Contacts of the helix formed by residues 60 - 79 (chain A) in PDB entry 1O4X
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 60 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59A LEU* 1.3 81.0 - - - +
61A PHE* 1.3 63.2 + - - +
62A LYS* 3.4 11.3 + - - +
63A ASN* 3.0 24.8 + - - +
64A MET* 3.0 22.3 + - - +
323D T 3.7 10.1 + - - -
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Residues in contact with PHE 61 (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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7A PRO* 5.4 8.3 - - + -
8A SER 3.2 27.4 - - - -
9A ASP* 4.1 14.1 - - - -
10A LEU* 4.1 19.7 - - + -
13A LEU* 4.0 21.1 - - + -
60A SER* 1.3 74.3 - - - +
62A LYS* 1.3 67.9 + - - +
64A MET* 4.4 4.5 - - - -
65A ALA* 3.0 34.4 + - + +
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Residues in contact with LYS 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A SER* 3.6 7.6 - - - +
61A PHE* 1.3 87.6 - - - +
63A ASN* 1.3 61.4 + - - +
65A ALA* 3.4 6.3 + - - +
66A LYS* 3.3 18.4 + - - +
322D T 3.1 46.5 + - - -
323D T 2.9 25.4 - - - +
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Residues in contact with ASN 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A LEU* 3.4 40.1 - - + +
60A SER* 3.0 20.1 + - - +
62A LYS* 1.3 74.8 - - - +
64A MET* 1.3 66.5 + - - +
66A LYS* 3.1 9.6 + - - +
67A LEU* 3.0 25.0 + - - +
323D T 3.3 32.2 - - - +
324D A 2.7 32.6 + - - -
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Residues in contact with MET 64 (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 LEU* 3.3 25.4 - - + +
17A ALA* 5.0 3.1 - - + -
54A PHE* 3.3 71.0 - - + +
57A LEU* 3.7 30.1 - - + -
59A LEU* 3.9 24.2 - - + +
60A SER 3.0 21.1 + - - +
61A PHE* 3.8 3.8 - - - +
63A ASN* 1.3 76.0 - - - +
65A ALA* 1.3 57.2 + - - +
67A LEU* 3.4 0.8 + - - -
68A LYS* 2.9 32.2 + - - +
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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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7A PRO* 5.6 8.5 - - + -
8A SER 5.8 0.7 - - - +
13A LEU* 4.1 6.3 - - - +
61A PHE* 3.0 34.8 + - + +
62A LYS* 3.5 8.5 - - - +
63A ASN 3.1 0.2 - - - -
64A MET* 1.3 75.4 - - - +
66A LYS* 1.3 59.1 + - - +
68A LYS* 4.2 2.6 - - - +
69A PRO* 2.9 27.7 - - - +
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Residues in contact with LYS 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 LYS 3.3 9.5 + - - +
63A ASN* 3.1 17.1 + - - +
65A ALA* 1.3 78.6 - - - +
67A LEU* 1.3 55.1 + - + +
69A PRO* 3.2 9.3 - - - +
70A LEU* 2.6 37.4 - - + +
323D T 4.5 19.4 + - - +
324D A 4.7 14.9 + - - +
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Residues in contact with LEU 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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46A PHE* 3.4 41.3 - - + -
50A THR* 4.0 15.0 - - + -
54A PHE* 3.8 24.7 - - + -
59A LEU* 3.9 15.9 - - + -
63A ASN* 3.0 37.2 + - - +
66A LYS* 1.3 78.1 - - + +
68A LYS* 1.3 64.7 + - - +
69A PRO 3.3 0.2 - - - -
70A LEU* 3.1 8.5 + - + +
71A LEU* 2.9 31.2 + - + +
324D A 3.4 13.5 - - - +
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Residues in contact with LYS 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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8A SER* 4.0 17.7 - - - +
12A GLU 5.1 0.4 - - - -
13A LEU* 2.9 32.3 - - + -
16A PHE* 3.7 44.7 - - + -
54A PHE* 3.9 11.6 - - + -
64A MET 2.9 18.9 + - - +
65A ALA* 4.2 2.2 - - - +
67A LEU* 1.3 72.1 - - - +
69A PRO* 1.3 67.5 - - + +
71A LEU* 3.2 1.4 + - - +
72A GLU* 2.8 47.3 + - - +
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Residues in contact with PRO 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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65A ALA 2.9 22.7 - - - +
66A LYS* 3.2 10.5 - - - +
68A LYS* 1.3 96.3 - - + +
70A LEU* 1.3 70.5 + - + +
72A GLU* 3.3 23.9 + - + +
73A LYS* 3.5 13.0 + - - +
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Residues in contact with LEU 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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38A MET* 3.4 25.3 - - + +
42A TYR* 5.4 0.3 - - - +
44A ASN* 4.9 12.6 - - - +
46A PHE* 4.7 17.5 - - + -
66A LYS* 2.6 40.6 - - + +
67A LEU* 3.1 8.5 + - + +
69A PRO* 1.3 86.4 - - + +
71A LEU* 1.3 62.9 + - + +
73A LYS* 3.2 30.6 + - + +
74A TRP 3.7 0.7 + - - -
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Residues in contact with LEU 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A PHE* 4.2 6.7 - - + -
20A PHE* 3.9 33.7 - - + -
34A VAL* 4.6 0.7 - - + -
38A MET* 4.0 29.8 - - + -
46A PHE* 5.2 4.5 - - + -
51A ILE* 4.2 19.1 - - + -
54A PHE* 3.6 46.2 - - + -
67A LEU* 2.9 22.8 + - + +
68A LYS 3.9 3.1 - - - +
70A LEU* 1.3 74.4 - - + +
72A GLU* 1.3 64.6 + - - +
73A LYS 3.2 0.2 - - - -
74A TRP* 3.2 5.7 + - - +
75A LEU* 3.0 22.5 + - - +
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Residues in contact with GLU 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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16A PHE* 3.9 27.3 - - + -
68A LYS* 2.8 35.6 + - - +
69A PRO* 3.4 13.9 - - - +
70A LEU 3.1 0.4 - - - -
71A LEU* 1.3 76.4 - - - +
73A LYS* 1.3 65.5 + - + +
75A LEU* 3.7 4.0 - - + +
76A ASN* 3.0 46.5 + - - +
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Residues in contact with LYS 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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42A TYR* 3.0 42.9 + - + +
69A PRO 3.5 12.1 + - - +
70A LEU* 3.2 22.1 + - + +
72A GLU* 1.3 77.6 - - - +
74A TRP* 1.3 64.7 + - - +
76A ASN* 3.5 7.3 + - - +
77A ASP* 3.1 16.3 + - - +
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Residues in contact with TRP 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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20A PHE* 3.4 30.3 - + + -
23A ARG* 5.1 0.2 - - + -
24A ARG* 4.0 24.7 - - + -
27A LEU* 4.8 2.5 - - + -
29A PHE* 3.8 25.4 - + - -
34A VAL* 3.6 31.1 - - + +
37A ALA* 3.7 29.2 - - + +
38A MET* 3.3 29.8 - - - -
41A LEU* 4.8 6.5 - - + +
42A TYR* 3.5 16.6 - + + -
70A LEU 3.7 0.6 + - - -
71A LEU* 3.2 9.0 + - - +
72A GLU 3.2 0.2 - - - -
73A LYS* 1.3 82.3 - - - +
75A LEU* 1.3 85.6 + - + +
77A ASP* 3.4 1.3 + - + +
78A ALA* 2.8 52.3 + - + +
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Residues in contact with LEU 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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16A PHE* 4.1 22.2 - - + -
19A THR* 4.2 22.2 - - + -
20A PHE* 4.2 17.0 - - + -
23A ARG* 3.4 39.5 - - + -
71A LEU 3.0 15.3 + - - +
72A GLU* 3.7 8.1 - - + +
73A LYS 3.3 0.2 - - - -
74A TRP* 1.3 92.7 - - + +
76A ASN* 1.3 60.7 + - - +
78A ALA* 3.3 2.9 + - - +
79A GLU* 2.6 40.1 - - - +
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Residues in contact with ASN 76 (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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72A GLU* 3.0 33.9 + - - +
73A LYS* 3.8 7.4 - - - +
75A LEU* 1.3 80.1 - - - +
77A ASP* 1.3 59.9 + - - +
79A GLU* 3.0 30.1 + - - +
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Residues in contact with ASP 77 (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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41A LEU* 5.2 9.2 - - + +
42A TYR* 2.9 32.7 + - + +
73A LYS 3.1 4.0 + - - +
74A TRP 3.8 0.4 - - - +
76A ASN* 1.3 74.4 - - - +
78A ALA* 1.3 63.4 + - - +
79A GLU 2.9 12.3 + - - -
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Residues in contact with ALA 78 (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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23A ARG* 5.4 0.4 + - + -
27A LEU* 3.3 32.8 - - + +
29A PHE* 5.3 3.1 - - + -
74A TRP* 2.8 47.0 + - + +
75A LEU 3.3 5.6 + - - +
77A ASP* 1.3 73.4 - - - +
79A GLU* 1.3 61.5 + - + +
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Residues in contact with GLU 79 (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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23A ARG* 2.5 61.9 + - + +
27A LEU* 3.8 1.2 - - - -
75A LEU* 2.6 36.6 - - + +
76A ASN* 3.0 15.3 - - - +
77A ASP 2.9 8.0 - - - -
78A ALA* 1.3 87.5 - - - +
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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