Contacts of the helix formed by residues 128 - 139 (chain A) in PDB entry 4Y6O
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 PRO 128 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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124A PHE* 3.1 34.3 - - + +
125A LYS 4.6 2.7 - - - +
126A LYS 3.6 7.2 - - - +
127A HIS* 1.4 88.4 - - - +
129A GLU* 1.3 77.1 + - - +
130A PRO 3.4 0.7 - - - -
131A PHE* 3.3 7.5 + - - +
132A PHE* 3.2 29.8 + - + -
218A THR* 3.7 21.5 - - + -
227A LEU* 3.8 21.1 - - + -
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Residues in contact with GLU 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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110A TYR* 4.1 19.2 + - + +
126A LYS 5.3 0.7 - - - +
127A HIS* 3.4 12.6 + - - +
128A PRO* 1.3 95.5 - - - +
130A PRO* 1.4 72.2 - - + +
132A PHE* 3.2 6.3 + - - +
133A ALA* 2.9 25.1 + - - +
218A THR* 3.8 22.2 + - - +
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Residues in contact with PRO 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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107A LEU* 3.5 5.6 - - + +
110A TYR* 3.6 43.7 - - + -
112A LEU* 3.8 19.5 - - + -
118A ILE* 3.5 25.2 - - + +
123A TYR* 4.3 9.4 - - + +
127A HIS* 3.4 19.5 - - + +
128A PRO 3.6 0.2 - - - -
129A GLU* 1.4 96.2 - - + +
131A PHE* 1.3 61.1 + - - +
133A ALA 3.3 0.3 + - - -
134A LEU 3.0 18.9 + - - -
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Residues in contact with PHE 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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118A ILE* 3.7 30.6 - - - +
119A PHE* 4.0 8.5 - + - -
124A PHE* 3.6 28.9 - + + -
127A HIS 5.1 0.8 + - - +
128A PRO 3.3 9.7 + - - +
130A PRO* 1.3 77.9 - - - +
132A PHE* 1.3 83.5 + + - +
134A LEU* 3.3 5.4 + - + +
135A ALA* 2.9 25.3 + - + +
190A PHE* 4.1 19.7 - + - -
230A PRO* 4.3 12.3 - - + -
232A ILE* 3.8 20.2 - - + -
234A PHE* 3.7 24.0 - + - -
10C MYK 3.9 24.9 - - + +
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Residues in contact with PHE 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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124A PHE* 3.7 29.8 - + - -
128A PRO* 3.2 30.8 + - + +
129A GLU* 3.2 7.8 + - - +
131A PHE* 1.3 91.8 - + - +
133A ALA* 1.3 58.3 + - - +
135A ALA* 3.4 3.8 + - - +
136A LYS* 3.1 27.0 + - - +
209A MET* 3.7 22.4 - - - -
213A ILE* 3.9 30.8 - - + +
217A VAL 6.4 0.2 - - - -
218A THR* 4.4 7.2 - - + +
219A PRO* 3.6 26.2 - - + -
227A LEU* 4.2 2.9 - - + -
228A VAL 3.6 22.7 - - - -
230A PRO* 3.9 7.0 - - + -
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Residues in contact with ALA 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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107A LEU* 4.2 6.5 - - + -
110A TYR* 3.4 29.4 - - + +
129A GLU 2.9 16.4 + - - +
130A PRO 3.5 5.4 - - - +
132A PHE* 1.3 75.6 - - - +
134A LEU* 1.3 62.0 + - - +
136A LYS* 3.4 9.7 + - - +
137A GLU* 3.2 20.6 + - - +
216A GLU* 6.4 1.8 - - - -
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Residues in contact with LEU 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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96A PHE* 5.3 0.4 - - + -
107A LEU* 3.9 26.6 - - + +
118A ILE* 4.2 12.8 - - + -
119A PHE* 3.6 35.9 - - + -
130A PRO 3.0 13.3 + - - +
131A PHE* 3.3 8.5 + - + +
133A ALA* 1.3 73.0 - - - +
135A ALA* 1.3 66.5 + - - +
137A GLU* 3.1 9.7 + - + +
138A LEU* 3.0 56.6 + - + +
10C MYK 4.9 5.4 - - + -
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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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131A PHE* 2.9 18.5 + - + +
132A PHE* 3.5 12.3 - - - +
133A ALA 3.3 0.2 - - - -
134A LEU* 1.3 75.3 - - - +
136A LYS* 1.3 55.5 + - - +
138A LEU 3.8 0.2 - - - -
139A TYR* 3.0 34.7 + - - +
190A PHE* 4.2 6.3 - - + -
213A ILE* 3.9 26.0 - - + -
10C MYK 4.0 27.7 - - + +
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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 PHE 3.1 11.0 + - - +
133A ALA* 3.5 11.2 - - - +
134A LEU 3.2 0.2 - - - -
135A ALA* 1.3 75.9 - - - +
137A GLU* 1.3 64.4 + - - +
138A LEU 3.4 0.2 + - - -
139A TYR* 3.7 12.3 + - - +
213A ILE* 3.4 30.9 - - + +
214A PHE* 2.9 51.6 + - + +
216A GLU* 2.8 35.6 + - + +
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Residues in contact with GLU 137 (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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106A ASN* 4.7 26.4 - - + +
133A ALA 3.2 9.8 + - - +
134A LEU* 3.1 16.4 + - + +
136A LYS* 1.3 80.1 - - - +
138A LEU* 1.3 70.7 + - + +
139A TYR 3.5 2.3 + - - +
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Residues in contact with LEU 138 (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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92A GLY 4.6 8.0 - - - +
93A ILE* 5.2 2.6 - - + +
94A PRO* 3.8 32.1 - - + +
96A PHE* 3.7 31.4 - - + -
134A LEU* 3.0 44.9 + - + +
135A ALA 3.8 0.4 - - - -
137A GLU* 1.3 88.5 - - + +
139A TYR* 1.3 66.7 + - - +
140A PRO* 3.2 8.0 - - - +
10C MYK 4.4 15.7 - - + +
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Residues in contact with TYR 139 (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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135A ALA 3.0 19.0 + - - +
136A LYS 3.7 3.3 + - - +
137A GLU 3.5 4.1 - - - +
138A LEU* 1.3 75.6 - - - +
140A PRO* 1.4 95.3 - - + +
141A GLY 3.9 0.3 + - - -
143A PHE* 3.9 20.1 - + - -
190A PHE* 4.3 22.2 - + - -
206A LEU* 3.4 35.0 - - + +
210A LYS* 3.7 39.9 - - + +
213A ILE* 4.8 8.3 - - + -
214A PHE* 3.7 37.6 - + + -
10C MYK 4.4 15.9 - - + -
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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