Contacts of the helix formed by residues 100 - 110 (chain D) in PDB entry 3UNF
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 100 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98D THR 5.3 2.2 - - - +
99D MET* 1.3 77.6 - - - +
101D VAL* 1.3 64.6 + - - +
102D GLU* 3.8 7.3 + - - +
103D SER* 2.7 33.6 + - - +
104D VAL* 3.1 23.7 + - - +
139D ASP* 3.4 17.9 - - + +
140D GLU* 3.2 27.4 - - - +
141D LYS* 5.5 8.1 - - - -
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Residues in contact with VAL 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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65D HIS* 5.1 0.9 - - + -
66D ILE* 4.5 24.2 - - + +
99D MET 4.0 0.2 + - - -
100D THR* 1.3 71.1 - - - +
102D GLU* 1.3 55.9 + - - +
104D VAL* 3.7 2.1 + - + +
105D THR* 2.7 34.1 + - - -
135D PHE* 4.0 30.1 - - + +
136D GLY 4.5 1.1 - - - -
137D GLY* 4.0 36.3 - - - +
138D VAL 4.3 1.1 - - - +
139D ASP* 3.0 22.9 + - + +
144D GLN* 3.7 15.9 - - + +
146D PHE* 4.3 10.3 - - + -
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Residues in contact with GLU 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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100D THR* 3.2 7.5 - - - +
101D VAL* 1.3 79.4 - - - +
103D SER* 1.3 57.9 + - - +
105D THR* 3.4 3.9 + - - -
106D GLN* 2.8 36.2 + - - +
139D ASP* 4.5 1.0 + - - -
141D LYS* 3.3 26.9 + - - +
144D GLN* 4.6 3.8 - - - +
146D PHE* 3.8 37.0 - - + -
154D PHE* 4.0 7.3 - - + -
58E LYS* 2.8 38.3 + - - +
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Residues in contact with SER 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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91D HIS* 6.3 0.2 - - - -
99D MET* 4.0 17.7 - - - +
100D THR* 2.7 27.3 + - - +
102D GLU* 1.3 75.9 - - - +
104D VAL* 1.3 60.7 + - - +
106D GLN* 3.5 14.4 + - - +
107D ALA* 2.8 29.8 + - - +
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Residues in contact with VAL 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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62D ILE* 4.5 14.6 - - + -
66D ILE* 3.6 27.8 - - + -
84D ALA* 4.6 9.4 - - + +
87D GLU* 6.4 0.2 - - + -
88D THR* 3.9 6.3 - - + -
99D MET* 3.6 33.4 - - + -
100D THR 3.1 18.4 + - - +
101D VAL* 3.9 4.5 - - + +
103D SER* 1.3 76.1 - - - +
105D THR* 1.3 61.8 + - - +
107D ALA* 3.3 5.1 + - - +
108D VAL* 3.2 22.9 + - - +
135D PHE* 4.2 24.2 - - + -
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Residues in contact with THR 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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101D VAL 2.7 22.3 + - - -
102D GLU 3.7 4.3 - - - -
104D VAL* 1.3 74.5 - - - +
106D GLN* 1.3 60.8 + - - +
108D VAL* 3.4 3.7 + - - +
109D SER* 3.0 30.9 + - - -
135D PHE* 3.5 44.3 - - + +
146D PHE* 3.7 18.2 - - + +
148D MET* 4.5 8.0 - - + +
154D PHE* 3.8 31.4 - - + -
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Residues in contact with GLN 106 (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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102D GLU* 2.8 27.3 + - - +
103D SER* 3.5 15.0 + - - +
104D VAL 3.3 0.2 - - - -
105D THR* 1.3 77.2 - - - +
107D ALA* 1.3 60.7 + - - +
109D SER* 3.3 5.0 + - - -
110D ASN* 2.9 39.9 + - - +
154D PHE* 3.8 30.2 - - + -
58E LYS* 4.8 6.6 + - - +
61E LEU* 6.0 1.6 - - - +
79E ARG* 4.4 13.1 - - - +
86E ARG* 5.5 4.9 + - - -
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Residues in contact with ALA 107 (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 LYS* 4.5 9.8 + - - +
84D ALA* 6.3 0.2 - - - -
87D GLU* 4.0 33.7 - - + +
99D MET* 5.1 3.1 - - + -
103D SER 2.8 17.2 + - - +
104D VAL* 3.5 9.0 - - - +
105D THR 3.3 0.2 - - - -
106D GLN* 1.3 77.4 - - - +
108D VAL* 1.3 62.5 + - + +
110D ASN* 3.3 24.5 + - - +
111D LEU* 4.1 7.6 + - - +
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Residues in contact with VAL 108 (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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80D LEU* 4.2 25.2 - - + +
83D LYS* 5.6 1.8 - - + -
84D ALA* 3.8 27.1 - - + +
104D VAL 3.2 14.9 + - - +
105D THR 3.8 5.8 - - - +
107D ALA* 1.3 76.2 - - + +
109D SER* 1.3 61.6 + - - +
110D ASN 3.3 0.9 + - - -
111D LEU* 3.3 24.1 + - + +
112D ALA* 4.1 2.4 + - - -
133D LEU* 4.2 14.8 - - + -
135D PHE* 3.7 20.0 - - + -
148D MET* 3.8 25.1 - - + +
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Residues in contact with SER 109 (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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105D THR 3.0 18.9 + - - -
106D GLN 3.5 7.2 - - - -
107D ALA 3.2 0.2 - - - -
108D VAL* 1.3 76.9 - - - +
110D ASN* 1.3 56.2 + - - +
111D LEU 3.3 0.2 - - - -
112D ALA* 3.0 27.5 - - - +
148D MET* 3.5 20.5 - - - +
152D GLY 3.0 23.5 + - - -
154D PHE* 3.3 15.7 - - - +
76E ALA* 5.0 0.3 - - - +
79E ARG* 2.9 23.9 + - - -
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Residues in contact with ASN 110 (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 LYS* 6.3 0.2 - - - +
106D GLN* 2.9 24.3 + - - +
107D ALA* 3.5 14.7 + - - +
108D VAL 3.2 1.4 - - - -
109D SER* 1.3 72.6 - - - +
111D LEU* 1.3 61.1 + - + +
112D ALA* 3.1 6.9 + - - +
113D LEU 5.0 0.5 + - - -
114D GLN* 3.4 20.1 + - - +
79E ARG* 3.0 23.1 + - - +
80E LEU* 5.6 2.6 - - - +
83E ASN* 4.9 13.7 + - - +
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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