Contacts of the helix formed by residues 80 - 99 (chain B) in PDB entry 3SE4
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 GLN 80 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22B GLN 5.6 1.8 + - - -
23B MET* 6.2 1.6 - - - +
25B ARG* 5.2 6.2 - - - +
79B TRP* 1.3 73.6 - - - +
81B MET* 1.3 66.7 + - - +
82B THR* 3.1 23.4 + - - +
83B LEU* 2.6 37.8 + - + +
84B LEU* 3.4 15.6 + - - +
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Residues in contact with MET 81 (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 SER* 3.5 43.3 - - - +
79B TRP 3.3 3.4 + - - -
80B GLN* 1.3 71.8 - - - +
82B THR* 1.3 66.4 + - - +
84B LEU* 3.1 14.1 + - + -
85B ASP* 3.0 43.0 + - - +
88B HIS* 6.2 0.4 - - - -
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Residues in contact with THR 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A GLN* 6.1 1.6 - - + -
80B GLN* 3.1 24.8 + - - +
81B MET* 1.3 75.2 - - - +
83B LEU* 1.3 69.0 + - + +
85B ASP* 3.1 17.0 + - - +
86B GLN* 3.2 38.3 + - - +
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Residues in contact with LEU 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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19B LEU* 3.4 29.5 - - + +
22B GLN* 4.2 28.0 - - + +
23B MET* 3.6 31.0 - - + +
80B GLN* 2.6 47.5 + - + +
81B MET 3.4 0.2 - - - -
82B THR* 1.3 82.9 - - + +
84B LEU* 1.3 65.4 + - - +
86B GLN* 4.0 8.7 - - - +
87B LEU* 3.1 22.9 + - - +
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Residues in contact with LEU 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B MET* 3.8 21.1 - - + -
70B PHE* 3.8 18.8 - - + +
75B SER* 3.6 24.5 - - - +
76B SER* 3.6 35.2 - - - +
79B TRP* 3.9 22.2 - - + +
80B GLN 3.4 3.6 + - - +
81B MET* 3.1 24.2 + - + +
83B LEU* 1.3 79.3 - - - +
85B ASP* 1.3 58.4 + - - +
87B LEU* 2.9 7.9 + - + +
88B HIS* 2.7 43.7 + - + +
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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
----------------------------------------------------------
236A HIS* 2.8 42.4 + - + +
238A PHE* 3.4 18.1 - - + -
81B MET* 3.0 35.1 + - - +
82B THR* 3.1 8.9 + - - +
84B LEU* 1.3 76.9 - - - +
86B GLN* 1.3 60.3 + - + +
88B HIS* 4.3 2.1 + - - -
89B THR* 2.8 29.1 + - - -
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Residues in contact with GLN 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A GLN* 4.4 19.6 - - + +
273A LYS* 5.2 19.2 - - + +
19B LEU* 3.4 27.8 - - + +
82B THR* 3.2 37.3 + - - +
83B LEU* 4.5 7.7 - - - +
84B LEU 3.2 0.4 - - - -
85B ASP* 1.3 75.9 - - + +
87B LEU* 1.3 67.8 + - - +
89B THR* 3.8 7.8 - - + +
90B GLY* 3.0 20.6 + - - -
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Residues in contact with LEU 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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16B THR* 3.9 22.7 + - + +
19B LEU* 3.3 20.3 - - + +
20B LEU* 3.9 32.3 - - + -
23B MET* 4.7 3.8 - - - -
66B ILE* 5.3 1.6 - - + -
70B PHE* 3.8 39.5 - - + -
83B LEU 3.1 20.2 + - - +
84B LEU* 2.9 9.6 + - + +
86B GLN* 1.3 78.0 - - - +
88B HIS* 1.3 61.1 + - + +
90B GLY 3.4 1.2 + - - -
91B LEU* 3.0 43.7 + - + +
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Residues in contact with HIS 88 (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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238A PHE* 3.6 25.1 - - + -
67B PHE* 3.4 38.7 - + + -
70B PHE* 2.8 41.9 + - + +
71B HIS* 3.5 25.8 + + - -
76B SER* 5.9 2.0 - - - -
81B MET* 6.3 0.2 - - - -
84B LEU* 2.7 37.7 + - + +
85B ASP* 3.6 2.0 + - - +
87B LEU* 1.3 84.3 - - + +
89B THR* 1.3 62.8 + - - +
91B LEU* 4.7 0.2 - - + -
92B HIS* 3.1 25.1 + - - +
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Residues in contact with THR 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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236A HIS* 4.7 4.2 + - - -
237A ALA* 5.3 0.7 + - - +
238A PHE* 3.3 24.4 + - - -
273A LYS 5.3 1.5 + - - +
274A GLY* 4.0 25.9 - - - -
275A ILE* 4.1 28.2 + - + +
85B ASP 2.8 17.4 + - - -
86B GLN* 3.2 8.9 + - - +
88B HIS* 1.3 74.3 - - - +
90B GLY* 1.3 61.9 + - - +
92B HIS* 3.8 3.1 - - - +
93B GLN* 3.2 28.2 + - + +
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Residues in contact with GLY 90 (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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12B LEU* 5.1 5.8 - - - +
15B ASN* 6.5 0.9 - - - -
16B THR* 4.4 4.0 - - - -
86B GLN 3.0 14.2 + - - -
87B LEU 3.8 2.2 - - - -
89B THR* 1.3 78.2 - - - +
91B LEU* 1.3 60.2 + - - +
93B GLN* 4.1 13.1 - - - +
94B GLN* 2.9 38.0 + - - +
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Residues in contact with LEU 91 (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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16B THR* 4.1 20.4 - - + +
63B LEU* 3.4 41.2 - - + +
66B ILE* 3.9 15.0 - - + -
67B PHE* 3.7 48.5 - - + +
87B LEU* 3.0 39.3 + - + +
88B HIS* 4.0 0.4 - - + +
90B GLY* 1.3 76.9 - - - +
92B HIS* 1.3 60.5 + - - +
93B GLN 3.4 0.2 - - - -
94B GLN* 3.5 3.2 + - - +
95B LEU* 2.9 36.7 + - - +
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Residues in contact with HIS 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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157A TYR* 3.7 10.1 + + - -
237A ALA* 3.9 11.9 - - + +
238A PHE* 2.8 44.2 + - + +
240A LYS* 6.0 0.9 - - + -
241A ARG* 3.0 36.3 + - + +
67B PHE* 4.8 6.4 - - + -
88B HIS 3.1 17.8 + - - +
89B THR 3.8 3.8 - - - +
91B LEU* 1.3 76.5 - - - +
93B GLN* 1.3 53.9 + - - +
95B LEU* 3.6 5.6 - - - +
96B GLN* 2.7 62.5 + - - +
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Residues in contact with GLN 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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275A ILE* 3.8 27.6 - - + +
298A ASP* 4.3 12.1 + - - -
12B LEU* 2.9 38.2 - - + +
89B THR* 3.2 17.0 + - - +
90B GLY* 4.5 6.5 - - - +
92B HIS* 1.3 76.7 - - - +
94B GLN* 1.3 64.7 + - - +
96B GLN* 4.0 11.4 - - - +
97B HIS* 3.2 30.2 + - + +
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Residues in contact with GLN 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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9B HIS* 3.6 20.0 + - - +
12B LEU* 3.0 35.6 + - + -
13B SER* 3.6 26.1 + - - +
16B THR* 2.9 28.5 + - - -
59B LEU* 5.8 0.5 - - - +
63B LEU* 3.6 30.5 - - + +
90B GLY 2.9 17.9 + - - +
91B LEU* 3.5 6.4 + - - +
92B HIS 3.3 0.4 - - - -
93B GLN* 1.3 76.5 - - - +
95B LEU* 1.3 66.2 + - - +
97B HIS* 3.6 5.7 - - - -
98B LEU* 3.1 25.2 + - - +
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Residues in contact with LEU 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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241A ARG* 4.0 22.7 - - - +
60B HIS* 3.1 30.9 + - + +
63B LEU* 3.3 33.7 - - + -
64B GLN* 3.6 29.6 - - + +
67B PHE* 4.7 13.2 - - + -
91B LEU 2.9 24.4 + - - +
92B HIS* 3.6 3.8 - - - +
94B GLN* 1.3 78.2 - - - +
96B GLN* 1.3 54.5 + - - +
98B LEU* 3.1 3.6 + - - +
99B GLU* 2.7 46.4 + - - +
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Residues in contact with GLN 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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157A TYR* 3.1 32.8 + - - +
92B HIS* 2.7 43.9 + - + +
93B GLN* 4.0 12.2 - - - +
94B GLN 3.3 0.2 - - - -
95B LEU* 1.3 75.1 - - - +
97B HIS* 1.3 51.0 + - + +
99B GLU* 3.1 14.1 - - + +
100B THR* 2.7 30.1 + - - -
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Residues in contact with HIS 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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3B CYS* 4.1 4.2 - - - -
5B LEU* 4.7 8.2 - - + +
6B PRO* 3.8 25.7 - - + +
9B HIS* 2.6 32.9 + + - -
12B LEU* 3.4 22.7 - - + -
93B GLN* 3.2 22.0 + - + +
94B GLN 3.6 5.1 + - - -
96B GLN* 1.3 77.0 - - + +
98B LEU* 1.3 71.3 + - - +
100B THR* 3.1 19.4 - - - +
101B CYS* 4.1 8.8 - - - -
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Residues in contact with LEU 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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9B HIS* 5.3 7.2 - - + +
56B MET* 3.5 45.4 - - + +
59B LEU* 4.1 17.7 - - + -
60B HIS* 3.3 47.3 - - + +
63B LEU* 4.4 12.1 - - + -
94B GLN 3.1 20.9 + - - +
95B LEU* 3.1 1.5 + - + +
97B HIS* 1.3 79.6 - - + +
99B GLU* 1.3 58.6 + - - +
100B THR 2.9 3.1 - - - -
101B CYS* 2.8 32.2 + - - +
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Residues in contact with GLU 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A THR* 4.6 10.7 + - - -
157A TYR* 4.2 7.7 + - - +
180A LEU* 5.4 7.5 - - + +
241A ARG* 2.9 35.9 + - - -
60B HIS* 3.3 37.8 + - + -
95B LEU* 2.7 19.9 + - - +
96B GLN* 3.1 25.3 + - + +
98B LEU* 1.3 68.6 - - - +
100B THR* 1.3 56.5 + - - +
101B CYS* 2.8 13.2 + - - -
102B LEU* 3.4 27.0 + - + +
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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