Contacts of the helix formed by residues 102 - 111 (chain D) in PDB entry 2Q41
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 ASP 102 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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239A TRP* 3.4 30.7 - - + -
86D TYR* 4.4 5.1 - - + -
99D THR* 2.8 25.1 + - - +
100D GLU 3.3 0.2 - - - -
101D ARG* 1.3 77.3 - - + +
103D GLU* 1.3 61.0 + - - +
104D CYS* 3.0 9.0 + - - +
105D ALA* 3.6 13.5 + - - +
106D TYR* 4.4 3.6 + - - +
267D VAL* 3.6 15.7 - - + +
268D PRO* 4.0 4.1 - - + +
269D THR* 2.5 42.6 + - - -
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Residues in contact with GLU 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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98D LEU* 5.3 4.7 - - + -
99D THR 3.3 15.5 + - - +
100D GLU* 2.8 36.7 + - - +
101D ARG 3.7 0.2 - - - -
102D ASP* 1.3 76.5 - - - +
104D CYS* 1.3 60.9 + - + +
106D TYR* 4.8 2.4 - - - +
107D GLN* 2.8 55.9 + - - +
131D ASP* 3.2 19.6 - - - +
136D ARG* 5.4 7.7 + - - +
164D PHE* 4.7 0.9 - - - -
166D ASP* 4.6 6.9 - - - +
167D VAL* 3.8 21.4 - - + +
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Residues in contact with CYS 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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239A TRP* 4.2 21.3 - - - -
324A PHE* 5.2 3.1 - - - -
102D ASP* 3.0 2.6 - - - -
103D GLU* 1.3 82.9 - - + +
105D ALA* 1.3 70.8 + - - +
107D GLN* 4.6 1.6 - - - -
108D GLU* 2.7 49.1 + - - +
136D ARG* 5.7 6.7 - - - +
137D GLU* 6.0 0.9 - - - -
308D LYS* 3.7 52.0 - - + +
309D PHE* 4.2 7.9 - - - -
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Residues in contact with ALA 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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239A TRP* 3.8 23.3 - - + -
102D ASP 3.6 5.8 + - - +
103D GLU 3.6 0.6 - - - -
104D CYS* 1.3 85.3 - - - +
106D TYR* 1.3 66.4 + - - +
108D GLU 3.7 0.3 - - - -
109D MSE 3.0 27.9 + - - +
266D SER 3.5 25.4 - - - +
267D VAL* 4.0 5.8 - - + -
309D PHE* 4.0 18.6 - - + -
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Residues in contact with TYR 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 ASP 4.4 4.2 + - - +
103D GLU* 5.1 2.7 - - - +
105D ALA* 1.3 78.0 - - - +
107D GLN* 1.3 64.4 + - + +
109D MSE 3.1 4.9 + - - +
110D ILE* 2.7 62.5 + - + +
134D VAL* 5.3 1.1 - - + -
201D ASP* 2.7 35.0 + - - -
202D SER 4.3 3.5 + - - -
234D GLN* 3.6 17.7 + - + +
267D VAL* 4.0 12.0 - - + +
270D TYR* 3.5 46.0 - + + +
275D ILE* 3.8 13.9 - - + -
277D PHE* 3.4 30.1 - + - -
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Residues in contact with GLN 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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98D LEU* 4.7 9.1 - - - +
103D GLU* 2.8 45.7 + - - +
104D CYS* 3.5 2.1 + - - +
105D ALA 3.2 0.8 - - - -
106D TYR* 1.3 85.8 - - + +
108D GLU* 1.3 56.8 + - - +
109D MSE 3.0 8.4 + - - -
110D ILE* 4.2 5.4 - - - -
111D THR* 3.0 32.0 + - - +
131D ASP* 3.6 18.6 + - - +
133D GLY* 2.9 34.9 - - - +
134D VAL* 3.9 7.9 - - + +
136D ARG* 5.1 4.7 + - - -
137D GLU* 3.8 14.3 - - + +
167D VAL* 5.0 3.5 - - - +
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Residues in contact with GLU 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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104D CYS* 2.7 30.0 + - + +
105D ALA 3.7 2.0 - - - +
107D GLN* 1.3 70.6 - - - +
109D MSE 1.3 58.9 + - - +
112D HIS* 3.5 24.1 - - + +
137D GLU* 3.8 24.6 - - + +
140D ARG* 4.1 1.9 + - - -
306D PRO 4.3 0.7 - - - +
307D LEU* 2.8 38.2 - - + +
308D LYS* 2.8 7.8 + - - +
309D PHE* 2.4 36.6 + - + +
310D TYR* 3.2 37.0 + - + +
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Residues in contact with MSE 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 ALA 3.0 13.4 + - - +
106D TYR 3.2 5.2 - - - +
108D GLU* 1.3 89.3 - - - +
110D ILE* 1.3 67.1 + - - +
111D THR 3.3 1.6 - - - -
113D LEU* 3.1 54.0 + - + +
265D THR* 3.2 42.4 - - + -
277D PHE* 3.8 13.0 - - + -
309D PHE* 3.2 23.1 - - - -
310D TYR* 3.5 23.8 - - + -
314D ILE* 3.7 20.4 - - + +
318D ALA* 5.6 2.9 - - + -
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Residues in contact with ILE 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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106D TYR* 2.7 54.0 + - + +
107D GLN* 3.8 3.8 - - - +
109D MSE 1.3 75.8 - - - +
111D THR* 1.3 76.2 + - + +
114D PRO* 3.1 20.3 - - - +
134D VAL* 4.1 14.1 - - + -
199D ILE* 3.8 19.1 - - + +
200D VAL 4.2 6.3 - - - +
201D ASP* 3.8 21.3 - - - +
232D CYS* 3.5 12.9 - - - +
234D GLN 4.6 2.9 - - - +
277D PHE* 3.6 27.1 - - + -
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Residues in contact with THR 111 (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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107D GLN 3.0 20.7 + - - +
109D MSE 3.3 0.2 - - - -
110D ILE* 1.3 86.1 - - + +
112D HIS* 1.3 70.0 + - - +
114D PRO* 3.2 3.2 - - - +
115D LEU* 2.8 33.9 + - - +
134D VAL* 3.4 44.9 - - + +
137D GLU* 3.1 17.5 - - + +
138D VAL* 3.9 15.7 - - + -
199D ILE* 3.8 7.6 - - + +
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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