + - - +
45A PHE* 3.2 66.6 + + + +
81A LEU* 4.5 0.3 - - - +
85A PHE* 3.7 27.8 - + + -
287A MET* 3.6 20.6 - - + -
288A THR* 4.5 10.8 - - + -
291A CYS* 5.5 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 42 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A SER* 2.9 31.0 + - - +
39A LEU* 3.4 14.3 + - + +
41A PHE* 1.3 75.3 - - - +
43A PHE* 1.3 75.7 + - + +
46A VAL* 3.4 29.4 + - + +
81A LEU* 4.0 18.1 - - + +
85A PHE* 3.8 33.1 - - + +
86A TRP* 3.7 52.3 - - + +
89A TYR* 4.6 5.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 43 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A LEU* 3.1 50.4 + - + +
40A VAL* 4.8 2.5 - - - +
42A ILE* 1.3 85.9 - - + +
44A GLY* 1.3 63.3 + - - +
46A VAL* 4.3 9.5 + - - +
47A GLY 4.8 2.9 + - - -
86A TRP* 4.7 12.6 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 44 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A VAL 3.0 22.1 + - - -
43A PHE* 1.3 73.9 - - - +
45A PHE* 1.3 64.4 + - - +
46A VAL 3.7 0.4 + - - -
47A GLY* 4.3 1.9 + - - -
48A ASN* 4.2 14.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 45 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A PHE* 3.2 67.2 + + + +
43A PHE 3.6 0.2 - - - -
44A GLY* 1.3 78.0 - - - +
46A VAL* 1.4 58.8 + - - +
47A GLY 3.4 0.3 + - - -
48A ASN* 3.4 5.2 + - + -
49A MET* 2.9 44.3 + - + +
81A LEU* 3.8 13.2 - - + -
85A PHE* 3.9 11.9 - + - -
290A CYS* 3.4 33.9 - - + -
291A CYS* 3.7 45.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 46 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A ILE* 3.4 21.3 + - + +
43A PHE* 4.7 5.8 - - - +
44A GLY 3.7 0.8 - - - -
45A PHE* 1.4 73.2 - - - +
47A GLY* 1.3 58.8 + - - +
49A MET* 4.2 2.6 - - - +
50A LEU* 3.1 37.1 + - + +
78A PHE* 4.6 9.2 - - + -
81A LEU* 3.8 24.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 47 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A PHE 4.8 3.4 + - - -
44A GLY 4.3 3.9 + - - -
45A PHE 3.5 0.6 - - - -
46A VAL* 1.3 77.4 - - - +
48A ASN* 1.3 61.3 + - - +
50A LEU* 5.0 1.1 - - - -
51A VAL* 3.3 33.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 48 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A GLY 4.2 11.5 + - - +
45A PHE* 3.4 9.2 + - + +
47A GLY* 1.3 70.0 - - - +
49A MET* 1.3 64.7 + - + +
51A VAL* 4.3 1.5 - - - -
52A ILE* 3.3 45.4 + - - +
291A CYS 4.9 2.3 - - - +
294A PRO* 3.3 31.4 - - - +
295A ILE* 4.5 19.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 49 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A PHE* 2.9 35.1 + - + +
48A ASN* 1.3 72.6 + - - +
50A LEU* 1.3 55.7 + - - +
53A LEU* 3.1 32.9 + - - +
74A ILE* 3.5 28.7 - - + +
77A LEU* 3.8 15.5 - - + -
78A PHE* 3.6 27.8 - - + -
81A LEU* 5.2 2.7 - - + -
290A CYS* 3.1 48.0 - - - +
294A PRO* 3.7 27.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 50 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A VAL* 3.1 25.0 + - + +
47A GLY* 4.4 2.0 - - - +
49A MET* 1.3 73.9 - - - +
51A VAL* 1.3 63.7 + - + +
53A LEU* 4.1 7.3 - - + +
54A ILE* 3.0 54.1 + - + +
78A PHE* 3.7 21.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 51 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A GLY* 3.3 22.4 + - - +
48A ASN* 4.4 2.5 - - - +
50A LEU* 1.3 77.9 - - + +
52A ILE* 1.3 66.3 + - + +
54A ILE* 3.8 8.7 - - + +
55A LEU* 3.3 34.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 52 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A ASN* 3.3 47.0 + - - +
49A MET 4.5 0.4 - - - +
51A VAL* 1.3 76.2 - - + +
53A LEU* 1.4 64.7 + - - +
55A LEU* 3.9 6.0 + - + +
56A ILE* 3.6 25.8 + - + +
70A LEU* 5.8 2.5 - - + -
74A ILE* 4.1 15.7 - - + -
294A PRO* 3.8 27.1 - - + +
295A ILE* 4.4 1.6 - - + +
297A TYR* 5.2 10.8 - - + -
298A ALA* 3.7 29.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 53 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A MET 3.1 20.1 + - - +
50A LEU* 4.2 8.3 - - + +
52A ILE* 1.4 75.0 - - - +
54A ILE* 1.3 65.0 + - + +
56A ILE* 3.4 11.3 - - - +
57A ASN* 3.1 34.2 + - + +
71A ASN* 3.2 47.3 - - - +
74A ILE* 3.8 27.6 - - + +
75A SER* 3.9 10.8 - - - +
78A PHE* 4.2 13.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 54 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A LEU* 3.0 44.6 + - + +
51A VAL* 3.8 11.2 - - + +
53A LEU* 1.3 79.1 - - + +
55A LEU* 1.3 64.5 + - + +
57A ASN* 4.6 4.5 - - + +
58A CYS* 3.1 44.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 55 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A VAL* 3.3 26.5 + - + +
52A ILE* 4.1 6.5 - - + +
54A ILE* 1.3 78.7 - - + +
56A ILE* 1.3 70.6 + - + +
58A CYS 4.2 8.0 + - - +
60A ARG* 4.0 18.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 56 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A ILE* 3.6 16.5 + - + +
53A LEU* 3.4 15.7 + - - +
55A LEU* 1.3 83.2 - - + +
57A ASN* 1.3 54.1 + - - +
60A ARG* 3.7 25.5 - - - +
66A ASP* 2.6 37.5 - - - +
67A ILE 4.5 11.2 - - - +
68A TYR* 5.1 1.8 - - + -
70A LEU* 3.9 17.0 - - + -
71A ASN* 3.4 37.9 - - + +
74A ILE* 5.5 0.7 - - + -
297A TYR* 3.8 30.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 57 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A LEU* 3.1 24.0 + - + +
54A ILE* 4.2 5.5 - - + +
55A LEU 3.5 0.2 - - - -
56A ILE* 1.3 78.6 - - - +
58A CYS* 1.3 59.5 + - + +
59A LYS 3.2 6.9 + - - -
66A ASP* 4.1 5.2 - - - +
68A TYR* 3.5 22.4 + - - -
71A ASN* 3.2 31.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 58 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A ILE* 3.1 35.3 + - + +
55A LEU 4.2 6.2 + - - +
56A ILE 3.8 0.8 - - - -
57A ASN* 1.3 71.9 - - - +
59A LYS* 1.3 89.0 + - - +
60A ARG 3.0 9.2 + - - -
61A LEU* 5.5 0.2 - - - +
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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