Contacts of the helix formed by residues 123 - 132 (chain A) in PDB entry 5IYB
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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119A VAL* 3.8 20.7 - - + +
120A ASP 3.6 14.6 + - - +
121A SER 3.1 3.2 - - - +
122A ASN* 1.3 80.2 - - - +
124A PRO* 1.3 70.3 - - - +
125A LYS* 2.7 45.7 + - - +
126A ILE* 3.1 11.8 + - + +
127A LYS* 3.0 24.5 + - - +
147A LEU* 5.2 1.9 - - - +
151A LYS* 4.1 16.6 - - - +
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Residues in contact with PRO 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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122A ASN 3.5 6.9 - - - +
123A ASN* 1.3 92.3 - - - +
125A LYS* 1.3 61.3 + - + +
127A LYS* 3.4 13.6 + - + +
128A ASP* 3.0 26.3 + - - +
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Residues in contact with LYS 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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123A ASN* 2.7 24.1 + - - +
124A PRO* 1.3 74.1 - - + +
126A ILE* 1.3 57.1 + - - +
128A ASP* 3.4 9.0 + - - +
129A ILE* 2.9 34.7 + - + +
147A LEU* 5.2 19.7 - - + -
116E GLN* 5.8 5.5 - - - +
119E VAL* 6.1 3.0 - - - +
120E ASP* 5.8 3.7 + - - -
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Residues in contact with ILE 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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119A VAL* 3.7 25.8 - - + +
120A ASP 3.5 17.3 - - - +
121A SER* 3.6 25.8 - - - -
123A ASN* 3.1 18.9 + - + +
125A LYS* 1.3 74.0 - - - +
127A LYS* 1.3 55.1 + - - +
129A ILE* 3.0 25.6 + - + +
130A LEU* 2.8 48.1 + - + +
144A VAL* 4.6 13.9 - - + -
147A LEU* 3.7 10.3 - - + -
235A VAL* 5.4 9.6 - - + -
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Residues in contact with LYS 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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121A SER 4.6 6.7 + - - +
123A ASN 3.0 12.3 + - - +
124A PRO* 3.4 14.6 - - + +
125A LYS 3.3 0.2 - - - -
126A ILE* 1.3 76.8 - - - +
128A ASP* 1.3 57.1 + - - +
130A LEU* 3.4 10.2 + - + +
131A ALA* 2.9 27.7 + - - +
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Residues in contact with ASP 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 PRO 3.0 13.2 + - - +
125A LYS* 3.5 12.8 - - - +
127A LYS* 1.3 74.3 - - - +
129A ILE* 1.3 55.6 + - + +
131A ALA* 3.3 8.6 + - - +
132A LYS* 2.7 63.8 + - - +
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Residues in contact with ILE 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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125A LYS* 2.9 22.1 + - + +
126A ILE* 3.3 31.0 - - + +
128A ASP* 1.3 77.2 - - - +
130A LEU* 1.3 65.7 + - + +
132A LYS* 3.2 27.8 + - - +
133A SER* 4.5 1.2 - - - -
140A ARG* 3.6 40.1 + - + +
143A HIS* 4.2 37.7 - - + +
144A VAL* 4.7 4.5 - - + -
147A LEU* 4.5 10.8 - - + -
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Residues in contact with LEU 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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121A SER* 5.1 13.5 - - - -
126A ILE* 2.8 35.8 + - + +
127A LYS* 3.7 9.9 - - + +
129A ILE* 1.3 76.6 - - + +
131A ALA* 1.3 61.0 + - - +
133A SER 4.1 0.3 - - - -
134A LYS* 3.3 40.1 + - + +
140A ARG* 4.2 34.8 - - - +
234A PHE* 4.5 17.0 - - + -
235A VAL* 5.2 14.4 - - + -
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Residues in contact with ALA 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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127A LYS* 2.9 18.0 + - + +
128A ASP* 3.5 13.0 - - - +
130A LEU* 1.3 75.4 - - - +
132A LYS* 1.3 51.9 + - - +
133A SER* 2.4 21.5 + - - -
134A LYS* 3.9 7.5 + - - +
187E ARG* 6.0 0.2 + - - -
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Residues in contact with LYS 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 ASP* 2.7 48.6 + - - +
129A ILE* 3.2 16.0 + - - +
131A ALA* 1.3 67.2 - - - +
133A SER* 1.3 71.5 - - - +
139A LYS* 4.8 10.9 - - + +
140A ARG* 5.5 0.9 + - - -
143A HIS* 5.4 16.4 + - + +
187E ARG* 4.4 37.3 - - - +
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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