Contacts of the helix formed by residues 102 - 116 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86A TYR* 4.3 2.8 - - + -
99A THR* 3.6 10.9 + - - +
101A ARG* 1.3 77.2 - - + +
103A GLU* 1.3 68.6 + - - +
104A CYS* 3.0 4.0 - - - +
105A ALA* 3.0 18.5 + - - +
106A TYR 3.9 2.1 + - - -
267A VAL* 3.9 13.8 - - + +
268A PRO* 3.5 9.0 - - + +
269A THR* 2.6 53.4 + - - +
239D TRP* 3.4 32.5 - - + -
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Residues in contact with GLU 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A LEU* 4.7 12.0 - - + +
99A THR 2.8 19.1 + - - +
100A GLU* 3.4 34.1 + - - +
102A ASP* 1.3 78.3 - - - +
104A CYS* 1.3 58.8 + - + +
106A TYR* 3.2 6.6 + - - +
107A GLN* 2.6 70.6 + - - +
131A ASP* 4.4 0.5 - - - +
136A ARG* 4.3 13.2 + - - +
166A ASP* 5.7 1.7 - - - +
167A VAL* 3.5 24.4 - - - +
267A VAL* 6.1 0.2 - - - -
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Residues in contact with CYS 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A GLU 4.9 0.4 + - - +
101A ARG 4.5 8.1 - - - -
102A ASP 3.0 2.7 - - - -
103A GLU* 1.3 85.2 - - + +
105A ALA* 1.3 59.0 + - - +
107A GLN* 4.5 6.5 - - - -
108A GLU* 2.9 55.0 + - - +
136A ARG* 5.6 3.4 - - - +
137A GLU* 5.6 0.4 - - - -
308A LYS* 3.6 26.2 - - + -
309A PHE* 3.9 11.3 - - - +
239D TRP* 4.2 18.4 - - - -
324D PHE* 4.8 4.5 - - - -
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Residues in contact with ALA 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A ASP 3.0 12.3 + - - +
104A CYS* 1.3 82.0 - - - +
106A TYR* 1.3 56.6 + - - +
109A MSE 2.8 35.3 + - - +
265A THR* 4.4 1.0 - - - +
266A SER 3.3 26.2 - - - +
267A VAL* 3.7 7.0 - - + -
309A PHE* 3.4 25.6 - - + -
239D TRP* 3.8 12.1 - - + -
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Residues in contact with TYR 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A GLN 5.6 1.3 - - - -
98A LEU* 6.3 0.9 - - + -
102A ASP 3.9 1.6 + - - +
103A GLU* 3.2 9.0 + - - +
105A ALA* 1.3 77.8 - - - +
107A GLN* 1.3 65.5 + - + +
109A MSE 3.1 2.7 + - - -
110A ILE* 2.8 50.6 + - + +
134A VAL* 5.1 3.4 - - + -
201A ASP* 3.0 28.1 + - - -
202A SER 4.1 0.3 + - - -
234A GLN* 2.8 38.2 + - - +
267A VAL* 4.0 6.4 - - + +
270A TYR* 3.4 47.6 - + + +
275A ILE* 4.1 19.1 - - + -
277A PHE* 3.7 25.6 - + - -
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Residues in contact with GLN 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A LEU* 5.3 2.0 - - - +
103A GLU* 2.6 58.6 + - - +
104A CYS* 4.4 1.6 - - - +
106A TYR* 1.3 78.9 - - + +
108A GLU* 1.3 63.1 + - - +
109A MSE 3.1 0.2 + - - -
110A ILE* 3.6 0.3 - - - +
111A THR* 3.1 26.9 + - - -
131A ASP* 3.1 17.3 + - - +
133A GLY* 3.3 12.7 - - - -
134A VAL* 3.7 28.5 - - + +
136A ARG* 2.6 29.3 + - - -
137A GLU* 2.7 24.8 - - + +
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Residues in contact with GLU 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104A CYS* 2.9 23.8 + - - +
107A GLN* 1.3 78.1 - - - +
109A MSE 1.3 57.2 + - - +
112A HIS* 2.9 53.2 + - + +
113A LEU 4.1 0.3 + - - -
137A GLU* 3.5 19.3 - - - +
140A ARG* 4.6 6.4 + - - +
307A LEU* 3.9 7.9 - - + +
308A LYS* 2.8 36.4 + - - +
309A PHE 2.6 27.6 + - - +
310A TYR* 3.0 23.6 + - + +
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Residues in contact with MSE 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A ALA 2.8 28.1 + - - +
106A TYR* 3.1 3.5 + - - +
107A GLN 3.1 0.6 - - - -
108A GLU* 1.3 76.7 - - - +
110A ILE* 1.3 56.1 + - - +
111A THR 2.8 13.9 + - - -
113A LEU* 3.1 58.3 + - + +
265A THR* 3.4 33.4 - - + +
277A PHE* 3.4 23.6 - - + -
309A PHE* 3.3 32.1 - - + +
310A TYR* 4.5 6.3 - - + -
314A ILE* 3.9 17.9 - - + -
318A ALA* 5.0 3.6 - - - -
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Residues in contact with ILE 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A TYR* 2.8 49.7 + - + +
107A GLN 3.6 6.1 - - - +
109A MSE 1.3 73.9 - - - +
111A THR* 1.3 68.7 + - - +
114A PRO* 3.5 14.5 - - - +
134A VAL* 4.0 22.2 - - + -
199A ILE* 3.8 15.5 - - + +
200A VAL 3.7 23.1 - - - +
201A ASP* 3.9 12.1 - - - +
232A CYS* 3.6 17.4 - - - +
234A GLN 4.5 1.6 - - - +
277A PHE* 3.4 29.8 - - + -
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Residues in contact with THR 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107A GLN 3.1 17.4 + - - -
108A GLU 4.2 0.4 - - - -
109A MSE 2.8 2.6 + - - -
110A ILE* 1.3 79.3 - - - +
112A HIS* 1.3 67.7 + - - +
113A LEU 3.4 0.2 - - - -
114A PRO* 3.0 18.5 - - - +
115A LEU* 3.1 40.9 + - + +
134A VAL* 3.1 31.7 + - - +
137A GLU* 3.6 20.9 - - + +
138A VAL* 3.9 11.8 - - + +
199A ILE* 4.1 5.3 - - + +
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Residues in contact with HIS 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A GLU* 2.9 48.8 + - + +
111A THR* 1.3 73.7 - - + +
113A LEU* 1.3 65.1 + - - +
115A LEU* 3.8 4.3 - - - -
116A CYS* 2.9 33.2 + - - +
137A GLU* 3.1 41.0 + - + +
140A ARG* 3.5 19.4 + - - -
141A HIS* 3.1 20.4 + - - -
296A ILE* 3.1 23.6 - - + +
307A LEU* 4.8 1.7 - - + +
310A TYR* 3.7 24.2 + + + -
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Residues in contact with LEU 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A GLU 4.1 0.2 + - - -
109A MSE 3.1 48.6 + - + +
112A HIS* 1.3 78.4 - - - +
114A PRO* 1.3 68.9 - - + +
117A SER* 2.7 22.5 + - - -
232A CYS* 5.1 1.1 - - - -
263A ALA* 4.2 19.3 - - + -
264A TRP 6.3 0.2 - - - -
265A THR* 6.0 0.2 - - - -
277A PHE* 4.1 16.2 - - + -
279A LEU* 4.4 15.7 - - + -
289A PHE* 4.5 1.0 - - - -
310A TYR* 4.3 2.7 - - + -
315A HIS* 3.2 53.4 + - + +
318A ALA* 4.5 5.6 - - + -
319A PHE* 4.7 3.8 - - + -
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Residues in contact with PRO 114 (chain A).
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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110A ILE 3.5 13.7 - - - +
111A THR 3.0 24.0 - - - +
113A LEU* 1.3 90.2 - - + +
115A LEU* 1.3 64.8 + - + +
117A SER* 2.9 19.6 + - - +
118A ILE* 3.8 9.9 + - - +
197A ALA* 5.6 0.9 - - + -
199A ILE* 4.5 10.3 - - + -
230A VAL* 3.9 24.9 - - + +
232A CYS* 3.4 26.2 - - + +
279A LEU* 3.6 17.9 - - + -
289A PHE* 4.3 3.1 - - + -
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Residues in contact with LEU 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A THR* 3.1 36.6 + - + +
112A HIS* 4.2 1.3 - - - -
114A PRO* 1.3 79.2 - - + +
116A CYS* 1.3 58.4 + - - +
117A SER 3.3 0.2 - - - -
118A ILE* 3.4 24.3 - - + +
121A PRO* 4.3 20.5 - - + +
124A VAL* 4.3 10.5 - - + -
138A VAL* 4.1 21.1 - - + -
141A HIS* 3.5 42.8 + - + +
144A ILE* 5.1 0.7 - - + -
197A ALA* 4.0 26.2 - - + -
199A ILE* 4.2 12.1 - - + -
294A ASN* 5.7 1.4 + - - -
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Residues in contact with CYS 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A HIS* 2.9 23.1 + - - +
115A LEU* 1.3 74.9 - - - +
117A SER* 1.3 58.8 + - - +
118A ILE 3.3 5.4 - - - -
141A HIS* 3.9 9.4 - - - -
292A PRO* 3.3 10.0 - - + +
293A LEU 2.8 24.3 + - - -
294A ASN* 3.2 27.0 + - - +
296A ILE* 3.5 38.6 - - - -
310A TYR* 3.6 20.0 - - - +
315A HIS* 4.4 0.2 - - - +
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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