Contacts of the helix formed by residues 56 - 76 (chain X) in PDB entry 5A0Q
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 ALA 56 (chain X).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6X ASN* 3.1 23.3 - - - +
27X PHE* 5.2 6.1 - - + -
38X PHE* 3.9 23.8 - - + -
40X LYS* 5.7 1.3 - - - +
54X GLY 3.6 0.2 + - - -
55X LEU* 1.3 72.0 - - - +
57X THR* 1.3 60.9 + - + +
59X VAL* 3.5 7.7 - - - +
60X GLN* 3.0 35.8 + - - +
123Y ALA* 3.7 23.6 - - + -
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Residues in contact with THR 57 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55X LEU* 3.7 12.4 - - + +
56X ALA* 1.3 78.5 - - + +
58X ASP* 1.3 71.2 + - - +
60X GLN* 3.8 3.1 - - - +
61X THR* 2.5 37.8 + - - -
89Y ALA* 5.2 5.4 - - - +
92Y LEU* 4.3 11.6 - - + +
121Y LEU* 3.4 42.2 - - + +
122Y ALA* 2.9 29.2 - - - +
123Y ALA* 4.7 3.4 - - + -
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Residues in contact with ASP 58 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55X LEU* 3.6 14.2 + - - +
57X THR* 1.3 85.8 + - - +
59X VAL* 1.3 59.8 + - - +
61X THR* 3.5 6.6 + - - -
62X VAL* 2.9 32.9 + - - +
102X TYR* 2.9 35.6 - - + +
103X TYR* 3.1 47.6 + - - +
104X THR* 3.7 8.0 - - + +
92Y LEU* 5.7 1.0 - - - +
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Residues in contact with VAL 59 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38X PHE* 4.6 7.6 - - + -
39X GLN 4.5 8.1 - - - +
40X LYS* 4.7 6.1 - - + +
42X PHE* 3.7 28.5 - - + -
52X LEU* 3.8 28.2 - - + +
53X ALA* 4.0 9.0 - - - -
54X GLY 4.1 1.6 - - - +
55X LEU 2.7 30.4 + - - +
56X ALA* 3.3 9.6 + - - +
58X ASP* 1.3 74.5 - - - +
60X GLN* 1.3 63.1 + - + +
62X VAL* 4.1 0.2 - - - -
63X ALA* 3.0 30.5 + - - +
104X THR* 3.5 18.2 - - - +
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Residues in contact with GLN 60 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38X PHE* 3.8 20.2 - - + -
42X PHE* 5.3 5.8 - - + -
56X ALA 3.0 17.7 + - - +
57X THR* 4.1 2.7 - - - +
59X VAL* 1.3 79.1 - - + +
61X THR* 1.4 61.1 + - - +
63X ALA* 3.8 5.0 - - - +
64X GLN* 2.9 32.8 + - + +
85Y ARG* 3.3 27.9 - - - +
122Y ALA 3.8 4.1 - - - +
123Y ALA* 3.5 8.5 - - - -
124Y LEU* 3.1 50.5 + - - +
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Residues in contact with THR 61 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57X THR* 2.5 30.8 + - - -
58X ASP* 3.4 10.9 + - - -
59X VAL 3.3 0.4 - - - -
60X GLN* 1.4 73.0 - - - +
62X VAL* 1.3 60.6 + - + +
64X GLN* 3.4 4.3 + - - +
65X ARG* 3.0 63.9 + - + +
102X TYR* 4.0 27.8 - - + -
85Y ARG* 4.8 0.2 - - - +
86Y ARG* 4.8 7.0 + - - +
89Y ALA* 4.1 17.3 - - + +
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Residues in contact with VAL 62 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52X LEU* 3.7 24.0 - - + -
58X ASP* 2.9 18.1 + - - +
61X THR* 1.3 77.9 - - + +
63X ALA* 1.3 58.4 + - - +
65X ARG* 4.5 4.5 - - + +
66X LEU* 2.9 29.6 + - + +
90X VAL* 4.3 15.7 - - + -
93X LEU* 4.2 13.5 - - + -
94X LEU* 3.6 35.0 - - + -
102X TYR* 4.7 11.9 - - + -
104X THR* 3.7 10.3 - - + -
106X PRO* 5.5 0.2 - - + -
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Residues in contact with ALA 63 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42X PHE* 3.8 38.6 - - + -
50X ILE* 6.2 1.3 - - - -
52X LEU* 4.5 6.4 - - + +
59X VAL 3.0 20.0 + - - +
60X GLN* 3.8 5.6 - - - +
61X THR 3.3 0.2 - - - -
62X VAL* 1.3 75.9 - - - +
64X GLN* 1.3 57.9 + - + +
66X LEU* 4.1 4.0 - - - +
67X LYS* 3.1 28.8 + - - +
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Residues in contact with GLN 64 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99Q LEU* 2.8 40.6 - - + +
102Q GLN* 2.6 43.9 - - - +
60X GLN* 2.9 24.5 + - - +
61X THR 3.7 3.6 - - - +
63X ALA* 1.3 75.6 - - + +
65X ARG* 1.3 66.9 + - + +
67X LYS* 3.5 4.8 + - - +
68X PHE* 3.2 16.1 + - - +
82Y ASN* 4.0 0.4 + - - -
85Y ARG* 1.9 39.2 - - - +
86Y ARG* 2.9 16.6 - - - +
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Residues in contact with ARG 65 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99Q LEU* 4.2 22.4 - - - +
61X THR* 3.0 44.5 + - + +
62X VAL* 4.2 2.0 - - - +
64X GLN* 1.3 79.0 - - - +
66X LEU* 1.4 57.1 + - - +
68X PHE* 3.4 8.6 - - + +
69X ARG* 3.1 31.6 + - + +
93X LEU* 4.0 27.4 - - + -
97X LYS* 5.7 4.2 - - - +
102X TYR* 4.5 18.9 + - + -
86Y ARG* 5.0 16.6 - - - +
89Y ALA* 5.5 5.5 - - - +
90Y ASP* 3.6 22.4 + - - +
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Residues in contact with LEU 66 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50X ILE* 3.6 28.5 - - + -
62X VAL* 2.9 20.2 + - + +
63X ALA* 4.2 3.8 - - - +
65X ARG* 1.4 75.0 - - - +
67X LYS* 1.3 60.4 + - - +
69X ARG* 3.3 2.9 + - + -
70X LEU* 2.9 36.4 + - + +
86X LEU* 3.8 26.9 - - + -
89X MET* 3.8 30.1 - - + -
90X VAL* 3.6 34.5 - - + +
93X LEU* 4.1 7.5 - - + +
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Residues in contact with LYS 67 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95Q GLN* 5.2 0.9 - - - +
98Q LEU* 5.7 8.1 - - + -
43X PRO 4.0 22.7 + - - +
63X ALA 3.1 17.8 + - - +
64X GLN* 4.1 4.3 - - - +
65X ARG 3.5 0.2 - - - -
66X LEU* 1.3 78.5 - - - +
68X PHE* 1.3 56.2 + - - +
70X LEU* 4.3 13.8 - - + +
71X ASN* 2.8 61.9 + - - +
74X GLU* 4.2 13.1 + - - -
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Residues in contact with PHE 68 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92Q LEU* 4.2 11.9 - - + -
95Q GLN* 3.3 48.7 - - + +
96Q ARG* 4.1 18.8 - - + -
99Q LEU* 4.2 22.0 - - + -
64X GLN 3.2 14.1 + - - +
65X ARG* 3.4 15.0 - - + +
67X LYS* 1.3 76.5 - - - +
69X ARG* 1.4 79.5 + - + +
70X LEU 3.2 0.2 + - - -
71X ASN* 3.2 4.2 + - - +
72X LEU* 3.1 51.6 + - + +
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Residues in contact with ARG 69 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99P VAL* 4.9 8.7 - - - +
100P TYR* 5.4 3.3 + - - -
65X ARG 3.1 17.0 + - - +
66X LEU* 3.9 4.3 - - - +
68X PHE* 1.4 92.1 - - + +
70X LEU* 1.3 61.0 + - - +
72X LEU* 3.7 12.1 + - + +
73X TYR* 3.6 17.7 + - - +
89X MET* 3.2 49.1 + - + +
92X ASN* 4.2 11.1 - - - +
93X LEU* 3.5 35.6 - - + +
96X GLU* 3.2 36.0 + - - -
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Residues in contact with LEU 70 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66X LEU* 2.9 23.3 + - + +
67X LYS* 3.9 17.3 - - + +
69X ARG* 1.3 75.4 - - - +
71X ASN* 1.3 58.7 + - - +
73X TYR* 3.3 9.1 + - + +
74X GLU* 2.9 50.8 + - + +
81X ILE* 3.7 44.2 - - + -
86X LEU* 3.8 26.2 - - + -
89X MET* 4.0 14.1 - - + -
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Residues in contact with ASN 71 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95Q GLN* 3.2 37.4 + - - +
98Q LEU* 4.8 7.5 - - - +
67X LYS* 2.8 50.5 + - - +
68X PHE 3.8 0.9 - - - +
70X LEU* 1.3 73.8 - - - +
72X LEU* 1.3 63.3 + - - +
74X GLU* 3.1 21.0 + - - +
75X LEU* 3.0 34.1 + - + +
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Residues in contact with LEU 72 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88Q ASN* 5.9 1.1 - - - +
91Q ARG* 3.9 32.1 - - + +
92Q LEU* 3.7 35.4 - - + +
95Q GLN* 4.0 13.7 - - + -
68X PHE* 3.1 34.5 + - + +
69X ARG* 3.9 11.9 - - + +
70X LEU 3.3 0.2 - - - -
71X ASN* 1.3 75.9 - - - +
73X TYR* 1.3 57.4 + - - +
75X LEU* 4.2 4.4 - - - +
76X LYS* 3.2 34.0 + - - +
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Residues in contact with TYR 73 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96P TYR* 2.4 35.6 + + - -
100P TYR* 4.0 33.4 - + + +
102P GLU* 3.5 3.8 + - - -
105P PRO* 3.9 2.9 - - - +
108P GLN* 4.5 3.8 - - - -
112P ARG* 4.6 6.7 - - - -
69X ARG 3.6 9.4 + - - +
70X LEU* 3.3 12.7 + - + +
71X ASN 3.2 0.2 - - - -
72X LEU* 1.3 77.1 - - - +
74X GLU* 1.3 60.2 + - + +
75X LEU 3.1 2.2 - - - -
76X LYS* 3.1 4.0 + - + -
77X GLU* 2.5 70.8 + - - +
79X ARG* 3.4 38.4 + - - -
81X ILE* 4.7 22.7 - - + -
85X THR* 5.4 0.4 - - + -
89X MET* 5.2 1.8 - - + -
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Residues in contact with GLU 74 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67Q LYS* 6.0 0.3 - - - +
67X LYS* 4.2 9.1 + - - -
70X LEU* 2.9 42.2 + - + +
71X ASN* 3.1 31.2 + - - +
73X TYR* 1.3 73.2 - - + +
75X LEU* 1.3 60.1 + - + +
77X GLU 2.9 22.8 - - - +
78X GLY* 3.9 8.2 - - - -
79X ARG 4.8 8.1 - - - +
80X GLN* 5.3 6.9 - - - +
81X ILE* 4.7 14.4 - - + +
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Residues in contact with LEU 75 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67Q LYS* 3.5 34.3 - - + +
68Q LEU 3.3 23.3 - - - +
69Q ASN* 4.0 13.9 - - - +
70Q GLU* 5.4 5.2 - - - +
91Q ARG* 3.2 49.2 + - + +
95Q GLN* 4.1 23.1 - - + +
71X ASN* 3.0 24.1 + - + +
72X LEU* 4.2 2.5 - - - +
74X GLU* 1.3 78.0 - - + +
76X LYS* 1.3 65.4 + - - +
77X GLU 3.2 3.3 + - - -
78X GLY* 4.7 1.0 + - - -
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Residues in contact with LYS 76 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108P GLN* 3.1 28.9 + - - +
111P GLN* 3.7 25.7 + - - +
112P ARG* 3.8 25.5 - - + +
88Q ASN* 3.9 23.3 + - - +
91Q ARG* 4.1 23.9 + - - +
72X LEU* 3.2 21.5 + - - +
73X TYR* 3.1 8.6 + - + +
75X LEU* 1.3 79.5 - - - +
77X GLU* 1.3 61.8 + - - +
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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
------------------------------------------------------------
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