Contacts of the helix formed by residues 73 - 95 (chain B) in PDB entry 5EJC
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 73 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B PRO* 3.8 17.7 - - - +
70B HIS* 3.0 20.3 + - - +
72B GLU* 1.3 82.7 - - - +
74B HIS* 1.3 65.5 + - - +
75B ALA 3.2 0.9 - - - -
76B LYS* 2.9 17.6 + - - +
77B VAL* 2.8 29.1 + - - -
940D GLN* 5.1 11.5 + - - +
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Residues in contact with HIS 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B LEU* 4.0 14.4 - - + +
58B LEU* 4.1 11.1 - - + +
62B VAL* 4.1 5.4 - - + -
67B LEU* 3.7 36.0 - - + +
68B PRO* 2.8 38.0 + - + -
70B HIS 3.4 2.7 - - - -
71B HIS* 3.4 43.8 + - + +
72B GLU 3.3 0.6 - - - -
73B SER* 1.3 76.1 - - - +
75B ALA* 1.3 58.4 + - - +
77B VAL* 4.6 1.8 - - - -
78B MSE 2.9 36.3 + - + +
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Residues in contact with ALA 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B GLU 4.3 6.6 + - - +
73B SER 3.2 1.2 - - - -
74B HIS* 1.3 78.7 - - - +
76B LYS* 1.3 62.3 + - - +
78B MSE 3.5 5.1 + - - +
79B MSE 3.2 25.7 + - - +
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Residues in contact with LYS 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B GLU 4.8 2.4 + - - +
73B SER* 2.9 17.9 + - - +
75B ALA* 1.3 78.0 - - - +
77B VAL* 1.3 63.3 + - + +
79B MSE 3.2 21.1 - - - +
80B TYR* 3.6 32.9 + - + +
941C LEU* 4.2 9.3 - - - +
940D GLN* 2.8 48.8 + - + +
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Residues in contact with VAL 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B ILE 3.6 24.2 - - - +
67B LEU* 4.6 1.6 - - + -
68B PRO* 3.9 28.9 - - + -
73B SER* 2.8 23.5 + - - +
74B HIS 3.9 3.1 - - - +
76B LYS* 1.3 73.7 - - + +
78B MSE 1.3 58.7 + - - +
79B MSE 3.0 1.3 - - - -
80B TYR* 2.7 31.8 + - + +
81B ARG* 3.1 22.9 + - + +
939D GLY 4.7 2.9 - - - +
940D GLN* 4.4 23.6 - - + +
943D ALA* 4.2 11.0 - - + -
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Residues in contact with MSE 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B LYS* 4.3 13.0 - - - +
66B ILE* 4.2 13.7 - - - -
67B LEU* 3.7 21.5 - - + -
74B HIS* 2.9 21.1 + - + +
75B ALA* 3.9 6.1 - - - +
77B VAL* 1.3 76.3 - - - +
79B MSE 1.3 57.1 + - - +
81B ARG* 3.2 17.6 + - + +
82B LYS* 2.8 67.3 + - + +
147B ASP* 4.8 0.4 - - - +
149B VAL* 4.1 13.9 - - + -
150B ASP* 3.1 27.1 - - - +
153B TRP* 5.9 0.9 - - + -
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Residues in contact with MSE 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B ALA 3.2 13.6 + - - +
76B LYS* 3.2 17.3 - - - +
77B VAL 2.9 0.8 + - - -
78B MSE 1.3 77.6 - - - +
80B TYR* 1.3 64.7 + - + +
82B LYS* 3.2 18.5 + - + +
83B GLU* 3.0 39.7 + - + +
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Residues in contact with TYR 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B LYS* 3.7 37.4 - - + +
77B VAL* 2.7 15.0 + - - +
79B MSE 1.3 76.9 - - + +
81B ARG* 1.3 56.8 + - - +
83B GLU* 3.2 9.1 + - - -
84B GLN* 2.9 29.2 + - - +
941C LEU* 3.9 23.1 - - + +
945C GLU* 3.9 19.3 + - - -
940D GLN* 3.7 17.3 - - - -
943D ALA* 3.6 31.2 - - + +
944D ALA* 4.2 6.5 - - + -
947D ARG* 3.2 51.6 - - - +
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Residues in contact with ARG 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B GLY 3.6 7.9 + - - -
66B ILE* 2.6 51.9 + - - +
77B VAL* 3.1 23.7 + - + +
78B MSE 3.5 24.0 - - + +
80B TYR* 1.3 76.8 - - + +
82B LYS* 1.3 57.1 + - - +
84B GLN* 3.7 2.2 + - - +
85B TYR* 3.0 24.6 + - - +
149B VAL* 4.2 2.0 - - - +
153B TRP* 3.2 66.5 + - + +
942D GLN* 4.7 10.1 + - - +
943D ALA* 3.5 33.9 - - - +
946D SER* 3.8 16.6 + - - -
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Residues in contact with LYS 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B MSE 2.8 53.6 + - + +
79B MSE 3.2 20.5 - - + +
81B ARG* 1.3 74.1 - - - +
83B GLU* 1.3 65.8 + - + +
85B TYR* 3.2 8.3 + - - +
86B LEU* 3.0 33.5 + - + +
147B ASP* 5.2 4.3 - - - -
149B VAL* 4.4 20.2 - - + -
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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
----------------------------------------------------------
79B MSE 3.0 35.8 + - + +
80B TYR* 3.2 13.7 + - - +
82B LYS* 1.3 76.5 - - + +
84B GLN* 1.3 53.6 + - - +
86B LEU* 3.2 11.1 + - + +
87B ASP* 2.8 41.1 + - - +
948C TYR* 3.8 20.4 + - - +
952C LYS* 5.5 1.0 - - - -
947D ARG* 3.5 26.9 + - - -
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Residues in contact with GLN 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B TYR 2.9 16.9 + - - +
81B ARG* 3.7 7.2 + - - +
83B GLU* 1.3 77.5 - - - +
85B TYR* 1.3 62.5 + - - +
87B ASP* 3.7 8.6 + - - +
88B VAL* 3.1 30.0 + - - +
115B GLU* 3.6 25.4 + - - +
153B TRP* 3.4 25.1 - - + -
156B ARG* 5.4 1.6 - - - +
943D ALA 4.5 0.7 - - - +
946D SER* 3.2 48.1 + - - -
947D ARG* 3.7 11.3 + - + +
950D ALA* 3.3 21.0 - - + +
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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
----------------------------------------------------------
81B ARG 3.0 16.4 + - - +
82B LYS 3.2 9.4 + - - +
84B GLN* 1.3 74.9 - - - +
86B LEU* 1.3 73.7 + - + +
89B LEU* 3.0 53.7 + - + +
104B GLN* 3.3 25.8 + - - -
107B VAL* 5.2 0.7 - - - +
108B TYR* 4.0 3.2 - + - -
111B MSE 3.2 40.7 - - + +
148B SER* 3.6 31.8 - - - -
149B VAL* 3.9 30.5 - - + -
152B TYR* 4.0 16.8 - + + -
153B TRP* 4.7 3.6 - - - +
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Residues in contact with LEU 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B LYS* 3.0 26.1 + - + +
83B GLU* 3.7 10.1 - - + +
85B TYR* 1.3 89.7 - - + +
87B ASP* 1.3 59.5 + - - +
89B LEU* 3.8 8.4 - - + +
90B HIS* 2.8 38.4 + - - +
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Residues in contact with ASP 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B GLU* 2.8 29.1 + - - +
84B GLN* 3.7 8.2 - - - +
86B LEU* 1.3 74.8 - - - +
88B VAL* 1.3 64.5 + - + +
90B HIS* 3.6 5.9 - - - +
91B ALA* 3.0 23.4 + - - +
948C TYR* 2.6 35.8 + - - -
952C LYS* 2.8 23.2 + - - -
947D ARG 5.3 0.5 - - - +
950D ALA* 6.0 2.2 - - + -
951D GLN* 3.6 17.2 + - + +
954D ILE* 3.8 10.5 - - + +
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Residues in contact with VAL 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B GLN 3.1 16.6 + - - +
87B ASP* 1.3 79.0 - - + +
89B LEU* 1.3 66.0 + - - +
91B ALA* 3.0 14.0 + - - +
92B LEU* 3.1 14.3 + - + +
111B MSE 3.6 44.2 - - + +
114B LEU* 3.5 29.6 - - + +
115B GLU* 3.7 23.6 - - + +
950D ALA* 4.3 15.9 - - + -
954D ILE* 4.2 6.7 - - + -
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Residues in contact with LEU 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B TYR* 3.0 47.4 + - + +
86B LEU* 3.8 9.6 - - + +
88B VAL* 1.3 77.4 - - - +
90B HIS* 1.3 64.6 + - - +
92B LEU* 3.1 19.7 + - + +
93B LYS* 3.3 35.1 + - + +
98B VAL* 4.4 10.1 - - + -
104B GLN* 6.0 0.7 - - - +
107B VAL* 4.0 26.7 - - + -
111B MSE 4.4 7.0 - - + -
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Residues in contact with HIS 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B LEU 2.8 22.6 + - - +
87B ASP* 3.6 5.8 - - - +
89B LEU* 1.3 74.2 - - - +
91B ALA* 1.3 64.4 + - - +
93B LYS* 3.0 25.3 + - + +
94B VAL* 3.0 23.0 + - + +
959C GLU* 2.7 36.4 + - - -
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Residues in contact with ALA 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B ASP 3.0 13.3 + - - +
88B VAL* 3.0 10.1 + - - +
90B HIS* 1.3 77.1 - - - +
92B LEU* 1.3 62.8 + - - +
94B VAL* 3.2 5.9 + - - +
95B VAL* 3.2 21.2 + - - +
114B LEU* 4.5 7.2 - - + -
954D ILE* 3.5 39.0 - - + -
957D VAL* 5.6 1.3 - - + -
958D PHE* 3.5 18.6 - - + -
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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
----------------------------------------------------------
88B VAL* 3.1 13.0 + - + +
89B LEU* 3.1 12.6 + - + +
91B ALA* 1.3 76.7 - - - +
93B LYS* 1.3 59.3 + - - +
95B VAL* 3.5 5.4 - - + +
96B ARG 3.2 3.5 + - - -
97B PHE* 2.8 42.3 + - + -
98B VAL* 3.6 20.5 + - + -
107B VAL* 4.4 2.0 - - + +
110B ARG* 3.8 29.2 - - + +
111B MSE 3.6 41.7 - - + +
114B LEU* 4.5 11.0 - - + -
119B LEU* 4.2 17.9 - - + -
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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
----------------------------------------------------------
89B LEU* 3.6 35.0 - - + +
90B HIS* 3.0 17.6 + - + +
92B LEU* 1.3 73.7 - - - +
94B VAL* 1.3 66.0 + - - +
96B ARG* 3.3 14.0 + - - +
98B VAL* 4.0 27.3 - - + +
99B SER* 5.0 6.5 - - - +
100B ASP* 3.7 23.9 + - - +
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Residues in contact with VAL 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B HIS* 3.0 29.5 + - + +
91B ALA* 3.4 9.0 - - - +
93B LYS* 1.3 78.6 - - - +
95B VAL* 1.3 57.6 + - - +
96B ARG* 3.3 5.5 + - - +
959C GLU* 3.5 41.5 - - + +
962C ILE* 4.1 21.2 - - + +
963C LEU* 5.5 9.9 - - + +
966C TYR* 3.7 18.5 - - - -
958D PHE* 3.7 25.8 - - + -
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Residues in contact with VAL 95 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B ALA 3.2 11.2 + - - +
92B LEU* 3.5 18.8 - - + +
94B VAL* 1.3 77.4 - - - +
96B ARG* 1.3 67.9 + - - +
97B PHE* 3.1 30.0 + - + -
119B LEU* 4.9 5.8 - - + -
121B ARG* 5.1 1.7 + - - -
962C ILE* 5.4 0.7 - - - -
966C TYR* 3.8 8.0 + - - -
957D VAL* 5.1 9.6 - - + +
958D PHE* 4.5 12.3 - - + -
961D GLU* 3.1 47.3 - - + +
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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) + - + + + + + -
------------------------------------------------------------
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