Contacts of the helix formed by residues 122 - 129 (chain A) in PDB entry 2YGE
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 122 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15A LEU* 4.0 22.0 - - + -
98A ASN* 3.6 28.0 - - + +
100A GLY 4.7 0.2 - - - +
101A THR* 3.8 18.4 - - - +
104A PHE* 4.2 20.0 - - + -
117A ILE* 3.4 29.9 + - + +
120A PHE* 3.3 7.8 - - + +
121A GLY* 1.3 84.9 - - - +
123A GLY* 1.3 61.1 + - - +
124A PHE 3.1 1.2 + - - -
125A TYR* 3.2 18.6 + - + +
1215A GDM 3.1 13.5 - - - +
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Residues in contact with GLY 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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33A GLU* 3.6 23.5 - - - +
34A LEU* 4.6 0.7 - - - +
37A ASN* 4.6 2.7 - - - -
117A ILE* 3.7 26.6 + - - -
118A GLY* 4.4 1.8 - - - -
121A GLY 3.7 1.4 - - - -
122A VAL* 1.3 71.8 - - - +
124A PHE* 1.3 62.3 + - - +
125A TYR 3.0 2.7 - - - -
126A SER* 2.7 27.6 + - - -
1215A GDM 3.4 4.8 + - - -
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Residues in contact with PHE 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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34A LEU* 4.3 4.1 - - - +
37A ASN* 3.9 12.0 - - - +
93A LEU* 3.9 19.5 - - + -
123A GLY* 1.3 76.8 - - - +
125A TYR* 1.3 88.1 + + - +
126A SER 3.1 1.6 + - - -
127A LEU* 3.1 47.9 + - + +
128A PHE* 5.1 3.1 - + - -
136A VAL* 3.7 20.9 - - + -
148A TRP* 3.7 37.5 - + - -
173A LEU* 3.9 12.8 - - + -
1215A GDM 3.0 53.8 + - + +
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Residues in contact with TYR 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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8A PHE* 4.7 4.5 - + - -
12A ILE* 3.5 44.4 - - + +
15A LEU* 4.0 19.3 - - + -
16A MET* 3.7 28.3 - - + -
19A ILE* 3.5 26.6 - - + +
92A ASN 4.6 0.5 + - - -
93A LEU* 3.7 8.5 - - - -
94A GLY 3.7 13.9 + - - -
98A ASN* 4.5 9.5 + - - -
101A THR* 6.0 0.4 - - - -
122A VAL* 3.2 19.5 + - + +
123A GLY 3.0 1.4 - - - -
124A PHE* 1.3 101.0 - + - +
126A SER* 1.3 61.6 + - - +
127A LEU 3.0 6.6 + - - -
128A PHE* 3.1 26.3 + + + +
148A TRP* 5.5 0.4 - + - -
1215A GDM 4.1 18.6 - - + -
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Residues in contact with SER 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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19A ILE* 4.5 3.6 - - - -
29A ILE* 4.1 22.7 - - - -
30A PHE* 3.4 24.0 + - - +
33A GLU* 3.5 8.0 - - - +
34A LEU* 4.9 0.9 - - - +
114A VAL* 5.6 0.7 - - - -
117A ILE* 3.9 21.0 - - - +
123A GLY 2.7 22.0 + - - -
125A TYR* 1.3 73.9 - - - +
127A LEU* 1.3 61.3 + - - +
128A PHE 2.9 6.3 - - - -
129A LEU* 3.0 29.0 + - - +
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Residues in contact with LEU 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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30A PHE* 4.2 12.1 - - - -
34A LEU* 4.3 12.1 - - + +
124A PHE* 3.1 55.3 + - + +
125A TYR 3.0 1.2 - - - -
126A SER* 1.3 79.6 + - - +
128A PHE* 1.3 79.0 + - + +
129A LEU 3.1 1.2 + - - -
130A VAL* 3.3 5.2 + - - +
131A ALA* 3.0 29.1 + - + +
134A VAL* 3.8 37.7 - - + -
173A LEU* 4.3 4.9 - - + -
175A LEU* 4.0 21.1 - - + -
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Residues in contact with PHE 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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16A MET* 3.6 32.8 - - + +
19A ILE* 3.9 11.9 - - + -
20A ILE* 3.7 28.6 - - + +
124A PHE* 5.1 3.4 - + - -
125A TYR* 3.1 28.9 + + + +
126A SER 2.9 1.4 - - - -
127A LEU* 1.3 93.2 - - + +
129A LEU* 1.3 59.0 + - - +
130A VAL 3.3 0.2 - - - -
131A ALA 3.5 19.4 - - - +
132A ASP 4.5 7.4 - - - -
133A ARG 4.6 0.2 - - - -
134A VAL* 3.9 20.0 - - + -
148A TRP* 5.5 0.9 - + - -
150A SER* 3.8 21.1 - - - -
151A ASN 4.4 2.2 - - - -
152A ALA* 3.7 22.2 - - + -
178A LYS* 3.0 21.8 + - - -
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Residues in contact with LEU 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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19A ILE* 3.6 17.7 - - + +
22A THR* 3.4 31.4 - - + -
24A TYR* 4.7 5.2 - - + -
27A LYS* 3.3 57.3 - - + +
29A ILE* 3.9 28.0 - - + -
30A PHE* 4.9 0.2 - - + -
114A VAL* 4.2 18.6 - - + -
126A SER* 3.0 22.1 + - - +
128A PHE* 1.3 78.8 - - - +
130A VAL* 1.3 60.5 + - + +
178A LYS* 3.1 18.6 + - - +
181A GLN* 4.4 0.2 - - - +
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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