Contacts of the helix formed by residues 77 - 98 (chain B) in PDB entry 3SE3
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 77 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B MET* 5.4 2.7 + - - +
76B TRP* 1.3 76.5 - - - +
78B GLU* 1.3 63.4 + - - +
79B THR* 3.1 15.9 + - - -
80B LEU* 2.9 47.6 + - + +
81B LEU* 2.8 27.5 + - - +
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Residues in contact with GLU 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B SER* 6.1 1.6 - - - +
76B TRP 3.2 5.4 + - - -
77B ASP* 1.3 74.9 + - - +
79B THR* 1.3 69.3 + - - +
81B LEU* 3.8 5.7 - - - +
82B ASP* 2.9 39.6 + - - +
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Residues in contact with THR 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A GLN* 5.5 12.1 - - + -
77B ASP* 3.1 13.1 + - - -
78B GLU* 1.3 87.4 - - - +
80B LEU* 1.3 62.3 + - + +
82B ASP* 3.5 6.1 - - + +
83B LYS* 3.0 27.3 + - + +
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Residues in contact with LEU 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B LEU* 3.8 19.8 - - + +
20B GLN* 3.3 39.5 - - + +
21B MET* 3.6 44.2 - - + +
77B ASP* 2.9 31.9 + - + +
79B THR* 1.3 77.7 - - + +
81B LEU* 1.3 71.2 + - - +
83B LYS* 3.0 5.3 + - + +
84B PHE* 2.9 19.4 + - - +
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Residues in contact with LEU 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B MET* 3.5 21.4 - - + +
67B PHE* 5.5 0.7 - - + +
72B SER* 6.0 1.1 - - - +
73B SER* 6.3 2.5 - - - -
76B TRP* 4.8 7.9 - - + +
77B ASP 2.8 21.1 + - - +
78B GLU* 3.8 7.2 - - - +
80B LEU* 1.3 69.7 - - - +
82B ASP* 1.3 67.7 + - - +
84B PHE* 2.7 21.3 + - - +
85B TYR* 3.0 31.8 + - + +
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Residues in contact with ASP 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A HIS* 2.9 36.6 + - + +
238A PHE* 3.3 18.8 - - + -
78B GLU* 2.9 25.9 + - - +
79B THR* 3.5 7.9 - - + +
81B LEU* 1.3 76.7 - - - +
83B LYS* 1.3 66.8 + - - +
84B PHE 2.6 2.1 + - - -
85B TYR* 2.9 22.0 + - - +
86B THR* 3.1 14.8 + - - +
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Residues in contact with LYS 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A GLN* 6.4 2.0 - - + -
273A LYS 5.4 9.0 - - - +
17B LEU* 3.3 32.0 - - + +
79B THR* 3.0 18.1 + - + +
80B LEU* 3.0 2.2 + - + +
82B ASP* 1.3 75.1 - - - +
84B PHE* 1.3 61.1 + - - +
86B THR* 3.4 10.8 - - - +
87B GLU* 3.2 21.7 + - - +
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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
----------------------------------------------------------
14B THR* 3.6 30.5 - - + -
17B LEU* 3.3 16.7 - - + +
18B LEU* 3.7 34.1 - - + -
21B MET* 4.4 12.6 - - + -
63B ILE* 3.8 19.5 - - + -
67B PHE* 4.1 21.1 - + + -
80B LEU 2.9 10.8 + - - +
81B LEU* 2.7 15.5 + - - +
82B ASP 2.6 0.6 + - - -
83B LYS* 1.3 75.0 - - - +
85B TYR* 1.3 80.1 - + - -
86B THR 3.1 1.1 - - - -
87B GLU* 3.2 3.5 + - + +
88B LEU* 3.1 48.6 + - + +
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Residues in contact with TYR 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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238A PHE* 3.4 39.7 - + + -
64B PHE* 3.6 32.9 - + + -
67B PHE* 2.4 45.9 + - + -
68B SER* 3.7 19.0 - - - -
73B SER* 5.6 4.9 + - - -
81B LEU* 3.0 34.0 + - + +
82B ASP* 2.9 13.3 + - - -
84B PHE* 1.3 82.9 - + - +
86B THR* 1.3 52.1 + - - +
88B LEU 3.2 1.7 + - - -
89B TYR* 2.6 37.2 + - - +
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Residues in contact with THR 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A HIS* 5.4 3.1 + - - -
238A PHE* 3.3 26.6 - - + -
274A GLY* 3.9 12.1 - - - -
275A ILE* 3.7 44.8 + - + +
82B ASP* 3.1 7.0 + - - +
83B LYS* 3.4 13.7 - - - +
85B TYR* 1.3 78.5 - - - +
87B GLU* 1.3 67.5 + - - +
89B TYR* 3.6 4.3 - - - +
90B GLN* 3.2 24.8 + - - +
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Residues in contact with GLU 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B GLY* 4.1 16.5 - - - -
13B ARG* 4.5 19.3 - - - +
14B THR* 3.3 24.9 - - + +
17B LEU* 4.2 12.3 - - + -
83B LYS 3.2 13.4 + - - +
84B PHE* 3.2 8.0 + - - +
86B THR* 1.3 83.7 - - - +
88B LEU* 1.3 58.0 + - - +
90B GLN* 3.5 19.0 + - - +
91B GLN* 3.1 32.3 + - - +
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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
----------------------------------------------------------
14B THR* 5.0 5.4 - - + -
60B ILE* 3.7 23.8 - - + -
63B ILE* 3.7 19.1 - - + -
64B PHE* 4.0 26.2 - - + +
84B PHE* 3.1 47.0 + - + +
85B TYR 3.7 5.4 - - - +
87B GLU* 1.3 73.7 - - + +
89B TYR* 1.3 60.4 + - - +
91B GLN* 3.4 25.4 - - - +
92B LEU* 2.8 35.8 + - + +
151B PHE* 4.9 9.0 - - + -
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Residues in contact with TYR 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A TYR* 3.6 21.3 + + - -
237A ALA* 4.1 18.0 + - + -
238A PHE* 3.5 42.8 - - + -
241A ARG* 3.6 30.7 - - + -
275A ILE* 5.2 11.9 - - + -
64B PHE* 4.6 10.5 - + + -
85B TYR 2.6 21.7 + - - +
86B THR* 3.3 5.8 + - + +
88B LEU* 1.3 75.0 - - - +
90B GLN* 1.3 66.2 + - - +
92B LEU* 3.0 10.2 + - + +
93B ASN* 3.2 43.4 + - - +
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Residues in contact with GLN 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275A ILE* 3.9 25.4 - - + +
298A ASP* 5.6 5.1 + - - +
86B THR* 3.2 9.7 + - - +
87B GLU* 3.7 24.5 + - - +
89B TYR* 1.3 81.9 - - - +
91B GLN* 1.3 62.7 + - + +
92B LEU 3.4 0.2 + - - -
93B ASN* 3.4 8.4 + - - +
94B ASP* 3.1 40.4 + - - +
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Residues in contact with GLN 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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10B GLY* 3.7 22.5 + - - -
11B SER* 4.4 1.1 - - - +
14B THR* 3.1 27.3 + - - -
60B ILE* 3.2 29.9 - - + +
87B GLU 3.1 21.9 + - - +
88B LEU* 3.1 19.6 + - - +
90B GLN* 1.3 78.5 - - + +
92B LEU* 1.3 63.9 + - - +
94B ASP* 3.3 11.2 + - - +
95B LEU* 3.2 27.5 + - + +
151B PHE* 4.0 12.9 - - - -
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Residues in contact with LEU 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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135A SER* 5.7 2.5 - - - -
241A ARG* 3.7 29.4 - - - +
57B TYR* 4.0 26.9 - - + +
60B ILE* 3.3 37.7 - - + -
61B SER* 4.2 24.7 - - - +
64B PHE* 4.9 14.1 - - + -
88B LEU* 2.8 22.3 + - + +
89B TYR* 3.6 6.1 - - + +
91B GLN* 1.3 72.2 - - - +
93B ASN* 1.3 55.1 + - - +
95B LEU* 3.1 7.9 + - + +
96B GLU* 2.6 37.6 + - - +
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Residues in contact with ASN 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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157A TYR* 3.6 11.2 + - - -
241A ARG* 3.2 10.4 + - - -
89B TYR* 3.2 51.0 + - - -
90B GLN* 3.8 9.3 - - - +
92B LEU* 1.3 74.6 - - - +
94B ASP* 1.3 66.0 + - - +
96B GLU* 3.4 11.0 - - - +
97B ALA* 2.9 25.5 + - - +
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Residues in contact with ASP 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 GLN* 3.1 30.4 + - - +
91B GLN* 3.5 12.2 - - - +
92B LEU 3.2 0.2 - - - -
93B ASN* 1.3 79.8 - - - +
95B LEU* 1.3 66.1 + - + +
97B ALA* 3.4 15.1 - - - +
98B CYS* 3.5 14.9 + - - -
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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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53B ILE* 5.3 15.2 - - + +
56B LEU* 4.2 21.5 - - + -
57B TYR* 3.8 43.9 - - + +
60B ILE* 4.4 16.2 - - + -
91B GLN* 3.3 15.0 - - + +
92B LEU* 3.1 10.2 + - + +
94B ASP* 1.3 81.7 - - + +
96B GLU* 1.3 67.2 + - - +
98B CYS* 3.1 21.1 + - + +
99B VAL* 4.8 0.7 - - - +
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Residues in contact with GLU 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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137A THR* 5.0 3.4 + - - +
155A ASN* 3.5 29.6 + - - +
157A TYR* 3.2 27.5 + - - -
180A LEU* 5.6 8.5 - - + -
241A ARG* 3.5 22.0 + - - -
57B TYR* 4.4 17.2 + - + +
92B LEU 2.6 19.4 + - - +
93B ASN* 3.4 12.4 + - - +
95B LEU* 1.3 77.0 - - - +
97B ALA* 1.3 65.8 + - - +
98B CYS 3.2 5.7 - - - +
99B VAL* 3.2 15.9 - - - +
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Residues in contact with ALA 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 ASN 2.9 15.3 + - - +
94B ASP* 3.4 9.4 - - - +
96B GLU* 1.3 76.9 + - - +
98B CYS* 1.3 69.8 + - - +
99B VAL* 2.9 14.0 + - - +
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Residues in contact with CYS 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 ASP 3.5 13.8 + - - +
95B LEU* 3.1 18.1 - - + +
96B GLU 3.5 0.8 - - - -
97B ALA* 1.3 76.5 - - - +
99B VAL* 1.3 70.2 + - - +
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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