Contacts of the helix formed by residues 82 - 93 (chain T) 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 T).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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-142J A 4.6 14.6 - - - +
-141J G 6.0 1.1 - - - +
85S GLN* 3.5 33.9 - - - +
88S ALA* 3.9 4.0 - - - -
78T ARG* 3.7 19.9 + - - +
80T THR* 3.1 19.4 + - + +
81T VAL* 1.3 78.5 - - - +
83T ALA* 1.3 65.0 + - - +
84T MET* 3.2 24.1 + - - +
85T ASP* 3.7 5.0 + - - -
86T VAL* 3.4 20.3 + - - +
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Residues in contact with ALA 83 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85S GLN* 3.6 6.8 + - - +
87S SER* 3.3 28.9 - - - +
88S ALA* 3.8 19.2 - - - +
91S ALA* 5.6 0.8 - - + +
82T THR* 1.3 74.7 - - - +
84T MET* 1.3 61.3 + - + +
86T VAL* 3.4 3.3 + - - +
87T VAL* 2.9 32.7 + - - +
100T PHE* 4.1 21.8 - - + +
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Residues in contact with MET 84 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78T ARG* 5.5 2.9 - - - +
82T THR* 3.2 14.5 - - - +
83T ALA* 1.3 78.2 - - - +
85T ASP* 1.3 59.9 + - - +
87T VAL* 3.2 5.0 + - - +
88T TYR* 2.9 65.6 + - + +
100T PHE 3.8 15.3 - - - +
101T GLY* 4.2 5.6 - - - -
102T GLY 4.1 19.7 - - - +
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Residues in contact with ASP 85 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69T ALA* 4.0 7.6 - - - +
72T TYR* 3.6 26.5 - - + +
73T THR* 3.0 31.1 + - - +
78T ARG* 2.8 42.5 + - - -
81T VAL* 4.1 8.5 - - + -
82T THR* 3.7 5.9 + - - +
83T ALA 3.4 0.2 - - - -
84T MET* 1.3 74.5 - - - +
86T VAL* 1.3 60.1 + - - +
88T TYR* 3.4 14.6 + - - +
89T ALA* 2.9 30.3 + - - +
81V ASN* 5.3 2.1 - - - +
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Residues in contact with VAL 86 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84S PHE* 4.9 2.5 - - + -
88S ALA* 3.8 23.3 - - + +
91S ALA* 4.3 13.7 - - + -
92S LEU* 3.8 37.0 - - + -
65T VAL* 4.8 2.4 - - + +
66T ILE* 6.3 0.2 - - + -
69T ALA* 4.4 6.5 - - + -
81T VAL* 4.2 14.1 - - + -
82T THR 3.4 15.5 + - - +
83T ALA* 3.4 10.2 + - - +
84T MET 3.3 0.4 - - - -
85T ASP* 1.3 78.5 - - - +
87T VAL* 1.3 56.2 + - - +
89T ALA* 3.4 5.8 + - - +
90T LEU* 2.9 38.1 + - + +
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Residues in contact with VAL 87 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91S ALA* 5.3 6.3 - - + -
83T ALA 2.9 21.0 + - - +
84T MET* 3.2 5.4 + - - +
86T VAL* 1.3 76.6 - - - +
88T TYR* 1.3 68.4 + - + +
90T LEU* 3.3 9.2 + - + +
91T LYS* 2.9 26.5 + - + +
96T THR* 5.2 8.7 - - + -
97T LEU* 4.2 21.0 + - + +
100T PHE* 3.5 35.0 - - + +
101T GLY 3.6 22.4 - - - +
102T GLY* 4.6 3.4 - - - -
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Residues in contact with TYR 88 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72T TYR* 3.5 39.6 - + + +
78T ARG* 6.3 0.2 - - - -
84T MET* 2.9 54.2 + - + +
85T ASP* 3.9 9.9 - - - +
87T VAL* 1.3 83.6 - - + +
89T ALA* 1.3 57.0 + - - +
91T LYS* 3.2 11.8 + - + +
92T ARG* 3.0 23.2 + - - +
102T GLY* 4.6 19.4 - - - -
80V TYR* 3.5 72.2 + + + +
81V ASN* 6.0 0.4 - - - -
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Residues in contact with ALA 89 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65T VAL* 3.3 30.7 - - + +
68T ASP* 3.8 9.0 - - + +
69T ALA* 3.5 17.7 - - + +
72T TYR* 4.0 6.5 - - - -
85T ASP 2.9 17.9 + - - +
86T VAL 3.8 4.3 - - - +
87T VAL 3.3 0.2 - - - -
88T TYR* 1.3 74.3 - - - +
90T LEU* 1.3 63.9 + - - +
92T ARG* 3.4 3.5 + - - +
93T GLN* 3.2 28.5 + - - +
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Residues in contact with LEU 90 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91S ALA* 4.4 3.4 - - + +
92S LEU* 5.3 1.8 - - + +
95S ALA* 3.8 24.2 - - + -
61T PHE* 3.7 31.0 - - + -
65T VAL* 3.8 18.8 - - + -
86T VAL* 2.9 33.1 + - + +
87T VAL* 3.7 7.4 - - + +
89T ALA* 1.3 73.7 - - - +
91T LYS* 1.3 63.0 + - - +
93T GLN* 3.5 3.6 + - + +
94T GLY 3.4 2.9 + - - -
95T ARG* 2.9 48.6 + - + +
96T THR* 4.1 2.2 - - - -
97T LEU* 4.1 24.9 - - + +
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Residues in contact with LYS 91 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72T TYR* 2.9 28.0 + - - -
87T VAL* 2.9 15.9 + - + +
88T TYR* 3.2 12.0 + - + +
90T LEU* 1.3 77.0 - - - +
92T ARG* 1.3 64.1 + - - +
94T GLY* 3.4 10.7 + - - -
96T THR* 3.3 26.8 + - + +
73V GLU* 4.4 6.8 + - - +
76V ARG* 3.3 39.2 - - - +
80V TYR* 3.5 26.2 - - - +
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Residues in contact with ARG 92 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68T ASP* 3.3 21.0 + - - +
72T TYR* 4.9 9.2 - - + +
88T TYR 3.0 15.5 + - - +
89T ALA* 3.8 7.6 - - - +
90T LEU 3.3 0.4 - - - -
91T LYS* 1.3 82.6 - - - +
93T GLN* 1.3 82.4 + - - +
94T GLY 3.2 1.1 + - - -
73V GLU* 4.0 23.3 - - - +
97V LEU* 2.8 29.3 + - + -
98V LEU* 2.7 42.3 + - + +
99V LEU 5.1 0.4 + - - -
100V PRO* 6.2 0.2 - - - +
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Residues in contact with GLN 93 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61T PHE* 5.3 3.6 - - + -
64T ASN* 2.8 37.3 + - - +
65T VAL* 3.8 22.9 - - + -
68T ASP* 2.7 25.0 + - - +
89T ALA 3.2 18.4 + - - +
90T LEU* 3.5 5.6 + - - +
91T LYS 3.3 0.6 - - - -
92T ARG* 1.3 94.6 + - - +
94T GLY* 1.3 61.8 + - - +
95T ARG* 3.4 12.3 + - + +
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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
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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