Contacts of the helix formed by residues 76 - 90 (chain L) in PDB entry 5A0Q
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 VAL 76 (chain L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41L LEU* 3.5 24.5 - - + -
73L ARG* 3.6 2.4 - - - +
75L SER* 1.4 74.3 + - - +
77L ALA* 1.3 53.4 + - - +
79L ALA* 4.0 0.2 - - - +
80L SER* 2.7 34.7 + - - -
101L ILE* 3.7 25.2 - - + +
103L GLY 3.6 16.2 - - - +
105L ASP* 3.0 32.3 - - - +
110L GLY* 4.0 11.2 - - - -
112L TYR* 3.4 30.5 - - + -
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Residues in contact with ALA 77 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99D GLU* 3.5 38.1 - - + +
75L SER* 3.2 9.5 + - - +
76L VAL* 1.3 77.9 - - - +
78L ALA* 1.3 57.5 + - - +
80L SER* 3.0 16.3 + - - -
81L LYS* 3.1 9.9 + - - +
105L ASP* 4.8 1.0 + - - -
112L TYR* 3.9 15.3 - - - +
120L ARG* 3.0 19.1 + - - +
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Residues in contact with ALA 78 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98D VAL* 4.0 32.8 - - + +
99D GLU* 4.4 6.0 - - - +
66L TYR* 5.3 2.0 - - - +
74L ILE* 3.8 16.2 - - + -
75L SER* 3.4 16.6 + - - +
77L ALA* 1.3 76.8 - - - +
79L ALA* 1.4 59.2 + - - +
81L LYS* 3.6 5.3 - - - +
82L LEU* 2.9 37.2 + - - +
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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
----------------------------------------------------------
37L ILE* 4.8 5.4 - - + -
41L LEU* 4.3 9.4 - - + -
59L LEU* 3.8 8.9 - - + +
63L CYS* 4.6 8.5 - - - -
74L ILE* 4.1 20.6 - - + +
75L SER 2.7 22.4 + - - +
76L VAL 4.0 3.1 - - - +
78L ALA* 1.4 69.8 - - - +
80L SER* 1.4 64.7 + - - +
82L LEU* 3.6 1.2 + - - +
83L LEU* 3.1 23.4 + - - +
101L ILE* 4.1 19.3 - - + -
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Residues in contact with SER 80 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76L VAL 2.7 21.3 + - - -
77L ALA 3.0 11.4 + - - -
79L ALA* 1.4 78.2 - - - +
81L LYS* 1.3 56.8 + - - +
83L LEU* 3.4 4.0 - - - +
84L ALA* 2.9 30.7 + - - +
101L ILE* 3.8 15.8 - - - +
112L TYR* 3.3 17.4 - - - -
114L VAL* 3.7 24.2 - - - +
120L ARG* 3.1 14.4 + - - +
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Residues in contact with LYS 81 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96D LEU* 3.1 24.4 - - - +
97D THR 3.3 18.8 - - - +
99D GLU* 4.7 8.5 - - + +
54K VAL* 5.2 6.3 + - - +
55K GLN* 3.8 13.3 + - - +
58K GLU* 3.2 29.0 + - - -
77L ALA 3.1 19.6 + - - +
78L ALA* 3.6 6.7 - - - +
79L ALA 3.2 0.2 - - - -
80L SER* 1.3 75.1 + - - +
82L LEU* 1.4 64.4 + - - +
84L ALA* 3.3 2.6 + - + +
85L ASN* 2.8 50.3 + - - +
120L ARG* 3.6 31.6 - - - +
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Residues in contact with LEU 82 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97D THR* 3.3 29.4 - - - +
98D VAL* 4.1 14.6 - - + -
59L LEU* 4.4 9.4 - - + -
62L GLN* 4.5 25.4 - - + +
63L CYS* 6.0 0.4 - - - -
66L TYR* 5.5 6.1 - - + -
74L ILE* 4.4 17.9 - - + -
78L ALA 2.9 31.7 + - - +
79L ALA* 4.0 4.9 - - - +
81L LYS* 1.4 74.2 - - - +
83L LEU* 1.4 56.9 + - - +
85L ASN* 3.5 8.3 + - - +
86L MET* 3.1 36.9 + - + +
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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
----------------------------------------------------------
55L TRP* 4.8 19.3 - - + +
56L GLU* 5.4 2.2 - - + -
59L LEU* 3.7 28.2 - - + +
79L ALA 3.1 18.3 + - - +
80L SER 3.4 3.8 - - - +
82L LEU* 1.4 75.8 - - - +
84L ALA* 1.3 63.5 + - - +
86L MET* 3.2 6.9 + - + +
87L VAL* 3.1 27.3 + - + +
97L MET* 5.9 0.7 - - - -
99L THR* 3.6 32.8 - - + +
101L ILE* 3.7 33.0 - - + -
114L VAL* 4.0 15.0 - - + -
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Residues in contact with ALA 84 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55K GLN* 4.9 2.0 - - - +
80L SER 2.9 18.6 + - - +
81L LYS* 3.3 6.5 + - + +
83L LEU* 1.3 71.6 - - - +
85L ASN* 1.3 68.7 + - - +
87L VAL* 3.5 11.1 - - - +
88L TYR* 3.1 23.0 + - - +
114L VAL* 4.2 8.5 - - + -
118L GLY* 4.2 13.5 - - - +
120L ARG* 3.8 27.8 - - + -
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Residues in contact with ASN 85 (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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96D LEU* 4.0 28.0 + - - +
97D THR* 4.1 18.0 + - - +
55K GLN* 3.5 19.2 + - - +
81L LYS* 2.8 43.1 + - - +
82L LEU* 3.7 8.0 - - - +
84L ALA* 1.3 77.0 - - - +
86L MET* 1.4 64.5 + - + +
88L TYR* 3.3 16.3 + - - +
89L GLN* 3.6 18.6 + - - +
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Residues in contact with MET 86 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55L TRP* 5.2 11.6 - - + +
58L LEU* 4.5 31.6 - - + +
59L LEU* 5.3 6.7 - - - -
62L GLN* 4.0 33.0 - - + +
82L LEU* 3.1 24.9 + - + +
83L LEU* 3.2 9.2 + - + +
85L ASN* 1.4 78.8 - - + +
87L VAL* 1.3 57.9 + - - +
89L GLN* 3.9 20.4 + - - +
90L TYR* 3.6 23.4 - - - -
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Residues in contact with VAL 87 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55L TRP* 4.7 10.3 - - + +
83L LEU* 3.1 20.5 + - + +
84L ALA* 3.5 15.3 - - - +
86L MET* 1.3 75.5 - - - +
88L TYR* 1.3 68.7 + - - +
89L GLN 3.3 0.7 - - - -
90L TYR* 3.3 19.2 + - + +
95L LEU* 4.2 4.5 - - + +
97L MET* 3.6 38.1 - - + -
99L THR* 6.2 1.3 - - + -
114L VAL* 5.0 3.6 - - + -
115L ASP 3.8 17.0 - - - +
116L SER* 3.5 31.4 - - - +
118L GLY* 4.4 2.2 - - - -
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Residues in contact with TYR 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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51K GLY* 5.3 0.4 - - - -
52K ASP* 1.9 35.7 + - - -
55K GLN* 2.7 58.6 - - + -
96K THR* 4.3 2.9 + - - -
98K TYR* 2.9 25.9 - + - -
84L ALA 3.1 18.8 + - - +
85L ASN 3.3 7.2 + - - +
87L VAL* 1.3 80.8 - - - +
89L GLN* 1.3 57.0 + - + +
91L LYS* 2.7 52.6 + - + +
116L SER 4.7 2.0 - - - -
117L GLU 4.3 9.6 - - - +
118L GLY* 5.0 2.0 - - - -
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Residues in contact with GLN 89 (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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85L ASN* 3.6 19.6 + - - +
86L MET* 4.1 19.8 - - - +
87L VAL 3.3 1.0 - - - -
88L TYR* 1.3 79.2 - - + +
90L TYR* 1.3 79.5 + - + +
91L LYS 3.2 2.9 + - - +
93L MET* 3.8 14.4 - - - +
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Residues in contact with TYR 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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55L TRP* 3.9 26.4 - + + -
86L MET 3.6 19.7 - - - -
87L VAL* 3.3 11.7 + - - +
88L TYR 3.0 0.8 - - - -
89L GLN* 1.3 93.4 + - + +
91L LYS* 1.3 61.8 + - - +
92L GLY 3.5 0.2 + - - -
93L MET* 3.4 33.9 + - + +
94L GLY 4.2 3.3 + - - -
95L LEU* 3.6 39.7 + - + +
116L SER 5.3 0.5 - - - +
101M PHE* 4.2 17.9 - + - -
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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
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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