Contacts of the helix formed by residues 66 - 87 (chain B) in PDB entry 4X5O
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 66 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A VAL 4.1 0.4 - - - -
138A TYR* 3.7 13.4 - - - -
142A ASN* 6.1 0.7 - - - -
64B ASP* 4.1 0.8 - - - +
65B TYR* 1.3 74.1 - - - +
67B PRO* 1.3 66.8 - - - +
68B ARG* 3.9 8.3 + - - +
69B GLN* 2.6 61.1 + - - +
70B MET* 2.9 10.9 + - - +
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Residues in contact with PRO 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A GLU* 3.3 52.0 - - + +
91A VAL* 3.3 18.3 - - - +
92A ILE* 4.1 13.7 - - + -
138A TYR* 3.3 16.6 - - - +
147A ILE* 4.6 5.2 - - + -
66B SER* 1.3 86.0 - - - +
68B ARG* 1.3 58.3 + - - +
70B MET* 3.6 3.1 + - - +
71B ALA* 3.3 18.9 + - - +
406B THR* 3.8 14.3 - - + +
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Residues in contact with ARG 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B SER* 3.1 9.4 + - - +
67B PRO* 1.3 76.2 - - - +
69B GLN* 1.3 71.7 + - + +
71B ALA* 3.2 19.0 + - - +
72B VAL* 3.4 9.5 + - - +
394B GLU* 3.3 23.8 + - - +
398B GLU* 4.1 15.9 + - - +
402B GLU 5.7 0.2 + - - -
403B LYS* 5.5 3.6 - - - +
404B ILE* 3.8 48.7 + - + +
406B THR* 3.7 17.2 - - + +
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Residues in contact with GLN 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B ARG* 3.4 28.9 - - - +
64B ASP 4.0 8.5 + - - +
65B TYR* 3.5 20.7 - - + -
66B SER* 2.6 54.0 + - - +
68B ARG* 1.3 78.8 - - + +
70B MET* 1.3 55.5 + - - +
72B VAL* 3.4 8.3 + - - +
73B ARG* 3.0 26.8 + - - +
390B PHE* 6.1 0.2 - - - -
394B GLU* 5.1 9.4 - - - +
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Residues in contact with MET 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A VAL* 3.1 59.7 - - + +
93A ASP* 4.0 8.7 - - + -
65B TYR* 3.7 22.2 - - + +
66B SER 2.9 10.6 + - - +
67B PRO 3.7 4.7 - - - +
68B ARG 3.2 0.2 - - - -
69B GLN* 1.3 73.8 - - - +
71B ALA* 1.3 56.0 + - - +
73B ARG* 3.4 48.2 - - + +
74B GLU* 2.7 48.3 + - + +
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Residues in contact with ALA 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A VAL* 5.7 0.2 - - - +
67B PRO 3.3 10.2 + - - +
68B ARG* 3.2 13.1 + - - +
70B MET* 1.3 80.2 - - - +
72B VAL* 1.3 63.4 + - - +
74B GLU* 3.4 9.6 + - - +
75B LYS* 3.2 37.2 + - - +
404B ILE* 4.0 11.7 - - + -
405B ARG 3.6 23.8 - - - +
406B THR* 4.9 2.5 - - - +
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Residues in contact with VAL 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B ARG 3.4 8.2 + - - +
69B GLN* 3.4 10.1 + - - +
70B MET 3.3 0.4 - - - -
71B ALA* 1.3 78.4 - - - +
73B ARG* 1.3 59.8 + - - +
75B LYS* 3.3 8.1 + - - +
76B VAL* 2.9 35.5 + - + +
390B PHE* 3.3 32.5 - - + +
393B VAL* 3.9 15.2 - - + +
394B GLU* 3.7 30.3 - - + +
397B LEU* 3.9 21.5 - - + -
404B ILE* 4.7 4.7 - - + -
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Residues in contact with ARG 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A ASP* 3.0 26.7 + - - -
65B TYR* 3.9 20.7 - - + -
69B GLN 3.0 14.3 + - - +
70B MET* 3.4 44.7 - - + +
72B VAL* 1.3 77.1 - - - +
74B GLU* 1.3 58.6 + - + +
76B VAL* 3.7 0.7 - - - +
77B PHE* 2.9 51.7 + - + +
172B TYR* 2.5 37.9 + - - -
390B PHE* 3.6 31.4 - - + -
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Residues in contact with GLU 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A LYS* 3.4 28.3 + - - -
91A VAL* 3.7 24.9 - - - +
150A TYR* 4.0 9.1 + - - -
70B MET* 2.7 31.0 + - + +
71B ALA* 3.7 8.4 - - - +
73B ARG* 1.3 74.0 - - + +
75B LYS* 1.3 59.2 + - + +
77B PHE* 3.7 3.6 - - - +
78B ASP* 2.8 33.9 + - - +
408B GLU* 4.5 3.6 - - - +
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Residues in contact with LYS 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71B ALA* 3.2 32.5 + - - +
72B VAL* 3.8 4.7 - - - +
74B GLU* 1.3 79.7 - - + +
76B VAL* 1.3 62.7 + - + +
78B ASP* 3.7 6.4 - - - +
79B VAL* 3.4 27.2 + - - +
393B VAL* 5.8 4.7 - - + -
397B LEU* 5.1 17.4 - - + +
404B ILE* 5.1 6.7 - - - +
405B ARG* 4.8 7.5 + - - +
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Residues in contact with VAL 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B VAL* 2.9 24.0 + - + +
75B LYS* 1.3 75.0 - - + +
77B PHE* 1.3 67.6 + - - +
79B VAL* 3.1 6.6 + - - +
80B ILE* 3.0 27.0 + - + +
202B LEU* 4.1 19.2 - - + +
386B VAL* 3.6 30.7 - - + -
389B ILE* 4.3 6.3 - - + -
390B PHE* 3.6 22.0 - - + -
393B VAL* 3.8 32.5 - - + -
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Residues in contact with PHE 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B ARG* 2.9 54.0 + - + +
74B GLU* 4.0 4.0 - - - +
76B VAL* 1.3 74.5 - - - +
78B ASP* 1.3 52.8 + - - +
80B ILE* 3.5 5.6 - - + +
81B ILE* 2.7 46.1 + - + +
152B ILE* 3.5 48.9 - - + -
172B TYR* 3.8 23.3 - + - -
173B GLN 5.7 0.2 - - - -
174B CYS* 4.7 4.5 - - + -
386B VAL* 3.6 31.6 - - + -
390B PHE* 3.8 11.4 - + - -
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Residues in contact with ASP 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B GLU 2.8 19.5 + - - +
75B LYS* 3.7 9.4 - - - +
76B VAL 3.2 0.2 - - - -
77B PHE* 1.3 76.7 - - - +
79B VAL* 1.3 57.8 + - - +
81B ILE* 3.9 5.1 - - - +
82B ARG* 2.9 60.5 + - - +
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Residues in contact with VAL 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B LYS 3.4 13.9 + - - +
76B VAL 3.1 8.5 + - - +
78B ASP* 1.3 76.9 - - - +
80B ILE* 1.3 65.5 + - - +
82B ARG* 4.0 19.4 - - - +
83B CYS* 3.4 20.0 + - + +
86B ARG* 5.8 0.2 + - - -
198B ILE* 4.2 7.6 - - + +
201B SER* 3.7 39.5 - - - +
202B LEU* 3.8 26.7 - - + +
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Residues in contact with ILE 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76B VAL* 3.0 24.1 + - + +
77B PHE* 3.5 15.3 - - + +
79B VAL* 1.3 76.6 - - - +
81B ILE* 1.3 62.3 + - - +
83B CYS* 3.2 6.1 + - - +
84B PHE* 3.1 40.0 + - + -
152B ILE* 4.5 4.0 - - + -
174B CYS* 3.5 27.6 - - - -
198B ILE* 3.5 30.7 - - + +
202B LEU* 4.7 7.2 - - + -
384B ILE* 3.9 26.5 - - + -
386B VAL* 4.8 5.2 - - + -
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Residues in contact with ILE 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A GLU* 5.9 0.7 - - - +
77B PHE* 2.7 29.4 + - + +
78B ASP* 4.0 4.9 - - - +
80B ILE* 1.3 72.8 - - - +
82B ARG* 1.3 66.6 + - - +
83B CYS 3.1 0.2 + - - -
84B PHE* 3.1 8.4 + - - +
85B LYS* 3.0 45.8 + - + +
150B TYR* 4.3 23.3 - - + +
152B ILE* 3.8 25.4 - - + -
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Residues in contact with ARG 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437A LYS* 6.1 3.1 - - - +
78B ASP* 2.9 51.5 + - - +
79B VAL* 4.0 17.8 - - - +
81B ILE* 1.3 79.0 - - - +
83B CYS* 1.3 59.8 + - - +
85B LYS* 4.2 6.1 - - - +
86B ARG* 3.5 40.2 + - - +
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Residues in contact with CYS 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79B VAL* 3.4 7.2 + - + +
80B ILE 3.2 8.9 + - - +
81B ILE 3.1 0.6 - - - -
82B ARG* 1.3 79.0 - - - +
84B PHE* 1.3 64.3 + - - +
85B LYS 3.2 0.4 - - - -
86B ARG* 3.1 28.4 + - - +
87B HIS* 3.2 22.6 - - - -
194B ILE* 3.6 20.4 - - - -
197B GLU* 3.7 28.0 - - + -
198B ILE* 3.6 30.1 - - + -
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Residues in contact with PHE 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80B ILE* 3.1 35.8 + - + -
81B ILE* 3.1 8.8 + - - +
83B CYS* 1.3 78.1 - - - +
85B LYS* 1.3 61.6 + - - +
87B HIS* 3.3 13.3 + - - +
88B GLY 3.6 0.2 + - - -
89B ALA* 3.6 20.5 + - - +
150B TYR* 3.4 46.9 - + + -
152B ILE* 5.4 0.4 - - + -
174B CYS* 4.0 19.3 - - - -
175B ASP 4.4 2.7 - - - -
176B PHE* 3.4 38.5 - + + -
194B ILE* 3.6 26.2 - - + -
198B ILE* 3.8 11.2 - - + -
382B LEU* 4.6 4.7 - - + -
384B ILE* 4.5 6.7 - - + -
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Residues in contact with LYS 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A GLU* 2.9 33.5 + - - -
408A GLU* 3.2 51.5 + - + +
409A THR 4.9 0.3 + - - -
437A LYS* 4.0 15.1 - - + +
81B ILE* 3.0 30.9 + - + +
82B ARG* 4.4 6.1 - - - +
84B PHE* 1.3 71.8 - - - +
86B ARG* 1.3 58.6 + - - +
87B HIS 3.0 5.6 - - - -
88B GLY* 2.8 20.8 + - - +
89B ALA 4.5 8.1 - - - +
91B VAL* 6.4 0.4 - - - -
150B TYR* 3.8 26.9 - - + +
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Residues in contact with ARG 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432A TRP* 3.4 26.1 + - + +
435A GLY* 3.7 22.1 + - - -
436A ILE 3.4 21.5 - - - +
437A LYS* 3.2 13.2 - - + +
438A ALA 3.2 25.8 + - - +
79B VAL 5.8 0.2 + - - -
82B ARG* 3.5 41.6 + - - +
83B CYS* 3.1 39.0 + - - +
85B LYS* 1.3 78.5 - - - +
87B HIS* 1.3 56.1 + - + +
88B GLY 3.3 0.9 - - - -
197B GLU* 3.1 33.8 + - - +
201B SER* 5.7 3.4 + - - -
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Residues in contact with HIS 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432A TRP* 3.2 37.8 - + - -
438A ALA 4.0 10.3 - - - +
439A GLU* 4.4 1.0 - - - +
83B CYS* 3.2 24.5 - - - +
84B PHE 3.3 8.2 + - - +
85B LYS 3.0 1.2 - - - -
86B ARG* 1.3 80.1 - - + +
88B GLY* 1.3 62.2 + - - +
89B ALA 3.6 1.3 - - - -
148B LYS* 3.0 24.6 + - - +
176B PHE* 4.6 4.0 - - + -
190B GLU* 3.0 25.3 + - + +
193B LYS* 4.3 4.0 - - + -
194B ILE* 3.4 38.5 - - + +
197B GLU* 2.6 32.2 + - - -
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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