Contacts of the helix formed by residues 93 - 105 (chain D) in PDB entry 1U8R
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 93 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115C ARG* 4.6 4.9 - - - -
91D GLY 3.7 6.2 - - - +
92D LEU* 1.3 96.0 - - + +
94D TRP* 1.3 67.5 + - - +
95D GLU* 3.5 14.6 - - - +
96D GLU* 3.0 50.1 + - - +
97D VAL* 3.4 8.3 + - - +
185D LYS* 5.6 1.6 - - - +
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Residues in contact with TRP 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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87D VAL* 4.1 18.5 - - + +
92D LEU 3.6 2.1 + - - -
93D PRO* 1.3 66.0 - - - +
95D GLU* 1.3 65.5 + - - +
96D GLU 2.8 11.9 + - - -
97D VAL* 3.2 20.3 - - - +
98D HIS 4.4 0.2 + - - -
127D PRO* 2.9 48.1 + - + +
128D PHE* 3.3 39.3 - + - -
170D LEU* 3.9 17.7 - - + -
181D ILE* 4.2 15.9 - - + -
184D LEU* 5.6 0.4 - - + -
185D LYS* 3.9 37.9 - - + +
189D VAL 5.3 0.4 - - - -
190D VAL* 4.0 26.0 - - + -
191D PRO* 4.3 10.5 - - + -
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Residues in contact with GLU 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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93D PRO* 4.0 13.7 - - - +
94D TRP* 1.3 79.8 + - + +
96D GLU* 1.3 66.8 + - + +
98D HIS* 5.3 2.9 - - - -
128D PHE* 5.4 0.7 - - - -
178D ILE* 3.8 21.7 - - + +
181D ILE* 3.8 25.3 - - + +
182D THR* 3.5 32.7 - - + +
185D LYS* 3.1 32.7 + - + +
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Residues in contact with GLU 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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111C ASP* 3.5 22.2 - - - +
92D LEU* 3.7 17.5 - - + +
93D PRO* 3.0 36.5 - - + +
94D TRP 2.8 3.6 + - - -
95D GLU* 1.3 91.6 - - + +
97D VAL* 1.3 67.9 + - - +
98D HIS 3.3 2.6 + - - -
99D ALA* 3.4 11.6 + - - +
100D GLU* 3.4 19.1 + - - +
178D ILE* 5.4 5.4 - - + -
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Residues in contact with VAL 97 (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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83D GLU* 4.4 10.8 - - + +
86D LEU* 3.5 32.2 - - + +
87D VAL* 3.4 32.8 - - + -
92D LEU* 3.5 13.9 - - + +
93D PRO 3.5 11.9 - - - +
94D TRP 3.2 15.5 - - - +
96D GLU* 1.3 75.8 - - - +
98D HIS* 1.3 69.6 + - - +
100D GLU* 3.2 1.7 + - - +
101D ALA* 2.9 26.0 + - - +
127D PRO* 5.2 0.2 - - + -
128D PHE* 3.8 19.7 - - + -
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Residues in contact with HIS 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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13D ARG* 4.3 10.1 + - - -
79D HIS* 3.2 13.6 - + - -
83D GLU* 3.3 9.2 - - - +
94D TRP 4.4 0.8 + - - +
95D GLU 6.0 1.8 - - - -
96D GLU 3.3 1.7 - - - +
97D VAL* 1.3 82.9 - - - +
99D ALA* 1.3 63.2 + - + +
101D ALA 3.3 0.2 + - - -
102D CYS* 2.9 37.5 + - + +
128D PHE* 4.7 5.6 - - + -
172D GLU* 2.9 27.4 + - + -
175D GLN* 2.4 49.9 + - + +
176D GLY* 4.1 7.3 + - - -
4001D CO 2.1 24.1 + - - -
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Residues in contact with ALA 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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96D GLU* 3.4 12.4 + - - +
97D VAL 3.3 0.4 - - - -
98D HIS* 1.3 86.7 - - + +
100D GLU* 1.3 63.0 + - - +
102D CYS* 3.5 16.3 + - - +
103D ARG* 3.3 20.8 + - - +
178D ILE* 6.2 4.5 - - + -
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Residues in contact with GLU 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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107C VAL 3.6 0.7 - - - +
109C SER* 2.8 35.6 + - - -
112C VAL* 3.4 25.5 - - + +
86D LEU* 3.9 13.0 - - + -
92D LEU* 4.2 6.0 - - + +
96D GLU 3.4 9.9 + - - +
97D VAL 3.2 7.4 + - - +
98D HIS 3.2 0.4 - - - -
99D ALA* 1.3 76.9 - - - +
101D ALA* 1.3 65.3 + - - +
103D ARG* 2.9 36.2 + - - +
104D TRP* 2.6 51.7 + - + +
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Residues in contact with ALA 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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79D HIS* 3.5 34.5 - - + +
82D ALA* 3.9 10.1 - - + -
83D GLU* 3.6 11.9 - - + +
86D LEU* 4.0 3.5 - - + +
97D VAL 2.9 16.4 + - - +
100D GLU* 1.3 72.4 - - - +
102D CYS* 1.3 57.5 + - - +
103D ARG 2.9 5.8 - - - -
104D TRP* 4.0 9.4 - - - -
105D GLU* 2.8 33.6 + - - +
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Residues in contact with CYS 102 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4D LEU 4.7 0.3 - - - +
10D MET* 3.9 9.9 - - - -
13D ARG* 3.5 21.8 - - - +
79D HIS* 3.8 2.9 + - + -
98D HIS* 2.9 27.5 + - - +
99D ALA* 3.6 12.6 - - - +
100D GLU 3.1 0.6 - - - -
101D ALA* 1.3 75.7 - - - +
103D ARG* 1.3 55.1 + - + +
105D GLU* 2.7 10.3 - - - +
106D HIS* 2.8 8.5 + - - -
4002D CO 1.9 47.9 + - - -
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Residues in contact with ARG 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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106C HIS 5.4 0.7 - - - -
107C VAL* 3.0 47.3 + - + +
109C SER* 3.9 10.9 - - - +
1D MET* 5.8 2.5 - - - -
3D GLU 5.2 4.7 - - - +
5D VAL* 3.9 18.5 - - + +
99D ALA* 3.3 20.8 + - - +
100D GLU* 2.9 42.5 + - - +
101D ALA 2.9 0.2 - - - -
102D CYS* 1.3 81.4 - - + +
104D TRP* 1.3 65.2 + - - +
105D GLU 3.2 1.1 - - - -
106D HIS* 3.2 22.1 + - - +
107D VAL* 4.1 5.0 - - - +
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Residues in contact with TRP 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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85C LEU* 4.9 8.7 - - + -
104C TRP* 3.3 46.2 - + - -
107C VAL* 4.0 21.3 + - + +
108C MET* 4.2 16.9 - - + +
112C VAL* 4.0 20.6 - - + -
116C LEU* 5.7 0.2 - - + -
82D ALA* 4.4 20.0 - - + -
85D LEU* 4.3 15.5 - - + -
86D LEU* 4.0 20.2 - - + -
90D ILE* 5.1 2.2 - - + -
100D GLU* 2.6 55.1 + - + +
101D ALA* 3.9 8.1 - - - +
103D ARG* 1.3 74.7 - - - +
105D GLU* 1.3 58.7 + - - +
106D HIS 2.8 12.2 + - - -
107D VAL* 2.9 21.3 + - + +
108D MET* 3.2 24.1 + - + +
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Residues in contact with GLU 105 (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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9D GLU* 3.9 6.4 - - - +
10D MET* 3.1 1.9 - - - +
13D ARG* 2.7 35.7 + - - -
75D VAL* 3.6 17.0 - - + +
78D LYS* 3.5 33.9 - - - +
79D HIS* 3.0 36.3 + - + +
82D ALA* 5.5 0.2 - - - +
101D ALA 2.8 11.0 + - - +
102D CYS* 2.7 8.8 - - - +
103D ARG 3.2 0.2 - - - -
104D TRP* 1.3 76.0 - - - +
106D HIS* 1.3 79.2 + - + +
107D VAL 3.5 0.2 - - - -
4002D CO 2.2 29.5 + - - -
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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