Contacts of the helix formed by residues 113 - 121 (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 ASP 113 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24A TYR* 4.6 11.6 + - - +
104A PHE* 4.4 2.6 - - - -
108A LEU* 4.4 0.2 - - - -
111A GLY 3.5 4.7 + - - +
112A ALA* 1.3 73.9 - - - +
114A VAL* 1.3 65.4 + - - +
115A SER* 3.3 22.2 + - - +
116A MET* 3.0 27.0 + - + +
117A ILE 4.4 0.3 + - - -
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Residues in contact with VAL 114 (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* 5.5 6.5 - - + -
22A THR* 4.9 5.4 - - - +
24A TYR* 3.4 44.5 - - + -
29A ILE* 4.6 4.3 - - + -
104A PHE* 3.9 11.4 - - + -
108A LEU* 3.8 25.4 - - + -
112A ALA 3.5 0.6 + - - -
113A ASP* 1.3 72.1 - - - +
115A SER* 1.3 57.3 + - - +
116A MET 3.0 0.2 - - - -
117A ILE* 2.9 36.7 + - + +
129A LEU* 4.2 29.6 - - + -
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Residues in contact with SER 115 (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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24A TYR* 4.0 9.8 + - - -
26A ASN* 4.7 3.4 + - - -
29A ILE* 4.0 33.2 - - - +
32A ARG* 2.7 36.2 + - - +
113A ASP* 3.3 20.8 + - - +
114A VAL* 1.3 79.1 - - - +
116A MET* 1.3 61.2 + - - +
117A ILE* 3.1 3.3 + - - -
118A GLY* 4.1 2.1 + - - -
119A GLN* 4.8 2.6 - - - +
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Residues in contact with MET 116 (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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104A PHE* 4.1 4.5 - - + -
107A ALA* 5.8 0.4 - - + -
112A ALA* 4.0 21.8 - - + -
113A ASP* 3.0 25.0 + - + +
115A SER* 1.3 75.1 + - - +
117A ILE* 1.3 65.2 + - - +
118A GLY 3.1 3.4 - - - -
119A GLN* 2.8 51.9 + - + +
120A PHE* 3.6 35.2 - - + -
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Residues in contact with ILE 117 (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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15A LEU* 5.1 0.2 - - + -
19A ILE* 3.7 29.2 - - + -
29A ILE* 4.5 3.6 - - + -
33A GLU* 4.0 17.7 - - + +
104A PHE* 3.3 30.6 - - + -
114A VAL* 2.9 21.6 + - + +
115A SER 3.1 2.8 - - - +
116A MET* 1.3 77.6 - - - +
118A GLY* 1.3 65.6 + - - +
120A PHE* 3.2 12.5 + - - +
122A VAL* 3.4 43.1 + - + +
123A GLY* 3.8 10.8 - - - -
126A SER* 3.9 20.9 - - - +
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Residues in contact with GLY 118 (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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32A ARG* 5.4 0.4 - - - -
33A GLU* 3.2 29.3 + - - -
115A SER 4.1 0.8 + - - -
116A MET 2.9 1.8 + - - -
117A ILE* 1.3 83.2 - - - +
119A GLN* 1.3 61.6 + - - +
120A PHE 3.1 0.2 - - - -
121A GLY* 3.2 13.2 + - - -
123A GLY* 4.4 5.4 - - - -
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Residues in contact with GLN 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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115A SER 4.8 2.3 + - - +
116A MET* 2.8 43.7 + - + +
118A GLY* 1.3 76.9 - - - +
120A PHE* 1.3 64.9 + - + +
121A GLY 3.4 0.6 + - - -
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Residues in contact with PHE 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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99A SER* 5.3 1.6 + - - -
100A GLY* 3.5 31.0 + - - +
103A ALA* 3.8 17.0 - - + -
104A PHE* 3.5 50.9 - + + -
107A ALA* 3.8 19.7 - - + -
116A MET* 3.6 43.1 - - + -
117A ILE 3.2 7.7 + - - +
118A GLY 3.1 1.0 - - - -
119A GLN* 1.3 82.2 - - + +
121A GLY* 1.3 62.8 + - - +
122A VAL* 3.3 4.6 + - + +
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Residues in contact with GLY 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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98A ASN* 3.7 6.6 + - - +
118A GLY 3.2 13.9 + - - -
119A GLN 3.4 1.4 + - - -
120A PHE* 1.3 79.7 - - - +
122A VAL* 1.3 65.0 + - - +
123A GLY 3.7 2.2 - - - -
1215A GDM 3.3 34.8 + - - +
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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