Contacts of the helix formed by residues 73 - 95 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A PRO* 3.8 17.2 - - - +
70A HIS* 3.0 20.2 + - - +
72A GLU* 1.3 81.6 - - - +
74A HIS* 1.3 64.2 + - - +
75A ALA 3.2 1.6 - - - -
76A LYS* 2.8 11.1 + - - -
77A VAL* 2.8 23.9 + - - +
940E GLN* 2.6 42.1 + - - +
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Residues in contact with HIS 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A LEU* 4.0 14.8 - - + +
58A LEU* 4.2 11.1 - - + +
62A VAL* 4.1 5.2 - - + -
67A LEU* 3.7 38.0 - - + +
68A PRO* 2.8 38.0 + - + -
70A HIS 3.4 2.7 - - - -
71A HIS* 3.4 42.9 + - + +
72A GLU 3.3 0.8 - - - -
73A SER* 1.3 75.1 - - - +
75A ALA* 1.3 58.5 + - - +
77A VAL* 3.4 2.1 + - - -
78A MSE 2.9 36.5 + - + +
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Residues in contact with ALA 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A GLU 4.3 6.8 + - - +
73A SER 3.2 0.8 - - - -
74A HIS* 1.3 77.4 - - - +
76A LYS* 1.3 62.9 + - - +
78A MSE 3.5 6.0 + - - +
79A MSE 3.2 21.0 + - - +
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Residues in contact with LYS 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A GLU 4.8 2.4 + - - +
73A SER* 2.8 12.4 + - - +
75A ALA* 1.3 80.4 - - - +
77A VAL* 1.3 60.1 + - - +
79A MSE 3.2 29.0 - - + +
80A TYR* 3.6 35.4 + - + +
940E GLN* 4.0 35.1 - - + +
941F LEU* 4.2 18.7 - - - +
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Residues in contact with VAL 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A ILE 3.6 24.7 - - - +
67A LEU* 4.6 1.6 - - + -
68A PRO* 3.9 28.7 - - + -
73A SER* 2.8 27.4 + - - +
74A HIS 3.9 3.6 - - - +
76A LYS* 1.3 68.9 - - - +
78A MSE 1.3 57.4 + - - +
79A MSE 3.0 1.8 - - - -
80A TYR* 2.7 31.6 + - + +
81A ARG* 3.1 23.0 + - + +
939E GLY 4.5 2.7 - - - +
940E GLN* 4.2 24.0 - - + -
943E ALA* 3.9 11.7 - - + -
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Residues in contact with MSE 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A LYS* 4.3 14.6 - - - +
66A ILE* 4.3 12.3 - - - -
67A LEU* 3.7 21.8 - - + -
74A HIS* 2.9 21.4 + - + +
75A ALA* 3.9 6.5 - - - +
77A VAL* 1.3 75.3 - - - +
79A MSE 1.3 56.2 + - - +
81A ARG* 3.2 18.4 + - + +
82A LYS* 2.8 34.8 + - + +
147A ASP* 4.8 1.6 - - - +
149A VAL* 4.1 21.8 - - + -
150A ASP* 3.1 26.9 - - - +
153A TRP* 6.0 0.9 - - + -
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Residues in contact with MSE 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A ALA 3.2 12.5 + - - +
76A LYS* 3.2 22.7 - - + +
77A VAL 3.0 0.4 + - - -
78A MSE 1.3 77.5 - - - +
80A TYR* 1.3 85.4 + - + +
82A LYS* 3.2 12.7 + - + +
83A GLU* 3.0 48.2 + - + +
945F GLU* 5.5 2.0 - - - +
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Residues in contact with TYR 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A LYS* 3.7 42.7 - - + -
77A VAL* 2.7 15.2 + - - +
79A MSE 1.3 98.3 - - + +
81A ARG* 1.3 57.0 + - + +
83A GLU* 3.2 3.2 + - - -
84A GLN* 2.9 28.3 + - - +
940E GLN* 3.9 18.2 - - + -
943E ALA* 3.7 27.4 - - + +
944E ALA* 4.2 6.5 - - + -
947E ARG* 3.1 56.3 - - + +
941F LEU* 4.1 7.3 - - + +
945F GLU* 2.5 29.0 + - - +
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Residues in contact with ARG 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A GLY 3.6 7.3 + - - -
66A ILE* 2.6 51.7 + - - +
77A VAL* 3.1 23.5 + - + +
78A MSE 3.5 24.5 - - + +
80A TYR* 1.3 76.4 - - + +
82A LYS* 1.3 57.5 + - - +
84A GLN* 3.6 0.6 + - - +
85A TYR* 3.0 24.8 + - - +
149A VAL* 4.2 1.5 - - - +
153A TRP* 3.2 65.5 + - + +
157A ARG* 4.5 6.0 - - - +
942E GLN* 4.5 2.2 + - - +
943E ALA* 3.4 33.7 + - - +
946E SER* 3.6 19.4 + - - -
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Residues in contact with LYS 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A MSE 2.8 16.5 + - + +
79A MSE 3.3 14.8 - - + +
80A TYR 3.2 0.2 - - - -
81A ARG* 1.3 73.8 - - - +
83A GLU* 1.3 65.4 + - + +
85A TYR* 3.2 7.9 + - - +
86A LEU* 3.0 40.7 + - + +
149A VAL* 4.4 24.9 - - + +
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Residues in contact with GLU 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A MSE 3.0 48.6 + - + +
80A TYR* 3.2 8.8 + - - +
82A LYS* 1.3 75.1 - - + +
84A GLN* 1.3 54.5 + - - +
86A LEU* 3.2 11.2 + - + +
87A ASP* 2.8 42.3 + - - +
947E ARG* 3.7 20.5 + - - -
948F TYR* 3.5 24.5 + - - +
952F LYS* 5.0 4.4 + - - +
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Residues in contact with GLN 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A TYR 2.9 16.9 + - - +
81A ARG* 3.7 5.6 + - - +
83A GLU* 1.3 77.5 - - - +
85A TYR* 1.3 62.6 + - - +
87A ASP* 3.7 8.8 - - - +
88A VAL* 3.1 30.5 + - - +
115A GLU* 3.7 19.1 - - - +
153A TRP* 2.8 36.4 - - + -
156A ARG* 5.2 0.7 + - - -
946E SER* 2.6 45.5 + - - -
947E ARG* 3.1 16.1 - - + +
950E ALA* 2.9 22.5 - - + +
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Residues in contact with TYR 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A ARG 3.0 15.8 + - - +
82A LYS* 3.2 11.6 + - - +
84A GLN* 1.3 75.2 - - - +
86A LEU* 1.3 74.7 + - + +
89A LEU* 3.0 52.7 + - + +
104A GLN* 3.3 25.6 + - - -
107A VAL* 5.2 0.7 - - - +
108A TYR* 4.0 3.0 - + - -
111A MSE 3.2 38.7 - - + +
148A SER* 3.6 31.9 - - - -
149A VAL* 4.0 29.4 - - + -
152A TYR* 4.0 16.8 - + + -
153A TRP* 4.7 3.6 - - - +
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Residues in contact with LEU 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A LYS* 3.0 37.2 + - + +
83A GLU* 3.7 9.9 - - + +
85A TYR* 1.3 88.5 - - + +
87A ASP* 1.3 58.5 + - - +
89A LEU* 3.8 8.1 - - + +
90A HIS* 2.8 37.5 + - - +
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Residues in contact with ASP 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A GLU* 2.8 28.7 + - - +
84A GLN* 3.7 8.6 - - - +
86A LEU* 1.3 74.3 - - - +
88A VAL* 1.3 64.0 + - + +
90A HIS* 3.3 6.3 + - - +
91A ALA* 3.0 22.9 + - - +
947E ARG 5.4 0.2 - - - +
950E ALA* 6.2 1.6 - - + -
951E GLN* 3.3 20.0 + - + +
954E ILE* 3.8 18.0 - - + +
948F TYR* 2.7 32.5 + - - -
952F LYS* 3.9 15.2 + - - -
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Residues in contact with VAL 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A GLN 3.1 16.4 + - - +
87A ASP* 1.3 78.4 - - + +
89A LEU* 1.3 66.3 + - - +
91A ALA* 3.0 15.2 + - - +
92A LEU* 3.1 15.0 + - + +
111A MSE 3.6 45.5 - - + +
114A LEU* 4.0 21.8 - - + -
115A GLU* 3.7 26.9 - - + +
950E ALA* 4.4 14.4 - - + -
954E ILE* 4.1 10.3 - - + -
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Residues in contact with LEU 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A TYR* 3.0 46.8 + - + +
86A LEU* 3.8 10.5 - - + +
88A VAL* 1.3 76.3 - - - +
90A HIS* 1.3 65.7 + - - +
92A LEU* 3.1 19.9 + - + +
93A LYS* 3.3 34.8 + - + +
98A VAL* 4.4 9.9 - - + -
104A GLN* 6.0 0.7 - - - +
107A VAL* 4.0 26.7 - - + -
111A MSE 4.4 6.1 - - + -
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Residues in contact with HIS 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A LEU 2.8 23.2 + - - +
87A ASP* 3.6 6.1 - - - +
89A LEU* 1.3 74.0 - - - +
91A ALA* 1.3 65.0 + - - +
93A LYS* 3.0 25.1 + - + +
94A VAL* 3.0 24.2 + - + +
958E PHE* 6.1 0.7 - + - -
959F GLU* 2.7 37.3 + - - -
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Residues in contact with ALA 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A ASP 3.0 12.2 + - - +
88A VAL 3.0 9.8 + - - +
90A HIS* 1.3 76.0 - - - +
92A LEU* 1.3 61.6 + - - +
94A VAL* 3.2 5.1 + - - +
95A VAL* 3.2 24.0 + - - +
114A LEU* 4.4 8.7 - - + -
954E ILE* 3.5 39.5 - - + -
957E VAL* 6.4 0.2 - - + -
958E PHE* 3.6 18.1 - - + -
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Residues in contact with LEU 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A VAL 3.1 11.4 + - - +
89A LEU* 3.1 12.9 + - + +
91A ALA* 1.3 76.1 - - - +
93A LYS* 1.3 61.9 + - - +
95A VAL* 3.5 5.0 + - + +
96A ARG 3.2 2.9 + - - -
97A PHE* 2.8 43.1 + - + -
98A VAL* 3.6 20.0 + - + -
107A VAL* 4.5 1.6 - - + +
110A ARG* 3.8 26.7 - - + +
111A MSE 3.6 41.3 - - + +
114A LEU* 3.9 22.7 - - + -
119A LEU* 4.2 11.4 - - + -
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Residues in contact with LYS 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A LEU* 3.6 35.2 - - + +
90A HIS* 3.0 20.7 + - + +
92A LEU* 1.3 74.5 - - - +
94A VAL* 1.3 66.4 + - - +
96A ARG* 3.3 15.2 + - - +
98A VAL* 4.0 28.7 - - + +
99A SER* 5.0 6.7 - - - +
100A ASP* 3.7 23.2 + - - +
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Residues in contact with VAL 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A HIS* 3.0 40.8 + - + +
91A ALA* 3.2 7.6 + - - +
93A LYS* 1.3 78.1 - - - +
95A VAL* 1.3 57.2 + - - +
96A ARG* 3.3 8.7 + - - -
958E PHE* 3.6 30.7 - - + -
959F GLU* 3.9 22.2 - - + +
962F ILE* 4.2 22.8 - - + +
963F LEU* 4.6 12.1 - - + +
966F TYR* 3.8 17.7 - - - -
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Residues in contact with VAL 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A ALA 3.4 12.1 - - - +
92A LEU* 3.6 13.5 - - + +
94A VAL* 1.3 76.9 - - + +
96A ARG* 1.3 68.8 + - - +
97A PHE* 3.1 25.2 + - + -
119A LEU* 4.9 3.1 - - + -
121A ARG* 4.6 6.1 + - - +
957E VAL* 4.2 18.6 - - + -
958E PHE* 3.5 32.8 - - + -
961E GLU* 4.1 36.1 - - + +
962F ILE* 4.8 0.4 - - + -
966F TYR* 4.2 8.7 + - - -
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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