Contacts of the helix formed by residues 80 - 104 (chain D) in PDB entry 5U8T
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 PRO 80 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63D LEU* 6.5 0.7 - - + -
66D SER* 3.8 17.5 - - - +
78D PRO 3.3 6.9 - - - +
79D TYR* 1.3 84.2 - - + +
81D HIS* 1.3 59.3 + - - +
82D GLN* 3.3 4.4 + - + +
83D LEU* 3.5 6.6 + - + +
84D MET* 2.9 38.2 + - + +
143D TYR* 3.0 28.7 - - + +
147D ARG* 3.4 1.8 - - - +
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Residues in contact with HIS 81 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79D TYR* 2.7 58.0 + - + +
80D PRO* 1.3 68.0 - - - +
82D GLN* 1.3 90.4 + - + +
83D LEU 3.1 2.9 - - - -
84D MET* 4.2 4.3 - - - -
85D LYS* 2.9 35.7 + - + +
172D THR* 3.4 29.5 + - - -
173D ASP* 4.8 6.7 - - - -
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Residues in contact with GLN 82 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80D PRO* 3.3 2.1 - - + -
81D HIS* 1.3 95.6 + - + +
83D LEU* 1.3 58.0 + - + +
85D LYS* 4.7 18.6 + - - +
86D ARG* 4.0 20.5 + - - +
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Residues in contact with LEU 83 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54D VAL 6.0 2.7 - - - +
58D GLN* 4.8 0.9 - - + +
59D ASP* 3.6 51.8 - - + +
62D ASP* 4.4 20.9 - - + +
80D PRO* 3.5 9.4 + - + +
82D GLN* 1.3 77.5 - - + +
84D MET* 1.3 65.1 + - - +
85D LYS 3.2 1.6 - - - -
86D ARG* 3.1 32.2 - - - +
87D LEU* 2.9 30.9 - - + +
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Residues in contact with MET 84 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63D LEU* 4.9 8.3 - - + -
79D TYR* 2.9 36.8 - - + +
80D PRO* 2.9 28.8 + - + +
81D HIS* 4.2 2.2 - - - -
83D LEU* 1.3 74.7 - - - +
85D LYS* 1.3 55.0 + - - +
87D LEU* 2.6 37.5 + - + +
88D LEU* 2.7 31.6 + - + +
140D ILE* 4.6 21.3 - - + -
143D TYR* 3.6 37.2 - - + -
144D ILE* 4.7 8.3 - - + -
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Residues in contact with LYS 85 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81D HIS* 2.9 27.7 + - + +
82D GLN* 4.7 17.5 + - - +
84D MET* 1.3 77.7 - - - +
86D ARG* 1.3 65.9 + - - +
87D LEU 3.0 0.2 + - - -
88D LEU* 3.2 7.0 + - - +
89D ASN* 3.0 25.2 + - + +
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Residues in contact with ARG 86 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54D VAL* 3.2 48.5 + - - +
59D ASP* 3.8 11.0 + - - -
82D GLN* 4.0 21.7 + - - +
83D LEU* 3.1 35.0 + - - +
85D LYS* 1.3 81.3 - - - +
87D LEU* 1.3 61.2 + - + +
89D ASN* 3.9 5.6 - - - +
90D ARG* 2.9 55.9 + - - +
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Residues in contact with LEU 87 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59D ASP* 3.5 44.2 - - + +
63D LEU* 4.3 26.0 - - + -
83D LEU* 2.9 30.1 - - + +
84D MET* 2.6 27.3 + - + +
86D ARG* 1.3 73.4 - - + +
88D LEU* 1.3 51.9 + - - +
89D ASN 2.9 4.3 - - - -
90D ARG* 2.5 35.7 + - - +
91D ILE* 2.8 22.0 + - + +
136D LEU* 6.0 3.6 - - + -
140D ILE* 6.0 1.1 - - + -
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Residues in contact with LEU 88 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A ASP* 3.8 23.8 - - - +
146A LEU* 3.7 42.2 - - + +
147A VAL* 4.6 7.4 - - + -
79D TYR* 5.2 9.6 - - - +
84D MET* 2.7 24.7 + - + +
85D LYS* 4.0 4.9 - - - +
87D LEU* 1.3 71.0 - - - +
89D ASN* 1.3 58.9 + - + +
91D ILE* 3.1 29.9 - - + +
92D SER* 4.3 3.3 + - - -
140D ILE* 6.3 1.3 - - + -
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Residues in contact with ASN 89 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85D LYS* 3.0 16.8 + - + +
86D ARG* 4.0 6.1 - - - +
87D LEU 2.9 0.8 - - - -
88D LEU* 1.3 77.4 - - + +
90D ARG* 1.3 59.9 + - - +
91D ILE 3.1 1.8 - - - -
92D SER* 3.0 9.9 + - - -
93D MET* 3.0 53.0 + - - +
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Residues in contact with ARG 90 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55B THR* 5.1 18.8 - - + -
54D VAL* 4.6 6.9 + - - +
56D PRO* 3.2 32.6 + - - +
59D ASP* 2.3 31.7 + - - -
86D ARG* 2.9 45.8 + - - +
87D LEU* 2.5 19.9 + - - +
89D ASN* 1.3 72.1 - - - +
91D ILE* 1.3 61.2 + - + +
93D MET* 3.2 26.4 - - + +
94D GLN* 3.5 11.0 + - + +
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Residues in contact with ILE 91 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146A LEU* 5.4 1.1 - - + +
147A VAL* 3.0 33.9 - - + +
87D LEU* 2.8 17.6 + - + +
88D LEU* 3.1 31.0 - - + +
90D ARG* 1.3 78.6 - - + +
92D SER* 1.3 78.2 + - - +
94D GLN* 3.8 6.7 + - - +
95D SER* 2.9 29.5 + - - -
133D LEU* 4.4 10.6 - - + +
136D LEU* 4.3 24.7 - - + -
137D LYS* 4.8 12.3 - - + -
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Residues in contact with SER 92 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88D LEU 4.4 3.8 - - - -
89D ASN* 3.0 13.1 + - - -
91D ILE* 1.3 90.4 - - - +
93D MET* 1.3 68.4 + - - +
95D SER* 3.6 9.6 - - - -
96D GLN* 2.9 28.9 + - - +
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Residues in contact with MET 93 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89D ASN* 3.0 45.4 + - - +
90D ARG* 3.2 20.2 - - + +
92D SER* 1.3 81.0 - - - +
94D GLN* 1.3 60.3 + - + +
96D GLN* 3.2 4.2 + - - +
97D LEU* 3.0 23.0 + - - +
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Residues in contact with GLN 94 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53B ILE* 4.5 3.2 - - + +
54B THR* 2.7 29.0 + - - -
55B THR* 3.1 13.9 - - - +
90D ARG* 3.5 12.8 + - - +
91D ILE* 4.0 5.9 - - - +
93D MET* 1.3 75.7 - - + +
95D SER* 1.3 62.6 + - - +
96D GLN 3.1 1.3 - - - -
97D LEU* 3.5 16.8 - - + -
98D ILE* 2.9 36.7 + - + +
129D MET* 3.3 31.3 - - + +
132D GLU* 2.9 26.3 - - - +
133D LEU* 5.4 6.7 + - + +
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Residues in contact with SER 95 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91D ILE* 2.9 24.5 + - - -
92D SER* 3.6 12.6 - - - -
93D MET 3.2 0.4 - - - -
94D GLN* 1.3 78.4 - - - +
96D GLN* 1.3 57.9 + - - +
98D ILE* 3.2 24.7 - - - +
99D GLU* 4.2 6.4 + - - +
133D LEU* 3.8 22.8 - - - +
137D LYS* 5.3 4.6 + - - -
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Residues in contact with GLN 96 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92D SER* 2.9 20.0 + - - +
93D MET* 3.6 4.0 - - - +
95D SER* 1.3 77.4 - - - +
97D LEU* 1.3 62.9 + - - +
99D GLU* 3.3 16.0 + - - +
100D ASN* 2.9 26.0 + - - +
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Residues in contact with LEU 97 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B ILE* 5.1 19.5 - - + -
93D MET 3.0 9.4 + - - +
94D GLN* 3.3 19.2 + - + +
96D GLN* 1.3 75.5 - - - +
98D ILE* 1.3 60.2 + - + +
100D ASN* 2.8 31.4 + - - +
101D ILE* 3.0 19.3 + - + +
129D MET* 3.9 26.9 - - + -
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Residues in contact with ILE 98 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94D GLN* 2.9 31.6 + - + +
95D SER* 3.2 17.9 - - - +
97D LEU* 1.3 76.9 - - + +
99D GLU* 1.3 74.9 + - + +
101D ILE* 3.2 14.0 - - + +
102D SER* 2.8 31.0 + - - -
126D LEU 6.1 0.2 - - - +
129D MET* 3.5 47.3 - - + +
130D GLU* 5.3 13.2 - - + +
133D LEU* 5.8 4.9 - - + -
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Residues in contact with GLU 99 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95D SER 4.3 6.3 - - - +
96D GLN* 3.3 11.3 + - - +
97D LEU 3.1 0.6 - - - -
98D ILE* 1.3 89.2 - - + +
100D ASN* 1.3 61.8 + - - +
102D SER* 3.6 8.7 - - - -
103D MET* 2.9 48.5 + - + +
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Residues in contact with ASN 100 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96D GLN* 2.9 31.9 + - - +
97D LEU* 2.8 11.5 + - - +
99D GLU* 1.3 79.4 - - - +
101D ILE* 1.3 57.1 + - - +
103D MET* 4.5 1.6 - - - +
104D GLY* 2.8 24.9 + - - -
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Residues in contact with ILE 101 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B TRP* 3.9 35.4 - - + +
53B ILE* 5.6 4.3 - - + -
97D LEU* 3.0 13.5 + - + +
98D ILE* 3.2 26.2 - - + +
100D ASN* 1.3 77.6 - - - +
102D SER* 1.3 56.8 + - - +
104D GLY* 3.6 4.2 - - - +
105D PHE* 3.0 23.9 + - - +
126D LEU* 5.5 1.8 - - + +
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Residues in contact with SER 102 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98D ILE* 2.8 22.6 + - - -
99D GLU* 3.7 10.5 - - - -
100D ASN 3.2 0.2 - - - -
101D ILE* 1.3 77.3 - - - +
103D MET* 1.3 72.5 + - - +
104D GLY 3.1 0.9 - - - -
105D PHE* 3.1 23.8 + - - +
106D LEU* 3.2 13.3 - - - +
126D LEU* 4.6 21.3 - - - +
22E HIS* 5.5 1.9 + - - +
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Residues in contact with MET 103 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99D GLU* 2.9 37.5 + - + +
100D ASN* 4.5 1.8 - - - +
102D SER* 1.3 84.6 - - - +
104D GLY* 1.3 59.8 + - - +
105D PHE 3.1 1.6 - - - -
106D LEU* 3.0 50.3 + - + +
107D ASP* 3.0 17.9 - - - +
22E HIS 4.7 14.4 - - - +
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Residues in contact with GLY 104 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100D ASN 2.8 21.1 + - - -
101D ILE* 3.7 5.8 - - - -
102D SER 3.1 0.4 - - - -
103D MET* 1.3 77.1 - - - +
105D PHE* 1.3 53.7 + - - +
106D LEU 3.1 2.7 - - - -
107D ASP* 3.2 36.3 + - - +
108D MET* 4.0 4.0 + - - +
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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