Contacts of the helix formed by residues 54 - 72 (chain A) in PDB entry 1F9O
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 SER 54 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53A THR* 1.3 71.0 - - - +
55A GLU* 1.3 68.8 + - - +
57A MET* 3.0 4.3 + - - +
58A SER* 3.0 23.4 + - - -
88A LEU* 3.6 12.1 - - - +
152A MET* 3.9 33.1 - - - +
153A HIS 4.0 7.4 - - - -
154A TRP* 2.9 12.9 + - - +
228A ALA* 3.6 19.1 - - - +
231A ALA* 3.3 20.5 - - - +
232A ASP* 4.7 1.3 - - - -
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Residues in contact with GLU 55 (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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36A HIS* 4.5 1.9 + - - -
53A THR* 3.6 15.4 + - - +
54A SER* 1.3 82.1 + - - +
56A ALA* 1.3 59.0 + - - +
58A SER* 2.6 23.4 + - - -
59A TYR* 3.2 26.5 + - + -
230A ASP* 4.9 7.5 - - - +
231A ALA* 3.5 10.3 - - + +
234A ARG* 4.0 13.2 - - - +
417A TRP* 3.5 19.2 - - + -
611A TRP* 3.6 15.3 - - + -
3C BGC 2.6 46.7 + - - -
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Residues in contact with ALA 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A PRO* 4.4 4.9 - - + +
35A TYR 4.9 4.3 - - - +
36A HIS* 5.4 4.0 - - - +
52A THR* 3.2 26.5 - - - +
53A THR* 3.2 13.6 + - - +
54A SER 3.1 0.8 - - - -
55A GLU* 1.3 78.9 - - - +
57A MET* 1.3 59.0 + - - +
59A TYR* 3.0 8.2 + - - +
60A TYR* 2.9 23.6 + - - +
610A PHE* 3.5 26.8 - - + -
611A TRP* 5.4 3.6 - - + -
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Residues in contact with MET 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A ILE* 4.3 12.6 - - - -
34A PRO* 3.5 26.2 - - - -
52A THR* 5.1 1.6 - - + -
53A THR 3.4 4.2 + - - +
54A SER 3.0 6.7 + - - +
56A ALA* 1.3 76.4 - - - +
58A SER* 1.3 57.1 + - - +
60A TYR* 2.9 27.5 + - + +
61A MET* 2.9 33.2 + - + +
80A SER 3.9 3.8 - - - +
83A VAL* 3.8 22.7 - - + -
84A THR* 3.2 28.9 - - - +
88A LEU* 3.1 36.6 - - + -
152A MET* 4.3 6.1 - - + -
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Residues in contact with SER 58 (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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54A SER 3.0 9.1 + - - -
55A GLU* 2.6 23.9 + - - -
57A MET* 1.3 76.6 - - - +
59A TYR* 1.3 58.8 + - - +
61A MET* 3.4 15.3 + - - +
62A TRP* 3.2 21.1 + - - +
152A MET* 5.0 1.9 - - - +
231A ALA 3.5 23.6 - - - -
234A ARG* 3.0 33.9 + - - -
235A ALA* 4.1 7.0 - - - -
238A ALA* 4.5 4.5 - - - +
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Residues in contact with TYR 59 (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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55A GLU* 3.2 23.8 - - + +
56A ALA 3.0 9.9 + - - +
58A SER* 1.3 79.9 + - - +
60A TYR* 1.3 64.9 + - - +
62A TRP* 3.7 25.7 - + + +
63A LEU* 3.2 23.2 + - - +
234A ARG* 3.5 33.2 + - - +
417A TRP* 3.0 23.8 + + - -
610A PHE* 4.3 6.7 - - + -
611A TRP* 3.7 37.2 - + + -
614A SER* 3.9 22.7 - - - -
615A GLU* 2.6 43.3 + - + -
618A VAL* 5.7 0.7 - - + -
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Residues in contact with TYR 60 (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 LYS* 4.5 7.5 + - + -
28A PHE* 3.7 29.7 - + - -
32A GLY 3.9 20.2 + - - -
34A PRO* 3.9 9.0 - - + -
56A ALA 2.9 11.0 + - - +
57A MET* 2.9 35.9 + - + +
59A TYR* 1.3 79.8 - - - +
61A MET* 1.3 59.6 + - - +
63A LEU* 3.4 6.5 + - + +
64A GLU* 3.1 48.7 + - + +
76A GLY 4.4 4.0 + - - -
79A LYS* 4.8 13.2 + - - +
80A SER* 3.9 26.6 + - - -
83A VAL* 4.9 4.0 - - + +
610A PHE* 3.9 16.1 - + + -
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Residues in contact with MET 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A MET 2.9 15.7 + - - +
58A SER* 3.6 11.4 - - - +
60A TYR* 1.3 78.7 - - - +
62A TRP* 1.3 56.6 + - - +
64A GLU 3.5 0.6 + - - +
65A ALA* 3.0 23.2 + - - +
77A PHE* 3.2 25.5 - - + -
80A SER* 3.3 24.9 - - - +
81A TRP* 3.4 50.3 - - + +
84A THR* 3.5 26.2 - - + +
152A MET* 4.9 4.0 - - + -
235A ALA* 3.5 33.2 - - + +
238A ALA* 4.3 5.8 - - + -
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Residues in contact with TRP 62 (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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58A SER 3.2 12.5 + - - +
59A TYR* 3.7 40.6 - + - +
61A MET* 1.3 76.4 - - - +
63A LEU* 1.3 66.1 + - - +
65A ALA* 3.3 6.4 + - + +
66A MET* 3.1 24.8 + - + +
234A ARG* 4.3 18.8 - - + -
237A GLN* 3.9 11.0 - - - -
238A ALA* 3.8 24.1 - - + +
241A TRP* 4.8 10.8 - + + -
245A TRP* 5.3 8.4 - + - -
420A GLN* 3.7 23.1 - - + -
424A GLU* 3.7 21.7 + - - -
503A ASN* 4.0 13.7 - - - -
615A GLU* 3.9 10.1 - - - -
618A VAL* 3.7 33.6 - - + +
622A VAL* 5.8 1.3 - - + -
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Residues in contact with LEU 63 (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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13A PHE* 3.7 9.0 - - + -
17A TYR* 3.9 26.7 - - + -
20A ILE* 3.8 39.7 - - + -
21A LYS* 4.4 7.4 - - + -
59A TYR 3.2 16.0 + - - +
60A TYR* 3.5 7.6 - - + +
62A TRP* 1.3 80.0 - - - +
64A GLU* 1.3 60.5 + - - +
66A MET* 3.2 6.6 + - - +
67A HIS* 3.0 25.3 + - - +
610A PHE* 4.8 6.3 - - + -
614A SER* 4.2 15.9 - - - +
617A ALA* 3.8 29.4 - - + -
618A VAL* 4.2 7.8 - - + +
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Residues in contact with GLU 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A TYR* 2.7 24.8 + - - -
21A LYS* 2.7 33.8 + - - +
60A TYR* 3.1 35.7 + - + +
61A MET 3.9 3.1 - - - +
62A TRP 3.3 0.2 - - - -
63A LEU* 1.3 78.0 - - + +
65A ALA* 1.3 60.6 + - - +
67A HIS* 3.3 10.2 + - - +
68A GLY* 2.9 23.7 + - - -
73A ASP 4.8 1.4 - - - +
76A GLY* 3.4 29.9 - - - +
77A PHE* 3.5 27.5 + - + +
80A SER* 4.2 1.8 - - - -
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Residues in contact with ALA 65 (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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61A MET 3.0 18.1 + - - +
62A TRP* 3.5 8.7 - - + +
63A LEU 3.2 0.2 - - - -
64A GLU* 1.3 75.8 - - - +
66A MET* 1.3 62.7 + - - +
68A GLY* 3.2 2.6 + - - -
69A ARG 3.1 17.2 + - - -
74A PHE* 4.1 4.6 - - - -
77A PHE* 3.8 8.2 - - + -
238A ALA 3.9 10.3 - - - +
242A ALA* 3.7 31.2 - - + -
245A TRP* 3.3 19.4 - - + -
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Residues in contact with MET 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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13A PHE* 3.2 30.5 - - + -
62A TRP* 3.1 15.1 + - - +
63A LEU* 3.4 10.1 - - - +
65A ALA* 1.3 76.4 - - - +
67A HIS* 1.3 61.5 + - - +
69A ARG* 3.4 9.8 + - - +
70A PHE* 3.4 30.9 + - + -
245A TRP* 3.8 30.0 - - + -
618A VAL* 3.4 39.9 - - + +
621A GLY* 3.7 14.6 - - - +
622A VAL* 3.8 16.6 - - + +
625A ILE* 4.4 7.2 - - + -
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Residues in contact with HIS 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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13A PHE* 3.6 11.6 - - - -
14A GLU* 6.1 2.6 - - + +
17A TYR* 3.2 63.6 + + + -
63A LEU 3.0 8.1 + - - +
64A GLU* 3.4 13.2 - - - +
65A ALA 3.2 0.2 - - - -
66A MET* 1.3 76.0 - - - +
68A GLY* 1.3 65.8 + - - +
70A PHE* 3.2 3.7 + - - +
71A SER* 2.9 53.7 + - - -
73A ASP* 4.0 19.8 + - + +
76A GLY* 5.9 2.5 - - - -
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Residues in contact with GLY 68 (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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64A GLU 2.9 12.9 + - - -
65A ALA 3.2 2.6 + - - -
67A HIS* 1.3 76.2 - - - +
69A ARG* 1.3 58.0 + - - +
71A SER* 4.2 0.2 - - - -
72A GLY* 2.7 31.4 + - - -
73A ASP 3.2 22.2 - - - -
74A PHE* 3.4 25.6 - - - -
249A GLN* 3.6 0.9 + - - -
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Residues in contact with ARG 69 (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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2A SER* 3.6 29.0 + - - -
3A SER* 2.8 36.2 + - - -
4A PRO 4.8 0.4 + - - -
5A ALA* 4.1 9.5 - - - +
65A ALA 3.1 4.9 + - - -
66A MET* 3.4 11.4 - - - +
67A HIS 3.2 0.2 - - - -
68A GLY* 1.3 77.2 - - - +
70A PHE* 1.3 80.6 + - + +
74A PHE* 3.7 1.0 - - - -
245A TRP* 3.6 47.1 - - + -
248A GLU* 4.4 2.6 + - - -
249A GLN* 3.2 17.2 + - - +
625A ILE* 3.7 39.4 - - + +
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Residues in contact with PHE 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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5A ALA* 4.0 12.1 - - + -
10A GLN* 3.7 51.4 + - + +
13A PHE* 3.7 25.1 - + + -
14A GLU* 4.5 10.0 - - + +
66A MET* 3.4 35.4 + - + +
67A HIS* 3.2 6.6 + - - +
69A ARG* 1.3 103.7 - - + +
71A SER* 1.3 59.1 + - - +
72A GLY 3.7 0.2 - - - -
249A GLN* 5.7 0.2 - - - -
621A GLY* 3.9 28.0 - - - -
624A ALA* 4.3 6.7 - - + -
625A ILE* 4.1 9.6 - - + -
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Residues in contact with SER 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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67A HIS* 2.9 42.9 + - - -
70A PHE* 1.3 78.4 - - - +
72A GLY* 1.3 61.6 + - - +
73A ASP* 3.0 26.2 + - - +
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Residues in contact with GLY 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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68A GLY 2.7 12.5 + - - -
70A PHE 3.7 0.8 - - - -
71A SER* 1.3 77.0 - - - +
73A ASP* 1.3 58.2 + - - +
74A PHE* 4.0 4.6 - - - -
249A GLN* 3.2 24.9 + - - -
251A LYS* 3.0 41.4 + - - +
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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