Contacts of the helix formed by residues 123 - 133 (chain A) in PDB entry 2YB6
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 ASN 123 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76A MET 5.2 1.8 + - - -
77A PHE* 3.9 20.4 - - - +
78A HIS 3.3 24.5 + - - +
79A PRO* 2.9 7.6 + - - +
81A VAL 3.5 13.0 + - - +
82A TYR* 5.4 0.9 - - - -
83A ALA* 5.8 3.3 - - - +
121A PRO 4.2 2.2 - - - -
122A ALA* 1.3 74.3 - - - +
124A SER* 1.3 57.4 + - - +
125A GLN* 3.1 13.3 + - - +
126A ALA* 3.0 28.6 + - - +
127A ALA* 2.9 28.1 + - - +
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Residues in contact with SER 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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121A PRO* 4.1 11.3 + - - +
122A ALA 3.9 1.9 + - - -
123A ASN* 1.3 70.2 + - - +
125A GLN* 1.3 60.2 + - - +
127A ALA* 3.4 7.3 + - - +
128A GLN* 2.9 31.4 + - - +
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Residues in contact with GLN 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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77A PHE* 3.7 11.7 - - + -
123A ASN* 3.1 8.2 + - - +
124A SER* 1.3 80.5 - - - +
126A ALA* 1.3 60.6 + - - +
128A GLN* 3.4 4.5 + - - +
129A LEU* 3.0 32.4 + - + +
140A ARG* 2.8 43.0 + - - +
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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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77A PHE* 3.5 29.1 - - + -
78A HIS 3.6 5.4 - - - +
79A PRO* 3.6 23.6 - - + -
123A ASN* 3.0 28.4 + - - +
125A GLN* 1.3 76.5 - - - +
127A ALA* 1.3 58.2 + - - +
129A LEU 3.4 0.5 + - - -
130A TYR* 2.9 31.4 + - - +
137A TYR* 3.6 4.5 - - + -
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Residues in contact with ALA 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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79A PRO* 3.8 11.8 - - + +
121A PRO* 3.5 34.5 - - + -
123A ASN 2.9 15.6 + - - +
124A SER* 3.7 7.4 - - - +
126A ALA* 1.3 76.8 - - - +
128A GLN* 1.3 62.1 + - - +
130A TYR* 3.3 3.4 + - - +
131A GLN* 3.0 40.5 + - - +
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Residues in contact with GLN 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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124A SER 2.9 17.1 + - - +
125A GLN* 3.9 4.9 - - - +
127A ALA* 1.3 76.6 - - - +
129A LEU* 1.3 61.6 + - + +
131A GLN* 3.2 16.0 + - - +
132A GLU* 2.8 63.8 + - + +
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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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77A PHE* 4.0 24.7 - - + -
125A GLN* 3.0 27.0 + - + +
126A ALA 4.0 2.5 - - - +
128A GLN* 1.3 76.0 - - + +
130A TYR* 1.3 63.0 + - - +
133A ASN* 2.8 51.3 + - + +
136A GLU* 4.0 32.1 - - + +
137A TYR* 3.9 16.7 - - + +
140A ARG* 4.1 15.0 - - + +
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Residues in contact with TYR 130 (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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79A PRO* 4.2 4.9 - - + -
114A ASP* 4.4 7.3 + - - -
115A GLU* 5.0 4.5 + - - -
116A PRO* 3.6 44.6 - - + +
126A ALA 2.9 19.0 + - - +
127A ALA* 3.6 4.3 - - - +
129A LEU* 1.3 76.3 - - - +
131A GLN* 1.3 70.4 + - + +
134A LYS* 2.7 63.9 + - - +
137A TYR* 3.7 40.3 - + + -
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Residues in contact with GLN 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 PRO* 4.8 22.6 + - - +
121A PRO* 5.0 1.6 - - - +
127A ALA* 3.0 33.4 + - - +
128A GLN* 3.2 24.0 + - - +
130A TYR* 1.3 89.8 - - + +
132A GLU* 1.3 77.9 + - + +
133A ASN 3.8 0.2 - - - -
134A LYS* 4.8 5.5 + - - +
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Residues in contact with GLU 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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128A GLN* 2.8 44.9 + - + +
131A GLN* 1.3 90.4 - - + +
133A ASN* 1.3 63.2 + - + +
134A LYS* 4.0 0.7 - - - -
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Residues in contact with ASN 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 LEU* 2.8 28.4 + - + +
131A GLN 3.8 0.2 - - - -
132A GLU* 1.3 82.2 - - + +
134A LYS* 1.3 66.1 + - - +
135A ARG* 3.1 9.8 - - - +
136A GLU* 3.0 33.2 + - - +
137A TYR 3.0 18.5 + - - -
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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