Contacts of the helix formed by residues 121 - 137 (chain A) in PDB entry 4I6J
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 GLU 121 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A LYS* 3.0 28.4 + - - +
119A ASP* 2.8 21.2 + - - +
120A SER* 1.3 80.7 - - - +
122A PRO* 1.3 75.6 - - + +
123A PHE* 3.5 1.3 - - + +
124A GLY* 3.2 5.5 + - - +
125A LYS* 2.8 22.2 + - - +
315A TYR* 3.4 16.5 - - + -
319A THR* 5.0 0.4 - - - +
407A ASP* 3.8 3.5 - - - +
408A PHE* 3.6 29.0 + - + +
409A SER* 2.8 35.1 + - - +
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Residues in contact with PRO 122 (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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120A SER 3.5 3.3 - - - +
121A GLU* 1.3 84.6 - - + +
123A PHE* 1.3 65.7 + - - +
125A LYS* 2.9 14.1 + - + +
126A GLU* 3.1 13.3 + - - +
318A ALA* 3.2 30.1 - - + +
319A THR 3.8 11.0 - - - +
321A ASN 3.6 15.9 - - - +
322A PRO* 3.5 30.7 - - + +
408A PHE* 3.7 22.2 - - + -
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Residues in contact with PHE 123 (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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121A GLU* 3.5 1.6 - - + +
122A PRO* 1.3 78.9 - - - +
124A GLY* 1.3 68.9 + - - +
126A GLU* 3.3 14.2 + - - +
127A ARG* 2.9 59.8 + - + +
408A PHE* 5.8 6.9 - - + -
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Residues in contact with GLY 124 (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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119A ASP* 3.4 26.4 + - - -
121A GLU* 3.2 8.2 + - - +
123A PHE* 1.3 87.9 - - - +
125A LYS* 1.3 62.9 + - - +
127A ARG* 3.3 14.9 - - - +
128A ASP* 2.8 27.6 + - - -
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Residues in contact with LYS 125 (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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118A TYR* 3.4 22.0 - - + +
119A ASP 3.5 17.8 + - - +
120A SER 3.4 4.0 - - - -
121A GLU 2.8 12.7 + - - +
122A PRO* 2.9 11.4 + - + +
124A GLY* 1.3 71.2 - - - +
126A GLU* 1.3 58.3 + - - +
128A ASP* 3.1 8.9 + - - +
129A ALA* 2.8 28.1 + - - +
154A ASP* 5.6 2.2 + - - -
319A THR* 2.6 47.9 + - - -
320A ASN* 3.1 18.4 + - - +
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Residues in contact with GLU 126 (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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122A PRO 3.1 8.3 + - - +
123A PHE* 3.6 17.2 - - + +
125A LYS* 1.3 76.3 - - - +
127A ARG* 1.3 67.1 + - - +
129A ALA* 2.9 20.5 + - + +
130A ALA* 3.1 13.0 + - - +
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Residues in contact with ARG 127 (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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26A TRP* 4.0 21.1 - - - -
28A ARG* 3.4 30.6 - - - +
98A PRO* 4.7 13.5 - - + +
119A ASP* 3.2 25.3 + - - -
123A PHE* 2.9 44.3 + - + +
124A GLY* 3.3 15.5 + - - +
126A GLU* 1.3 77.2 + - - +
128A ASP* 1.3 86.4 + - - +
130A ALA* 3.4 6.7 + - - +
131A ILE* 3.1 37.5 + - + +
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Residues in contact with ASP 128 (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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26A TRP* 4.2 2.5 - - - -
28A ARG* 2.7 35.8 + - - -
116A PHE* 3.3 21.0 - - + -
118A TYR* 5.7 2.1 - - + -
119A ASP* 4.2 7.6 + - - +
124A GLY 2.8 17.9 + - - +
125A LYS* 3.5 7.0 - - - +
127A ARG* 1.3 108.6 + - - +
129A ALA* 1.3 66.4 + - - +
131A ILE* 3.8 5.7 - - - +
132A MET* 2.9 32.5 + - - +
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Residues in contact with ALA 129 (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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125A LYS 2.8 12.8 + - - +
126A GLU* 2.9 13.4 + - + +
128A ASP* 1.3 76.3 - - - +
130A ALA* 1.3 64.5 + - - +
132A MET* 2.9 24.3 + - - +
133A LYS* 3.0 13.4 + - - +
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Residues in contact with ALA 130 (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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126A GLU 3.1 7.5 + - - +
127A ARG* 3.7 9.6 - - - +
129A ALA* 1.3 79.2 - - - +
131A ILE* 1.3 65.7 + - + +
132A MET 3.2 0.2 + - - -
133A LYS* 3.2 11.3 + - - +
134A MET* 2.9 27.3 + - - +
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Residues in contact with ILE 131 (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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26A TRP* 4.4 13.5 - - + -
98A PRO* 3.8 13.5 - - + +
99A ALA* 3.6 36.3 - - + +
102A PHE* 4.3 7.9 - - + -
114A LEU* 4.0 25.8 - - + -
116A PHE* 4.9 5.4 - - + -
127A ARG* 3.1 34.4 + - + +
128A ASP* 3.8 8.1 - - - +
129A ALA 3.2 0.2 - - - -
130A ALA* 1.3 77.3 - - + +
132A MET* 1.3 62.6 + - + +
134A MET* 3.7 19.0 + - + +
135A ALA* 3.3 19.2 + - - +
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Residues in contact with MET 132 (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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116A PHE* 4.8 7.4 - - + -
128A ASP* 2.9 33.0 + - - +
129A ALA* 2.9 16.6 + - - +
131A ILE* 1.3 74.5 - - + +
133A LYS* 1.3 60.8 - - - +
135A ALA* 3.6 5.8 - - - +
136A LYS* 3.0 28.9 + - - +
142A VAL* 3.6 39.9 - - + +
144A THR* 4.6 10.1 - - + -
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Residues in contact with LYS 133 (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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129A ALA 3.0 10.9 + - - +
130A ALA* 3.5 13.0 - - - +
132A MET* 1.3 73.0 - - - +
134A MET* 1.3 59.3 + - - +
135A ALA 2.9 10.3 + - - -
136A LYS* 3.2 11.1 + - + +
137A GLU* 3.1 50.4 + - + +
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Residues in contact with MET 134 (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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99A ALA* 4.3 9.6 - - - -
100A ASP 4.8 0.4 - - - -
102A PHE* 3.5 19.7 - - + -
103A PRO* 3.9 27.6 - - + -
106A PHE* 3.4 29.5 - - + -
130A ALA 2.9 17.3 + - - +
131A ILE* 3.7 28.7 - - + +
133A LYS* 1.3 76.6 - - + +
135A ALA* 1.3 56.6 + - - +
137A GLU* 4.2 16.1 - - - +
138A ALA* 3.6 16.6 - - - +
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Residues in contact with ALA 135 (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 PHE* 4.3 16.4 - - + -
114A LEU* 5.1 2.7 - - + -
131A ILE 3.3 15.6 + - - +
132A MET* 3.2 8.5 + - - +
133A LYS 2.9 1.2 - - - -
134A MET* 1.3 79.0 - - - +
136A LYS* 1.3 69.8 + - - +
138A ALA* 3.3 2.9 + - - -
139A GLY 3.1 4.2 + - - -
140A VAL* 2.9 42.4 + - + +
142A VAL* 4.2 13.0 - - + -
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Residues in contact with LYS 136 (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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132A MET 3.0 16.1 + - - +
133A LYS* 3.5 9.2 - - + +
135A ALA* 1.3 73.0 - - - +
137A GLU* 1.3 59.9 + - + +
138A ALA 2.5 15.9 + - - -
139A GLY* 2.7 15.1 + - - -
140A VAL 3.9 6.8 + - - -
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Residues in contact with GLU 137 (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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133A LYS* 3.1 44.3 + - + +
134A MET* 4.2 13.7 - - - +
135A ALA 4.3 0.7 - - - -
136A LYS* 1.3 77.5 - - + +
138A ALA* 1.3 64.5 + - - +
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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