Contacts of the helix formed by residues 80 - 100 (chain B) in PDB entry 3FIE
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 THR 80 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79B THR* 1.3 89.3 - - - +
81B ASP* 1.3 65.1 + - - +
82B ALA* 3.7 9.5 + - - +
83B GLU* 2.8 47.0 + - - +
84B LYS* 3.0 16.1 + - - +
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Residues in contact with ASP 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B TYR* 3.8 31.4 + - + -
11B ASN* 5.3 5.2 - - - +
79B THR 5.3 0.5 - - - +
80B THR* 1.3 74.2 - - - +
82B ALA* 1.3 56.4 + - - +
84B LYS* 3.4 17.6 + - - +
85B ASP* 2.9 29.8 + - - +
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Residues in contact with ALA 82 (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 THR* 3.7 10.0 + - - +
81B ASP* 1.3 79.1 - - - +
83B GLU* 1.3 62.4 + - + +
85B ASP* 3.3 7.5 + - - +
86B ARG* 3.2 28.9 + - - +
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Residues in contact with GLU 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B ASN 3.6 2.2 - - - +
77B TYR* 3.6 14.6 - - + -
78B LEU* 2.8 37.4 + - + +
79B THR* 3.2 8.1 + - - -
80B THR* 2.8 45.2 + - - +
82B ALA* 1.3 74.6 - - + +
84B LYS* 1.3 62.0 + - - +
86B ARG* 3.3 30.1 + - - +
87B TYR* 2.9 30.1 + - - +
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Residues in contact with LYS 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B TYR* 3.9 33.3 + - + +
47B PRO* 3.4 22.5 - - + +
48B GLU* 2.8 42.1 + - - +
78B LEU* 3.6 29.2 - - + +
79B THR* 4.1 17.2 + - - +
80B THR 3.0 14.5 + - - +
81B ASP* 3.7 14.3 + - - +
83B GLU* 1.3 77.2 - - - +
85B ASP* 1.3 57.7 + - - +
87B TYR* 4.0 0.5 - - - +
88B LEU* 2.9 31.5 + - - +
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Residues in contact with ASP 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B ASN* 3.4 2.5 - - - +
10B TYR* 2.7 38.2 + - + +
81B ASP 2.9 16.8 + - - +
82B ALA* 3.6 7.6 - - - +
83B GLU 3.2 0.4 - - - -
84B LYS* 1.3 78.3 - - - +
86B ARG* 1.3 61.8 + - - +
88B LEU* 3.8 2.2 - - - +
89B LYS* 2.9 60.4 + - - +
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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
----------------------------------------------------------
77B TYR* 4.8 9.3 - - - -
82B ALA* 3.2 17.2 + - - +
83B GLU* 3.3 35.5 + - - +
85B ASP* 1.3 77.3 - - + +
87B TYR* 1.3 55.1 + - - +
89B LYS* 3.2 2.8 + - - +
90B THR* 2.7 40.0 + - - +
198B GLU* 4.0 28.7 + - - -
379B ASN* 6.2 0.2 - - - -
381B LEU* 4.6 22.5 - - + +
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Residues in contact with TYR 87 (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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45B ILE* 3.7 18.4 - - + -
47B PRO* 3.5 31.0 - - + -
77B TYR* 3.9 17.7 - - + +
78B LEU* 3.6 17.0 - - + -
83B GLU 2.9 18.1 + - - +
84B LYS 4.0 1.3 - - - +
86B ARG* 1.3 76.9 - - - +
88B LEU* 1.3 60.6 + - - +
90B THR* 3.8 3.7 - - - -
91B THR* 3.0 45.7 + - - -
155B VAL* 3.7 12.8 - - - +
156B LEU 3.2 17.0 + - - -
157B GLY* 3.8 13.2 - - - -
195B PHE* 2.9 30.3 + + - +
197B PRO* 3.6 19.3 - - + -
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Residues in contact with LEU 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B PHE* 3.7 30.1 - - + +
9B ASN 4.2 0.2 - - - -
10B TYR* 3.9 24.0 - - + +
37B PHE* 3.9 29.4 - - + -
45B ILE* 3.7 35.7 - - + -
47B PRO* 4.6 5.8 - - + -
84B LYS 2.9 18.6 + - - +
85B ASP* 3.8 3.4 - - - +
87B TYR* 1.3 82.9 - - - +
89B LYS* 1.3 58.8 + - - +
91B THR* 3.3 1.9 + - - -
92B ILE* 2.9 46.0 + - + +
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Residues in contact with LYS 89 (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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8B PHE 3.3 22.0 - - - +
9B ASN* 2.9 33.9 - - - +
85B ASP* 2.9 49.0 + - - +
86B ARG* 3.9 2.2 - - - +
88B LEU* 1.3 75.3 - - + +
90B THR* 1.3 60.4 + - - +
92B ILE* 3.8 8.4 - - + +
93B LYS* 3.2 23.0 + - - +
381B LEU* 3.8 22.1 - - + +
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Residues in contact with THR 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B ARG* 2.7 27.7 + - - +
87B TYR* 3.8 6.1 - - - -
88B LEU 3.2 0.2 - - - -
89B LYS* 1.3 75.9 - - - +
91B THR* 1.3 63.5 + - - +
93B LYS* 3.4 3.9 + - - +
94B LEU* 3.1 30.7 + - + +
197B PRO* 4.1 20.0 - - + -
198B GLU* 6.0 1.3 - - - +
380B LEU* 3.6 38.5 - - + +
381B LEU* 3.6 20.6 - - - +
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Residues in contact with THR 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B ILE* 5.4 3.8 - - + -
45B ILE* 4.1 18.8 - - + -
87B TYR* 3.0 39.0 + - - -
88B LEU 3.8 4.0 - - - -
90B THR* 1.3 73.6 - - - +
92B ILE* 1.3 67.0 + - - +
94B LEU* 3.2 10.1 + - - +
95B PHE* 3.0 51.6 + - + -
155B VAL* 4.6 7.2 - - + -
195B PHE* 4.2 16.9 - - + -
197B PRO* 4.9 0.9 - - - +
225B LEU* 4.9 2.7 - - + -
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Residues in contact with ILE 92 (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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5B ILE* 4.0 3.6 - - + -
6B ASN 3.3 25.6 - - - +
7B SER* 4.3 6.1 - - - +
8B PHE* 4.1 15.7 - - + +
39B ILE* 3.3 36.1 - - + -
88B LEU* 2.9 30.2 + - + +
89B LYS* 3.8 9.6 - - + +
90B THR 3.3 0.2 - - - -
91B THR* 1.3 77.0 - - - +
93B LYS* 1.3 57.4 + - - +
95B PHE* 3.1 8.5 + - - +
96B LYS* 2.9 55.0 + - - +
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Residues in contact with LYS 93 (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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89B LYS 3.2 14.8 + - - +
90B THR* 3.6 7.0 - - + +
91B THR 3.3 0.2 - - - -
92B ILE* 1.3 81.0 - - - +
94B LEU* 1.3 56.6 + - + +
96B LYS* 3.3 13.2 + - + +
97B ARG* 2.9 26.5 + - - +
380B LEU* 2.6 33.0 + - + +
381B LEU* 3.5 25.8 + - + -
383B ASP* 3.0 19.7 + - - -
386B TYR* 2.9 34.4 + - + -
387B THR* 4.3 5.8 - - - +
388B VAL* 3.9 18.7 - - + +
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Residues in contact with LEU 94 (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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90B THR* 3.1 19.5 + - + +
91B THR 3.2 4.0 + - - +
93B LYS* 1.3 74.4 - - + +
95B PHE* 1.3 60.9 + - - +
97B ARG* 3.2 5.1 + - - +
98B ILE* 2.9 32.1 + - - +
195B PHE* 3.4 39.0 - - + -
197B PRO* 4.3 7.0 - - + -
221B PRO* 3.9 19.7 - - + +
222B ALA* 4.1 9.5 - - + +
225B LEU* 3.6 15.7 - - + -
380B LEU* 4.7 6.7 - - + -
386B TYR* 3.5 41.1 - - + +
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Residues in contact with PHE 95 (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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5B ILE* 4.3 7.9 - - + -
39B ILE* 3.8 30.5 - - + -
40B MET* 4.2 16.4 - - - -
43B VAL* 4.2 21.5 - - + -
91B THR* 3.0 43.9 + - + -
92B ILE 3.1 7.6 + - - +
94B LEU* 1.3 76.9 - - - +
96B LYS* 1.3 57.4 + - - +
98B ILE* 3.2 7.5 + - - +
99B ASN* 2.9 28.9 + - - +
108B LEU* 3.6 33.1 - - + +
111B ILE* 6.2 0.9 - - + -
153B LEU* 5.6 0.2 - - + -
155B VAL* 4.6 11.9 - - + -
225B LEU* 3.8 17.0 - - + -
229B LEU* 4.1 25.4 - - + -
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Residues in contact with LYS 96 (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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5B ILE* 4.0 24.0 - - + -
7B SER* 2.9 28.5 + - - -
92B ILE* 2.9 33.8 + - - +
93B LYS* 3.5 13.4 - - + +
95B PHE* 1.3 74.0 - - - +
97B ARG* 1.3 61.6 + - - +
99B ASN* 3.1 9.7 + - - +
100B SER* 2.8 24.9 + - - -
388B VAL* 3.5 24.1 - - + +
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Residues in contact with ARG 97 (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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93B LYS 2.9 13.6 + - - +
94B LEU* 3.5 12.1 - - - +
95B PHE 3.2 0.2 - - - -
96B LYS* 1.3 77.6 - - - +
98B ILE* 1.3 63.0 + - - +
100B SER* 2.7 22.3 + - - -
220B ASP* 3.1 20.8 + - - -
222B ALA* 3.9 9.3 - - + +
360B PHE* 3.2 39.9 + - + -
362B VAL* 3.5 19.0 - - - +
386B TYR* 3.0 28.5 + - + -
387B THR 3.5 11.7 - - - -
388B VAL* 3.0 40.9 + - - +
389B SER 3.2 19.8 + - - -
390B GLU* 3.4 15.2 + - - +
391B GLY* 3.2 11.3 - - - -
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Residues in contact with ILE 98 (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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94B LEU 2.9 14.4 + - - +
95B PHE* 3.5 9.2 - - - +
97B ARG* 1.3 75.8 - - - +
99B ASN* 1.3 61.9 + - - +
100B SER 3.3 0.9 + - - -
101B ASN 3.5 4.0 - - - +
104B GLY* 3.1 46.9 - - - +
107B LEU* 4.6 10.5 - - + -
108B LEU* 4.0 14.1 - - + -
222B ALA* 3.7 22.2 - - + +
225B LEU* 3.6 37.7 - - + -
226B ALA* 4.0 10.5 - - + +
229B LEU* 4.0 15.0 - - + -
356B LEU* 6.3 0.4 - - + -
360B PHE* 3.5 14.2 - - + -
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Residues in contact with ASN 99 (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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2B PRO* 5.0 2.0 - - - +
3B VAL* 3.2 36.6 + - - +
5B ILE* 3.8 13.3 - - + +
95B PHE 2.9 16.3 + - - +
96B LYS* 3.1 11.2 + - - +
98B ILE* 1.3 77.6 - - - +
100B SER* 1.3 56.8 + - - +
101B ASN 3.3 0.4 - - - -
105B GLU* 2.9 48.2 - - - +
108B LEU* 3.7 18.9 - - + +
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Residues in contact with SER 100 (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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276A ASN* 5.2 5.2 - - - +
96B LYS 2.8 11.0 + - - -
97B ARG* 2.7 20.8 + - - -
99B ASN* 1.3 77.8 - - - +
101B ASN* 1.3 57.6 + - - +
102B PRO* 4.2 4.2 - - - +
105B GLU* 4.4 3.9 - - - +
360B PHE* 4.2 4.9 - - - -
388B VAL* 3.5 26.6 + - - -
389B SER* 4.3 10.0 + - - -
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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