Contacts of the helix formed by residues 77 - 98 (chain L) in PDB entry 5T0G
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 LEU 77 (chain L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15K PHE* 4.6 22.4 - - + -
20K ARG* 5.8 10.1 - - + -
21K LEU* 4.8 18.8 - - + +
159K SER* 5.8 10.5 - - - +
161K THR* 5.9 1.8 - - - +
28L ALA* 5.5 11.1 - - + +
74L ILE* 5.1 0.7 - - - +
75L ALA 3.9 3.1 + - - +
76L GLY* 1.3 71.6 - - - -
78L THR* 1.3 61.0 + - - +
79L ALA* 3.4 10.3 - - + +
80L ASP* 4.4 20.6 - - - +
81L ALA* 3.1 22.2 + - - +
126L ARG* 5.9 0.2 - - - +
129L GLY* 4.1 25.5 + - - +
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Residues in contact with THR 78 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159K SER 5.0 0.5 + - - -
160K GLY 3.7 0.2 - - - -
161K THR* 3.5 38.9 + - + +
162K PHE 5.7 0.4 - - - +
60L GLN* 5.6 10.5 - - + +
62L LYS* 5.7 5.4 - - - +
74L ILE* 6.0 5.6 - - + -
76L GLY 3.4 8.7 + - - +
77L LEU* 1.3 73.6 - - - +
79L ALA* 1.3 65.9 + - - +
81L ALA* 3.7 7.4 - - + -
82L ARG* 2.9 58.0 + - - +
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Residues in contact with ALA 79 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117K SER 5.5 3.8 - - - +
120K ALA* 5.4 4.9 - - + -
121K LEU* 4.4 22.4 - - + +
159K SER 4.1 18.5 + - - +
77L LEU* 3.4 8.0 - - + +
78L THR* 1.3 83.8 + - - +
80L ASP* 1.3 71.4 + - - +
82L ARG* 3.1 12.5 + - - +
83L LEU* 3.0 20.3 + - - +
126L ARG* 5.9 0.7 - - - +
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Residues in contact with ASP 80 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15K PHE* 5.3 0.2 - - - -
77L LEU* 4.4 17.1 + - + +
79L ALA* 1.3 85.0 - - - +
81L ALA* 1.3 57.3 + - - +
83L LEU* 3.5 15.0 - - - +
84L LEU* 2.9 35.9 + - + +
126L ARG* 3.6 28.1 + - - -
127L PRO 4.2 0.7 - - - +
128L TYR* 3.3 52.4 - - + -
129L GLY 4.4 12.4 + - - +
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Residues in contact with ALA 81 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74L ILE* 3.5 36.1 - - + +
77L LEU 3.1 23.1 + - - +
78L THR* 3.5 9.9 - - + +
80L ASP* 1.3 80.3 - - - +
82L ARG* 1.3 59.9 + - + +
84L LEU* 3.5 7.1 + - - +
85L CYS* 2.9 26.1 + - - +
129L GLY 5.0 2.1 + - - -
130L VAL* 6.1 3.1 - - - -
132L LEU* 5.6 4.4 - - - +
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Residues in contact with ARG 82 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113K THR* 5.1 1.4 - - - +
114K GLN* 5.2 16.0 - - - +
117K SER* 3.1 36.0 + - - +
118K ASN* 5.1 6.1 - - - +
160K GLY* 2.4 37.8 + - - -
162K PHE* 4.4 13.5 - - - +
64L LEU* 6.0 6.3 - - + -
78L THR* 2.9 47.1 + - - +
79L ALA* 3.7 9.5 - - - +
81L ALA* 1.3 74.9 - - + +
83L LEU* 1.3 57.2 + - - +
85L CYS* 3.1 12.6 + - + +
86L ASN* 2.6 42.3 + - - +
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Residues in contact with LEU 83 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118K ASN* 5.8 2.5 - - - +
121K LEU 5.7 4.5 - - - +
79L ALA 3.0 13.8 + - - +
80L ASP* 3.5 19.5 - - - +
82L ARG* 1.3 74.3 - - - +
84L LEU* 1.3 71.3 + - + +
86L ASN* 3.0 23.0 + - - +
87L PHE* 3.1 11.5 + - + +
115L LYS* 5.5 7.9 - - - -
128L TYR* 4.4 30.5 - - + +
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Residues in contact with LEU 84 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80L ASP* 2.9 22.9 + - + +
81L ALA* 3.8 5.2 - - - +
83L LEU* 1.3 78.2 - - + +
85L CYS* 1.3 57.3 + - - +
87L PHE* 3.4 18.1 + - + +
88L MET* 2.8 26.9 + - - +
112L ILE* 5.3 15.1 - - + +
115L LYS* 4.2 25.6 - - + -
116L THR* 4.5 12.8 - - + -
128L TYR* 4.3 33.2 - - + -
130L VAL* 4.6 22.9 - - + -
132L LEU* 4.8 15.3 - - + +
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Residues in contact with CYS 85 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64L LEU* 4.0 16.2 - - + -
66L VAL* 5.2 0.7 - - + -
72L ILE* 6.3 1.3 - - + -
81L ALA 2.9 15.1 + - - +
82L ARG* 3.3 17.0 - - + +
83L LEU 3.0 0.6 - - - -
84L LEU* 1.3 75.2 - - - +
86L ASN* 1.3 62.0 + - - +
88L MET* 3.1 7.5 + - - +
89L ARG* 2.8 77.2 + - - +
132L LEU* 6.4 2.5 - - + -
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Residues in contact with ASN 86 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118K ASN* 3.6 24.4 + - - +
82L ARG* 2.6 35.6 + - - +
83L LEU* 3.4 9.7 + - - +
85L CYS* 1.3 75.6 - - - +
87L PHE* 1.3 65.9 + - - +
89L ARG* 3.3 10.1 + - - +
90L GLN* 3.0 21.1 + - - +
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Residues in contact with PHE 87 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83L LEU* 3.1 10.4 + - + +
84L LEU* 3.5 21.3 - - + +
86L ASN* 1.3 74.7 - - - +
88L MET* 1.3 64.9 + - - +
90L GLN* 3.1 13.7 + - + +
91L GLU* 3.0 54.8 + - + +
111L LEU* 4.3 21.1 - - + -
112L ILE* 4.0 33.7 - - + -
115L LYS* 4.5 34.1 - - + -
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Residues in contact with MET 88 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66L VAL* 3.6 24.0 - - + -
70L ILE* 3.6 30.1 - - + -
72L ILE* 4.8 8.1 - - + -
84L LEU 2.8 18.3 + - - +
85L CYS* 3.1 10.7 + - - +
87L PHE* 1.3 80.5 - - + +
89L ARG* 1.3 61.7 + - - +
91L GLU* 3.5 4.3 + - - +
92L CYS* 3.3 24.8 + - - -
108L LEU* 3.5 34.9 - - + +
112L ILE* 4.6 16.6 - - + -
132L LEU* 6.3 7.6 - - + -
134L ILE* 4.3 16.2 - - + -
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Residues in contact with ARG 89 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64L LEU* 3.6 8.7 - - - +
65L HIS 3.5 19.2 + - - -
66L VAL* 3.4 41.7 + - - +
85L CYS* 2.8 59.4 + - - +
86L ASN* 3.6 8.5 - - - +
88L MET* 1.3 72.1 - - - +
90L GLN* 1.3 69.4 + - - +
92L CYS* 3.1 14.1 + - - +
93L LEU* 3.1 24.6 + - + +
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Residues in contact with GLN 90 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86L ASN 3.0 12.9 + - - +
87L PHE* 3.2 17.5 - - + +
89L ARG* 1.3 76.8 - - - +
91L GLU* 1.3 69.2 + - - +
93L LEU* 3.2 25.0 + - - +
94L ASP* 2.9 55.3 + - - +
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Residues in contact with GLU 91 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87L PHE* 3.0 54.4 + - + +
88L MET* 4.0 5.6 - - - +
89L ARG 3.3 0.2 - - - -
90L GLN* 1.3 79.6 - - - +
92L CYS* 1.3 64.9 + - - +
94L ASP* 3.5 26.5 + - - +
95L SER 3.7 1.2 + - - -
103L LEU* 3.6 22.1 - - + +
108L LEU* 3.7 26.7 - - + -
111L LEU* 3.4 26.4 - - + +
112L ILE* 5.6 1.3 - - + -
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Residues in contact with CYS 92 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66L VAL* 3.8 16.6 - - - -
67L ASP* 3.7 38.1 - - + +
70L ILE* 5.2 3.4 - - - -
88L MET* 3.3 25.4 + - - -
89L ARG* 3.1 10.2 + - - +
91L GLU* 1.3 80.5 - - - +
93L LEU* 1.3 64.6 + - - +
94L ASP 3.0 1.4 + - - -
95L SER* 3.6 1.9 + - - -
96L ARG* 3.1 21.1 + - - +
101L ARG 5.1 0.3 - - - +
102L PRO* 5.3 3.6 - - - +
103L LEU* 5.7 4.2 + - - +
108L LEU* 5.3 3.3 - - - +
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Residues in contact with LEU 93 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89L ARG* 3.1 26.7 + - + +
90L GLN* 3.2 30.1 - - - +
92L CYS* 1.3 79.3 - - - +
94L ASP* 1.3 61.8 + - - +
96L ARG* 3.6 9.3 - - - -
97L PHE* 2.9 32.5 + - + +
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Residues in contact with ASP 94 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90L GLN* 2.9 53.8 + - - +
91L GLU* 3.5 24.1 - - - +
92L CYS 3.0 2.4 + - - -
93L LEU* 1.3 78.1 - - - +
95L SER* 1.3 58.6 + - - +
97L PHE* 3.0 6.6 + - - +
98L VAL* 2.9 33.9 + - + +
103L LEU* 5.7 0.9 - - + -
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Residues in contact with SER 95 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91L GLU 3.7 1.0 + - - -
92L CYS 3.6 3.8 + - - -
94L ASP* 1.3 79.5 - - - +
96L ARG* 1.3 58.1 + - - +
98L VAL* 4.8 1.6 - - - -
99L PHE* 3.0 31.9 + - - +
100L ASP 2.8 25.3 + - - -
101L ARG* 2.4 30.5 + - - +
102L PRO 3.8 2.9 + - - -
103L LEU* 3.6 33.3 - - - +
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Residues in contact with ARG 96 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92L CYS 3.1 20.8 + - - +
93L LEU* 3.6 11.0 - - - +
94L ASP 3.2 0.2 - - - -
95L SER* 1.3 77.7 - - - +
97L PHE* 1.3 55.8 + - - +
100L ASP* 3.2 51.3 + - - +
101L ARG* 3.3 17.1 + - - +
102L PRO* 4.0 13.5 - - + +
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Residues in contact with PHE 97 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93L LEU* 2.9 18.2 + - + +
94L ASP* 3.0 3.6 + - - +
96L ARG* 1.3 78.8 - - - +
98L VAL* 1.3 85.3 + - + +
100L ASP* 3.7 7.7 + - - +
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Residues in contact with VAL 98 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94L ASP* 2.9 22.4 + - + +
95L SER* 4.8 1.1 - - - -
97L PHE* 1.3 92.2 - - + +
99L PHE* 1.3 87.5 + - + +
100L ASP* 4.7 0.9 - - - +
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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