Contacts of the strand formed by residues 119 - 134 (chain D) in PDB entry 2IVB
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 GLY 119 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A THR* 2.6 29.5 + - - +
81B ARG* 5.6 1.1 + - - -
124B ILE* 4.3 2.0 - - - -
112D VAL* 4.7 1.8 - - - +
113D HIS* 3.5 6.1 + - - -
117D GLY 3.5 2.1 + - - -
118D ASP* 1.3 82.6 + - - +
120D ILE* 1.3 61.3 + - - -
150D TYR* 4.3 4.0 - - - -
151D LEU 3.4 10.8 - - - -
153D THR* 3.6 17.5 - - - -
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Residues in contact with ILE 120 (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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92A PRO* 3.9 8.5 - - + +
93A THR* 3.8 28.0 - - - +
96A ARG* 3.4 30.5 - - + +
124B ILE* 3.4 36.3 - - + -
112D VAL* 4.9 1.3 - - - -
119D GLY* 1.3 81.0 - - - +
121D ILE* 1.3 64.4 + - - +
122D ALA* 4.1 7.0 - - - -
150D TYR* 3.4 7.8 - - - -
151D LEU* 2.9 46.7 + - + +
1160F AZI 3.5 23.8 - - - +
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Residues in contact with ILE 121 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A THR* 5.1 3.4 + - - +
96A ARG* 3.4 20.2 - - - +
97A PHE* 5.0 10.8 - - + -
142A ALA* 3.1 39.9 - - + -
144A ILE* 4.2 16.4 - - + -
112D VAL* 4.0 30.7 - - + +
116D PHE* 4.3 4.7 - - + -
120D ILE* 1.3 79.9 - - - +
122D ALA* 1.3 65.4 + - - +
123D ALA* 3.3 4.2 + - - -
126D PHE* 5.6 4.7 - - + -
148D GLY* 3.9 23.3 - - - -
149D LYS 3.7 0.7 - - - -
150D TYR* 3.8 24.0 - - + -
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Residues in contact with ALA 122 (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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151B LEU* 4.7 3.1 - - + -
120D ILE* 3.7 4.7 - - - -
121D ILE* 1.3 70.2 - - - +
123D ALA* 1.4 52.1 + - - +
124D ILE* 2.8 14.5 + - + -
125D ASN* 3.3 32.2 + - + +
126D PHE* 4.2 3.5 - - - -
148D GLY* 4.3 3.1 - - - -
149D LYS 2.9 13.7 + - - +
151D LEU* 2.9 39.3 - - + -
1160F AZI 3.5 13.5 - - - +
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Residues in contact with ALA 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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96A ARG* 3.5 37.6 - - + +
99A GLU* 3.5 24.3 - - + +
100A MET* 4.8 9.0 - - + +
103A VAL* 5.7 4.3 - - - +
104A TYR* 5.7 2.9 - - - -
121D ILE* 3.3 4.1 + - - -
122D ALA* 1.4 67.5 - - - +
124D ILE* 1.3 62.8 + - - +
126D PHE* 4.3 24.8 - - + +
1160F AZI 3.2 7.5 + - - -
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Residues in contact with ILE 124 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A GLU* 4.1 3.1 - - - +
119B GLY* 4.6 0.7 - - - -
120B ILE* 3.9 20.4 - - + -
151B LEU* 3.9 18.8 - - + +
152B PRO 3.6 17.5 - - - +
153B THR* 3.3 35.3 + - - +
154B LYS 5.6 0.3 + - - -
81D ARG* 6.1 4.0 - - - +
122D ALA* 2.8 1.5 + - + -
123D ALA* 1.3 83.3 - - - +
125D ASN* 1.3 62.5 + - - +
126D PHE* 2.8 17.1 + - - +
92F PRO* 3.9 28.7 - - + -
96F ARG* 3.9 18.4 - - - +
1160F AZI 3.9 7.9 - - - +
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Residues in contact with ASN 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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141A ARG* 3.2 21.6 + - - +
151B LEU* 6.0 9.3 - - + +
152B PRO 4.9 6.0 + - - +
122D ALA* 3.3 15.9 + - + +
124D ILE* 1.3 77.7 - - - +
126D PHE* 1.3 58.8 + - - +
147D ASP 3.2 0.6 - - - +
148D GLY* 3.1 25.6 - - - -
149D LYS* 3.8 33.7 - - + +
151D LEU* 5.9 1.7 - - + +
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Residues in contact with PHE 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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100A MET* 4.4 13.9 - - + -
104A TYR* 4.1 23.3 - + + +
141A ARG* 4.9 2.5 - - - -
154B LYS 5.1 2.4 - - - +
156B PHE* 3.6 19.8 - - + +
121D ILE* 5.6 4.5 - - + -
122D ALA 4.2 10.5 - - - -
123D ALA* 4.3 18.4 - - - +
124D ILE 2.8 16.5 + - - +
125D ASN* 1.3 84.4 + - - +
127D LYS* 1.3 73.6 + - - +
128D LEU* 3.8 15.5 - - + -
146D LEU* 3.4 50.7 - - + -
147D ASP 3.3 14.1 - - - -
148D GLY* 4.2 3.8 - - - -
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Residues in contact with LYS 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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141A ARG* 4.9 0.6 - - - +
156B PHE* 3.8 27.7 - - + -
126D PHE* 1.3 79.4 - - - +
128D LEU* 1.3 62.7 + - - +
129D ASP* 3.7 35.5 + - - +
145D THR* 3.4 6.8 - - - +
146D LEU* 3.8 0.2 - - - -
147D ASP* 3.0 58.3 + - + +
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Residues in contact with LEU 128 (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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100A MET* 4.8 2.9 - - - -
104A TYR* 3.2 66.9 - - + +
107A THR* 6.3 0.2 - - + -
108A LEU* 4.5 18.8 - - + -
156B PHE* 3.4 21.2 - - + -
39D ALA* 5.3 1.2 - - - +
41D ALA* 3.5 20.1 - - + +
126D PHE* 3.8 5.1 - - + -
127D LYS* 1.3 78.0 + - - +
129D ASP* 1.3 64.6 + - - +
130D VAL* 5.5 1.1 - - + -
144D ILE* 4.7 3.8 - - + -
145D THR 3.1 13.5 - - - +
146D LEU* 3.6 26.2 - - + -
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Residues in contact with ASP 129 (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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41D ALA* 5.0 3.4 - - - -
127D LYS* 3.7 24.8 + - - +
128D LEU* 1.3 76.4 - - - +
130D VAL* 1.3 65.8 + - - +
131D LYS* 4.0 20.3 - - - +
143D VAL 4.6 0.3 - - - +
144D ILE* 3.4 6.1 - - - +
145D THR* 3.0 52.2 + - - +
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Residues in contact with VAL 130 (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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108A LEU* 3.7 30.1 - - + -
111A LEU* 4.3 26.0 - - + +
112A VAL* 4.7 12.8 - - + -
115A LYS* 3.3 44.2 + - + +
116A PHE* 4.6 14.1 - - + -
40D GLU* 4.8 2.4 + - - +
41D ALA* 5.6 0.9 - - + -
128D LEU* 5.5 2.9 - - + -
129D ASP* 1.3 81.6 - - - +
131D LYS* 1.3 62.7 + - - +
132D LYS 4.2 0.2 - - - -
142D ALA* 4.9 1.6 - - + -
143D VAL 3.7 2.2 - - - -
144D ILE* 4.1 16.2 - - + -
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Residues in contact with LYS 131 (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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115A LYS* 5.3 0.4 - - - +
116A PHE* 4.6 1.6 - - - -
129D ASP* 4.0 13.0 - - - +
130D VAL* 1.3 74.4 - - - +
132D LYS* 1.3 69.1 + - - +
133D VAL* 3.8 21.4 + - + -
142D ALA* 3.3 5.5 - - - -
143D VAL* 2.7 53.8 + - + +
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Residues in contact with LYS 132 (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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115A LYS* 3.5 39.3 + - + +
116A PHE* 3.7 24.0 - - + -
130D VAL 4.2 1.4 + - - -
131D LYS* 1.3 79.2 - - - +
133D VAL* 1.3 70.3 + - - +
140D GLU* 3.1 33.0 - - + +
141D ARG 3.6 4.3 - - - -
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Residues in contact with VAL 133 (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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131D LYS* 4.0 24.7 - - + +
132D LYS* 1.3 80.2 - - - +
134D ALA* 1.3 75.4 + - + +
140D GLU* 3.4 7.4 - - - +
141D ARG* 2.8 42.7 + - + +
143D VAL* 3.8 28.9 - - + -
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Residues in contact with ALA 134 (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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133D VAL* 1.3 89.8 - - + +
135D ASP* 1.3 64.0 + - - +
136D PRO* 3.5 9.4 - - + +
139D GLY 3.9 5.6 - - - +
140D GLU* 4.7 2.5 - - - +
141D ARG* 4.7 2.1 - - - +
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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