Contacts of the strand formed by residues 112 - 127 (chain D) in PDB entry 5IXG
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 VAL 112 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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108D THR* 3.4 0.2 - - - -
109D LEU 2.9 30.0 + - - +
110D HIS* 3.7 11.7 - - - +
111D GLY* 1.3 81.7 - - - +
113D THR* 1.3 63.2 + - - +
114D LYS* 3.8 22.4 - - + -
148D ASP 3.6 20.4 - - - +
149D PHE* 3.3 28.3 - - + +
150D GLY* 4.8 1.3 - - - +
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Residues in contact with THR 113 (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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106D ASN* 3.8 28.0 - - + +
107D LEU 3.2 4.5 - - - +
108D THR* 2.7 32.8 + - - +
111D GLY 4.0 2.4 + - - -
112D VAL* 1.3 74.8 - - - +
114D LYS* 1.3 72.1 + - - +
115D PRO* 4.8 0.3 - - - +
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Residues in contact with LYS 114 (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 ASN* 3.7 4.9 - - - -
107D LEU* 2.9 32.0 + - - +
112D VAL* 3.8 12.6 - - + -
113D THR* 1.3 82.4 - - - +
115D PRO* 1.3 81.1 - - + +
148D ASP* 3.7 31.9 - - + +
149D PHE* 3.6 29.1 - - + -
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Residues in contact with PRO 115 (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 GLY 3.3 12.1 - - - +
106D ASN* 3.4 10.2 - - - +
113D THR 4.8 0.7 - - - +
114D LYS* 1.3 100.4 - - + +
116D LEU* 1.4 60.9 + - - +
144D PHE* 6.2 0.3 - - - +
149D PHE* 5.5 1.4 - - - -
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Residues in contact with LEU 116 (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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89D TYR* 2.9 40.1 + - + -
105D GLY 2.9 17.6 + - - +
107D LEU* 4.0 30.5 - - + -
114D LYS 3.6 0.2 + - - -
115D PRO* 1.4 75.9 - - - +
117D THR* 1.3 72.5 + - - +
118D LEU* 3.8 25.1 - - + -
142D GLY* 4.7 0.4 - - - -
143D GLU 3.7 32.3 - - - +
144D PHE* 4.6 10.3 - - + -
149D PHE* 5.9 1.6 - - + -
165D LEU* 3.9 17.0 - - + -
201D OTP 5.6 1.3 - - + -
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Residues in contact with THR 117 (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 SER* 4.1 14.4 - - - -
103D VAL 3.1 10.8 - - - +
104D VAL* 4.1 23.7 - - + +
116D LEU* 1.3 83.0 - - - +
118D LEU* 1.3 76.1 + - - +
119D LYS* 4.1 2.9 + - + +
141D VAL 4.1 0.3 - - - +
142D GLY* 3.9 9.0 - - - -
143D GLU 4.9 0.3 + - - -
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Residues in contact with LEU 118 (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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89D TYR* 3.6 37.7 - - + +
102D SER* 3.2 4.3 - - - -
103D VAL* 2.8 39.2 + - + +
116D LEU* 3.8 22.4 - - + -
117D THR* 1.3 80.6 - - - +
119D LYS* 1.3 60.2 + - - +
120D ILE* 4.4 0.2 - - - +
140D ALA* 4.4 4.7 - - + -
141D VAL 3.3 6.5 - - - +
142D GLY* 4.1 15.9 - - - +
165D LEU* 4.5 8.3 - - + -
167D ILE* 4.6 9.9 - - + -
201D OTP 4.0 41.7 - - + -
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Residues in contact with LYS 119 (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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143A GLU* 3.2 32.6 + - - +
162A LYS* 3.8 23.2 - - - +
164A LYS* 4.4 7.5 - - - +
101D VAL 3.8 9.6 - - - +
102D SER* 4.3 3.6 - - - -
117D THR* 4.0 4.2 - - + +
118D LEU* 1.3 72.5 - - - +
120D ILE* 1.3 66.1 + - - +
121D ASP* 3.0 27.0 + - - +
140D ALA* 3.2 4.4 - - - -
141D VAL* 2.8 52.8 + - + +
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Residues in contact with ILE 120 (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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93D ILE* 4.8 3.4 - - + -
100D PRO* 3.8 33.0 - - + +
101D VAL* 2.8 27.9 + - - +
102D SER* 3.8 28.3 - - - +
103D VAL* 4.1 14.6 - - + -
118D LEU 4.4 0.4 - - - +
119D LYS* 1.3 73.4 - - - +
121D ASP* 1.3 62.0 + - - +
122D SER* 3.3 29.2 - - - +
123D PHE* 4.1 8.1 - - + -
138D VAL* 4.4 10.1 - - + -
139D ASP 3.8 4.7 - - - +
140D ALA* 4.3 8.1 - - + -
201D OTP 4.7 11.2 - - + -
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Residues in contact with ASP 121 (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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162A LYS* 5.2 1.6 + - - -
119D LYS* 3.0 33.8 + - - +
120D ILE* 1.3 74.4 - - - +
122D SER* 1.3 62.3 + - - +
139D ASP* 2.8 22.4 + - + +
141D VAL* 3.7 27.2 - - - +
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Residues in contact with SER 122 (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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27C GLY 4.5 14.2 + - - -
28C LEU 5.2 1.0 + - - -
29C SER* 5.7 1.0 - - - -
30C VAL* 5.7 0.7 - - - +
120D ILE* 3.3 10.7 - - - +
121D ASP* 1.3 80.5 - - - +
123D PHE* 1.3 61.5 + - - +
137D GLY 4.3 0.4 + - - -
138D VAL* 3.2 7.1 - - - -
139D ASP* 3.1 40.9 + - - +
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Residues in contact with PHE 123 (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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44D LEU* 3.9 18.4 - - + -
46D ARG* 3.6 22.9 - - - -
99D LYS* 3.2 43.0 + - + +
100D PRO* 4.0 38.6 - - + +
120D ILE* 4.1 9.9 - - + -
122D SER* 1.3 76.7 - - - +
124D LYS* 1.3 65.6 + - - +
125D CYS* 3.5 24.9 - - - -
136D CYS* 4.3 2.2 - - + -
137D GLY 3.3 3.8 - - - -
138D VAL* 3.6 17.5 - - + -
201D OTP 3.8 24.9 - - + -
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Residues in contact with LYS 124 (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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25C PHE 2.9 24.5 + - - -
26C GLY* 3.0 13.2 + - - +
27C GLY 3.7 31.2 - - - +
28C LEU* 3.5 15.3 - - + +
123D PHE* 1.3 77.3 - - - +
125D CYS* 1.4 72.3 + - - +
126D MET* 3.9 22.2 - - - +
136D CYS* 3.2 2.6 - - - +
137D GLY 2.7 32.6 + - - -
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Residues in contact with CYS 125 (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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28C LEU* 4.8 0.2 - - - -
46D ARG* 3.4 28.2 - - - +
123D PHE* 3.5 12.6 - - - -
124D LYS* 1.4 78.7 - - - +
126D MET* 1.3 66.1 + - - +
134D GLU* 3.5 17.5 - - - +
135D VAL 3.2 5.8 - - - +
136D CYS* 2.1 46.4 - - - -
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Residues in contact with MET 126 (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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25C PHE* 3.6 38.8 - - + +
28C LEU* 4.1 21.1 - - + -
124D LYS* 3.9 28.9 - - - +
125D CYS* 1.3 78.3 - - - +
127D PRO* 1.4 86.4 - - + +
128D HIS* 3.4 0.6 + - - -
129D PRO* 4.2 7.0 - - + -
134D GLU* 3.5 6.4 - - - +
135D VAL* 2.9 42.1 + - + -
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Residues in contact with PRO 127 (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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126D MET* 1.4 98.3 - - + +
128D HIS* 1.3 66.1 + - - +
129D PRO* 3.5 8.3 - - - +
132D LYS* 6.0 2.7 - - - -
133D ARG 4.1 6.3 - - - +
134D GLU* 4.4 4.7 - - + -
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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