Contacts of the helix formed by residues 118 - 127 (chain A) in PDB entry 1AYU
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 118 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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116A GLY 3.2 7.0 + - - +
117A ASN* 1.3 68.6 - - - +
119A LYS* 1.3 65.6 + - - +
121A LEU* 3.4 8.3 - - - +
122A LYS* 2.9 26.2 + - - +
178A TRP* 2.8 40.4 + - + -
197A ALA 4.2 0.7 - - - +
198A ARG* 3.6 1.6 - - - -
199A ASN* 3.0 44.6 + - - +
200A LYS 3.7 0.5 + - - -
201A ASN 4.2 0.2 + - - -
202A ASN* 3.0 48.2 + - + +
203A ALA 4.9 0.7 - - - -
206A ILE* 3.7 3.9 - - + +
207A ALA* 4.1 6.3 - - + -
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Residues in contact with LYS 119 (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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117A ASN* 3.2 14.8 + - - +
118A GLU* 1.3 81.2 - - - +
120A ALA* 1.3 60.2 + - - +
122A LYS* 3.1 11.8 + - + +
123A ARG* 2.9 31.4 + - - +
199A ASN* 5.3 8.3 + - - +
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Residues in contact with ALA 120 (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 ARG* 4.9 4.2 + - - +
113A ILE* 4.4 2.2 - - - +
114A PRO* 3.7 26.5 - - + -
117A ASN* 3.3 22.8 + - - +
119A LYS* 1.3 77.9 - - - +
121A LEU* 1.3 52.8 + - - +
123A ARG* 3.2 35.0 + - - +
124A ALA* 2.7 35.2 + - - +
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Residues in contact with LEU 121 (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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113A ILE* 4.0 14.1 - - + +
117A ASN 3.0 14.2 + - - +
118A GLU* 3.4 10.3 - - - +
119A LYS 3.1 0.2 - - - -
120A ALA* 1.3 76.5 - - - +
122A LYS* 1.3 56.0 + - - +
124A ALA* 3.1 3.6 + - - +
125A VAL* 2.9 36.3 + - + +
131A VAL* 3.9 30.3 - - + -
133A VAL* 4.2 7.2 - - + -
166A ALA* 5.5 2.7 - - + -
178A TRP* 3.5 33.4 - - + -
206A ILE* 3.9 27.1 - - + +
207A ALA* 4.1 9.6 - - + -
210A ALA* 4.0 15.5 - - + -
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Residues in contact with LYS 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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1A ALA* 4.9 10.7 + - + -
2A PRO 3.9 9.2 + - - -
3A ASP* 5.0 9.3 + - - +
118A GLU 2.9 13.5 + - - +
119A LYS* 3.4 11.2 - - + +
121A LEU* 1.3 74.4 - - - +
123A ARG* 1.3 58.7 + - - +
125A VAL* 3.2 4.7 + - - +
126A ALA* 2.9 29.7 + - + +
169A TYR* 3.7 39.1 - - + +
178A TRP* 3.5 18.5 - - + -
198A ARG* 4.2 20.6 - - - +
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Residues in contact with ARG 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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1A ALA* 5.4 4.5 - - - -
111A ARG* 5.5 9.6 - - - +
114A PRO* 5.9 0.6 - - - +
117A ASN* 4.9 5.3 - - - +
119A LYS* 2.9 13.2 + - - +
120A ALA* 3.3 36.8 - - - +
122A LYS* 1.3 79.2 - - - +
124A ALA* 1.3 56.1 + - - +
126A ALA* 3.4 6.0 + - - +
127A ARG* 2.8 52.2 + - + +
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Residues in contact with ALA 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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111A ARG* 4.6 3.8 - - - +
113A ILE* 4.2 22.4 - - + -
120A ALA 2.7 16.8 + - - +
121A LEU 3.1 8.7 + - - +
123A ARG* 1.3 72.9 - - - +
125A VAL* 1.3 62.2 + - - +
127A ARG* 4.6 3.8 - - - +
128A VAL* 2.8 33.5 + - - +
129A GLY 3.4 4.7 + - - +
131A VAL* 4.2 13.5 - - + -
212A PHE* 4.4 12.3 - - + -
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Residues in contact with VAL 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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7A TYR* 2.7 53.9 + - + -
121A LEU* 2.9 23.8 + - + +
122A LYS 3.7 4.9 - - - +
124A ALA* 1.3 75.2 - - - +
126A ALA* 1.3 52.3 + - - +
129A GLY 3.3 15.3 + - - +
131A VAL* 3.8 21.5 - - + -
166A ALA* 4.5 15.7 - - + +
168A GLY* 4.0 25.6 - - - +
169A TYR* 4.2 13.7 - - + -
178A TRP* 4.5 10.3 - - + -
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Residues in contact with ALA 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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1A ALA* 3.7 27.4 - - + -
2A PRO* 4.5 5.2 - - + +
5A VAL* 5.1 2.9 - - - -
7A TYR* 3.0 17.7 + - - -
10A LYS* 5.9 0.2 + - - -
122A LYS 2.9 18.0 + - - +
123A ARG 3.6 3.6 - - - +
125A VAL* 1.3 77.0 - - - +
127A ARG* 1.3 64.8 + - - +
169A TYR* 3.6 22.6 - - - +
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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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1A ALA* 4.8 16.6 - - - +
7A TYR* 4.9 0.3 + - - -
40A LYS* 4.1 8.3 + - - +
123A ARG* 2.8 39.3 + - + +
124A ALA* 4.1 1.8 - - - +
126A ALA* 1.3 83.1 - - - +
128A VAL* 1.3 72.6 + - + +
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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