Contacts of the helix formed by residues 82 - 93 (chain L) in PDB entry 6L49
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 THR 82 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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198J A 4.6 16.2 - - - +
199J G 5.4 4.0 - - - +
85K GLN* 3.5 31.0 - - - +
88K ALA* 4.0 2.7 - - - -
78L ARG* 3.5 33.3 + - - +
80L THR* 3.2 6.6 + - + +
81L VAL* 1.3 85.7 - - - +
83L ALA* 1.3 64.8 + - - +
84L MET* 3.5 16.2 + - - +
85L ASP* 3.5 13.8 + - - -
86L VAL* 3.8 7.4 - - - +
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Residues in contact with ALA 83 (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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85K GLN* 3.8 6.6 + - - +
87K SER* 3.4 31.0 - - - +
88K ALA* 3.7 21.0 - - - +
91K ALA* 5.6 0.9 - - + -
82L THR* 1.3 74.6 - - - +
84L MET* 1.3 62.1 + - + +
85L ASP 3.2 0.2 - - - -
86L VAL* 3.0 6.6 + - + +
87L VAL* 3.0 32.6 + - + +
100L PHE* 5.0 11.9 - - + +
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Residues in contact with MET 84 (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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78L ARG* 5.8 0.7 - - - +
82L THR* 3.3 11.8 - - - +
83L ALA* 1.3 80.7 - - + +
85L ASP* 1.3 59.2 + - - +
87L VAL* 3.4 4.5 + - + +
88L TYR* 2.9 69.7 + - + +
100L PHE 3.6 18.6 - - - +
101L GLY* 4.3 4.7 - - - -
102L GLY 4.1 20.9 - - - +
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Residues in contact with ASP 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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69L ALA* 3.7 22.6 - - + +
72L TYR* 3.4 29.8 - - + +
73L THR* 2.7 23.8 + - - +
78L ARG* 2.9 37.8 + - - -
81L VAL* 4.2 0.7 - - + -
82L THR* 3.5 14.4 + - - +
83L ALA 3.2 0.6 - - - -
84L MET* 1.3 79.2 - - - +
86L VAL* 1.3 56.6 + - - +
88L TYR* 4.6 4.5 - - - -
89L ALA* 2.9 30.3 + - - +
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Residues in contact with VAL 86 (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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88K ALA* 3.8 27.4 - - + +
91K ALA* 4.2 14.8 - - + -
92K LEU* 3.8 37.2 - - + +
65L VAL* 4.7 3.1 - - + -
66L ILE* 6.4 0.2 - - + -
69L ALA* 4.4 13.5 - - + -
81L VAL* 4.8 3.8 - - + -
82L THR 3.8 15.0 - - - +
83L ALA* 3.0 8.2 + - - +
85L ASP* 1.3 74.6 - - - +
87L VAL* 1.3 59.6 + - - +
89L ALA* 3.4 5.4 + - - +
90L LEU* 2.9 39.2 + - + +
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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
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91K ALA* 5.4 5.4 - - + -
83L ALA* 3.0 15.0 + - + +
84L MET* 3.4 8.7 + - + +
86L VAL* 1.3 78.6 - - + +
88L TYR* 1.3 62.1 + - + +
90L LEU* 3.3 9.6 + - + +
91L LYS* 2.9 27.9 + - + +
96L THR* 4.9 7.1 + - - +
97L LEU* 4.1 18.8 - - + +
100L PHE* 3.4 36.8 - - + +
101L GLY 3.9 23.8 - - - +
102L GLY* 4.6 7.2 - - - +
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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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72L TYR* 3.3 36.0 + + + +
84L MET* 2.9 56.9 + - + +
85L ASP* 3.9 6.1 - - - +
87L VAL* 1.3 78.4 - - + +
89L ALA* 1.3 60.4 + - - +
91L LYS* 3.2 7.8 + - + +
92L ARG* 2.9 23.9 + - - +
102L GLY* 4.8 13.5 - - - -
80N TYR* 3.5 74.0 + + + +
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Residues in contact with ALA 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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65L VAL* 3.5 33.4 - - + +
68L ASP* 3.7 16.8 - - + +
69L ALA 4.0 3.8 - - - +
72L TYR* 3.4 7.5 - - + -
85L ASP 2.9 19.2 + - - +
86L VAL* 3.8 5.2 - - - +
88L TYR* 1.3 75.8 - - - +
90L LEU* 1.3 62.9 + - - +
92L ARG* 3.4 4.0 + - - +
93L GLN* 3.2 30.0 + - - +
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Residues in contact with LEU 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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91K ALA* 4.5 2.5 - - + +
95K ALA* 3.7 32.5 - - + -
61L PHE* 4.3 6.3 - - + -
65L VAL* 4.3 27.4 - - + -
86L VAL* 2.9 32.2 + - + +
87L VAL* 3.6 7.9 - - + +
89L ALA* 1.3 73.5 - - - +
91L LYS* 1.3 62.3 + - - +
93L GLN* 3.5 3.3 + - + +
94L GLY 3.4 2.4 + - - -
95L ARG* 2.9 54.8 + - + +
96L THR* 3.9 6.5 - - - -
97L LEU* 3.8 28.9 - - + +
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Residues in contact with LYS 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 VAL* 2.9 16.2 + - - +
88L TYR* 3.2 14.8 + - + +
90L LEU* 1.3 76.9 - - - +
92L ARG* 1.3 63.4 + - + +
94L GLY* 3.4 11.4 + - - -
96L THR* 3.5 36.0 + - + +
98L TYR* 5.5 0.2 - - - -
102L GLY* 5.8 7.6 + - - -
76N ARG* 5.2 9.6 - - - +
80N TYR* 4.2 19.1 - - + +
65R ASP* 2.4 35.9 + - - +
68R GLU* 6.0 2.0 - - - -
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Residues in contact with ARG 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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68L ASP* 3.3 25.5 + - - +
72L TYR* 3.3 25.8 - - - +
88L TYR 2.9 10.7 + - - +
89L ALA* 3.4 6.3 + - - +
90L LEU 3.4 0.2 - - - -
91L LYS* 1.3 79.2 - - + +
93L GLN* 1.3 64.8 + - - +
94L GLY 3.3 1.8 + - - -
73N GLU* 3.0 37.2 + - - +
76N ARG* 5.3 8.3 - - - +
80N TYR* 6.5 0.2 - - + -
97N LEU* 2.9 49.2 + - - +
98N LEU* 3.7 20.6 + - - +
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Residues in contact with GLN 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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61L PHE* 5.8 3.2 - - + -
64L ASN* 3.8 31.9 + - - +
65L VAL* 4.6 13.0 - - + -
68L ASP* 3.6 21.1 + - - +
89L ALA 3.2 18.8 + - - +
90L LEU* 3.5 6.7 + - + +
91L LYS 3.3 0.2 - - - -
92L ARG* 1.3 82.5 + - - +
94L GLY* 1.3 62.2 + - - +
95L ARG* 3.2 15.4 + - + +
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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