Contacts of the helix formed by residues 72 - 87 (chain H) in PDB entry 3X0X
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 ASP 72 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70H GLY 3.7 3.2 + - - -
71H ALA* 1.3 73.0 - - - +
73H TRP* 1.3 65.1 + - - +
74H PRO* 3.4 20.2 - - - +
75H THR* 2.6 34.0 + - - -
76H ALA* 2.9 16.6 + - - +
324H GLN* 3.8 19.0 - - + +
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Residues in contact with TRP 73 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61H LEU* 3.6 37.9 - - + -
71H ALA 4.0 0.4 + - - -
72H ASP* 1.3 69.4 - - - +
74H PRO* 1.4 60.7 - - + +
76H ALA* 3.3 8.5 + - + +
77H ILE* 2.9 41.7 + - + +
98H LEU 5.1 0.2 - - - -
102H PRO* 3.8 13.2 - - + -
253H ILE* 3.5 35.0 - - + -
257H ILE* 4.2 10.5 - - + -
320H ALA* 4.4 8.7 - - - +
323H LEU* 3.7 25.8 - - + -
324H GLN* 2.7 40.5 + - + +
327H TRP* 3.2 61.0 - + + +
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Residues in contact with PRO 74 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72H ASP* 3.4 21.1 - - - +
73H TRP* 1.4 90.5 - - + +
75H THR* 1.3 54.0 + - - +
77H ILE* 2.7 24.2 + - + +
78H GLU* 2.8 25.0 + - - +
317H ARG 6.0 0.2 - - - +
320H ALA* 4.2 26.4 - - + +
321H HIS* 4.0 30.5 - - + +
324H GLN* 3.9 10.3 - - + +
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Residues in contact with THR 75 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20H PRO* 3.6 30.3 - - + -
21H VAL* 5.1 7.5 - - + +
71H ALA* 4.3 11.9 - - + -
72H ASP* 2.6 33.9 + - - -
74H PRO* 1.3 73.8 - - - +
76H ALA* 1.3 61.7 + - - +
77H ILE 3.2 0.5 + - - -
78H GLU* 3.3 9.2 + - - +
79H VAL* 3.2 21.7 + - + +
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Residues in contact with ALA 76 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60H LEU* 3.8 21.1 - - + +
61H LEU* 3.6 32.1 - - + -
71H ALA* 4.7 1.3 - - + -
72H ASP 2.9 13.6 + - - +
73H TRP* 3.4 13.9 - - + +
75H THR* 1.3 76.9 - - - +
77H ILE* 1.3 64.1 + - + +
79H VAL* 3.4 6.2 - - - +
80H VAL* 3.2 25.1 + - - +
98H LEU* 4.8 3.8 - - + +
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Residues in contact with ILE 77 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73H TRP* 2.9 28.3 + - + +
74H PRO* 2.7 12.3 + - + +
76H ALA* 1.3 78.0 - - + +
78H GLU* 1.3 69.2 + - - +
79H VAL 3.1 1.6 - - - -
80H VAL* 3.0 18.4 + - + +
81H ARG* 3.0 16.2 + - - +
256H LEU* 3.7 34.8 - - + -
257H ILE* 4.5 22.7 - - + -
260H ASN* 3.3 37.0 - - + +
316H ALA 6.1 0.7 - - - +
317H ARG* 6.5 0.4 - - + -
320H ALA* 4.6 10.3 - - + -
323H LEU* 5.1 1.8 - - + -
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Residues in contact with GLU 78 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21H VAL* 4.6 20.8 - - + +
74H PRO* 2.8 23.3 + - - +
75H THR* 3.8 9.9 - - - +
77H ILE* 1.3 75.7 - - - +
79H VAL* 1.3 55.7 + - - +
81H ARG* 3.2 32.0 + - - +
82H GLU* 3.0 32.2 + - - +
317H ARG* 4.3 25.6 + - - +
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Residues in contact with VAL 79 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20H PRO* 3.4 42.4 - - + +
21H VAL* 4.0 6.3 - - + +
24H ALA* 4.1 12.3 - - + +
57H LEU* 4.4 8.5 - - + -
60H LEU* 4.0 13.9 - - + -
75H THR 3.2 12.5 + - - +
76H ALA 3.4 8.7 - - - +
77H ILE 3.1 0.2 - - - -
78H GLU* 1.3 73.9 - - - +
80H VAL* 1.3 63.7 + - - +
81H ARG 3.1 4.6 + - - -
82H GLU* 3.5 1.7 + - - +
83H ILE* 3.1 42.0 + - + +
94H PHE* 3.9 15.0 - - + -
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Residues in contact with VAL 80 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76H ALA 3.2 17.0 - - - +
77H ILE* 3.0 15.3 + - + +
79H VAL* 1.3 75.4 - - - +
81H ARG* 1.3 58.1 + - - +
83H ILE* 4.0 7.7 - - - +
84H ALA* 3.1 24.9 + - - +
91H GLY* 4.1 12.7 - - - +
94H PHE* 4.6 7.6 - - + -
95H GLY* 4.3 12.1 - - - +
98H LEU* 4.2 20.6 - - + -
257H ILE* 4.8 13.2 - - + +
260H ASN* 4.5 4.8 - - + +
261H VAL* 3.7 28.7 - - + +
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Residues in contact with ARG 81 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77H ILE* 3.0 10.0 + - - +
78H GLU* 3.2 34.9 + - - +
80H VAL* 1.3 75.5 - - - +
82H GLU* 1.3 68.7 + - - +
84H ALA* 3.0 3.1 + - - +
85H ALA* 2.9 26.1 + - - +
260H ASN* 3.3 48.9 + - + +
263H LEU* 3.8 12.6 - - - +
264H GLY* 3.8 8.2 - - - +
267H HIS* 3.9 12.2 + - - -
313H ASP* 2.8 50.6 + - - +
316H ALA* 4.1 5.1 - - - +
317H ARG* 3.7 17.8 - - - +
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Residues in contact with GLU 82 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21H VAL* 4.3 10.3 - - + +
24H ALA* 3.9 13.2 - - + +
25H ARG* 3.8 53.9 + - + +
28H ALA* 4.7 7.7 - - + +
78H GLU 3.0 10.9 + - - +
79H VAL* 3.5 9.4 - - - +
81H ARG* 1.3 79.7 - - - +
83H ILE* 1.3 64.5 + - - +
85H ALA* 3.2 14.6 + - - +
86H ALA* 3.3 12.5 + - - +
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Residues in contact with ILE 83 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24H ALA* 4.2 19.7 - - + +
27H LEU* 5.8 0.9 - - + -
28H ALA* 6.2 0.9 - - - +
31H TRP* 5.0 14.5 - - + -
52H LEU* 4.5 17.7 - - + -
57H LEU* 4.6 1.6 - - + -
79H VAL* 3.1 24.8 + - + +
80H VAL* 4.2 4.3 - - - +
82H GLU* 1.3 78.8 - - - +
84H ALA* 1.3 59.4 + - - +
85H ALA 3.2 0.3 + - - -
86H ALA* 3.2 6.9 + - - +
87H ASP* 2.9 28.1 + - - +
90H LEU* 3.9 36.6 - - + +
91H GLY* 4.1 4.9 - - - -
94H PHE* 3.6 36.1 - - + -
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Residues in contact with ALA 84 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80H VAL 3.1 19.6 + - - +
81H ARG 3.0 4.9 + - - +
83H ILE* 1.3 76.2 - - - +
85H ALA* 1.3 62.8 + - - +
87H ASP 3.3 23.1 + - - -
88H GLY* 3.7 4.7 + - - -
91H GLY* 4.0 7.6 - - - -
261H VAL* 3.5 43.3 - - + +
264H GLY* 3.9 3.1 - - - -
265H ILE* 3.7 11.5 + - + +
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Residues in contact with ALA 85 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32H ARG* 4.7 7.9 - - - +
81H ARG 2.9 11.7 + - - +
82H GLU* 3.4 15.0 - - - +
84H ALA* 1.3 80.5 - - - +
86H ALA* 1.3 60.1 + - - +
87H ASP* 4.6 0.3 - - - -
264H GLY* 3.2 23.5 - - - +
265H ILE* 5.2 0.2 - - - -
267H HIS* 4.8 5.6 - - + -
268H GLY* 3.6 24.9 - - - +
381H PHE* 4.4 10.4 - - - -
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Residues in contact with ALA 86 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27H LEU 5.2 0.2 - - - +
28H ALA* 4.0 23.8 - - + +
31H TRP* 4.4 9.8 - - + +
32H ARG* 3.5 34.6 - - + +
35H ALA* 3.9 22.3 - - - +
82H GLU 3.3 7.5 + - - +
83H ILE* 3.2 8.6 + - - +
85H ALA* 1.3 80.4 - - - +
87H ASP* 1.3 62.9 + - + +
380H ARG* 5.5 2.6 + - - -
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Residues in contact with ASP 87 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31H TRP* 5.9 3.4 - - + -
35H ALA* 4.8 5.5 - - - +
38H ARG* 3.2 32.2 + - - +
39H ASP* 5.1 6.4 + - - +
83H ILE 2.9 16.7 + - - +
84H ALA* 3.3 7.5 - - - -
85H ALA 3.3 2.2 - - - -
86H ALA* 1.3 82.0 - - + +
88H GLY* 1.3 62.5 + - - +
89H SER* 3.1 10.3 + - - -
90H LEU* 3.0 43.4 + - + +
91H GLY 3.2 15.4 + - - -
212H GLN* 5.0 2.4 + - - -
380H ARG* 6.3 0.4 - - - +
384H ASN* 5.8 0.7 - - - -
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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