Contacts of the helix formed by residues 123 - 132 (chain A) in PDB entry 1IER
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 PRO 123 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7A ASN* 4.0 8.1 - - - +
121A ALA 3.2 12.8 - - - +
122A ASP* 1.3 83.0 - - - +
124A HIS* 1.3 63.5 + - + +
126A CYS* 3.4 8.6 + - + +
127A ASP* 2.8 29.3 + - - +
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Residues in contact with HIS 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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68A MET* 4.4 20.1 - - + +
71A GLN* 4.7 11.4 + - - -
72A ARG* 3.3 45.3 + - + +
122A ASP* 3.3 2.5 + - - +
123A PRO* 1.3 84.4 - - + +
125A LEU* 1.3 57.5 + - - +
127A ASP* 3.3 15.6 + - - +
128A PHE* 2.9 36.4 + + + +
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Residues in contact with LEU 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 TYR* 5.3 0.4 - - + -
12A VAL* 3.8 28.3 - - + -
16A VAL* 4.4 6.1 - - + -
68A MET* 3.6 31.4 - - + -
72A ARG* 4.2 5.4 - - - +
113A LEU* 4.0 22.7 - - + +
114A HIS* 5.3 0.2 - - - -
117A GLY* 3.6 29.6 - - - -
122A ASP* 3.2 23.1 + - - +
124A HIS* 1.3 76.7 + - - +
126A CYS* 1.3 67.1 + - - +
128A PHE* 3.2 5.5 + - - +
129A LEU* 2.9 38.5 + - + +
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Residues in contact with CYS 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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114A HIS* 3.8 33.4 - - - +
117A GLY* 3.7 5.4 - - - -
118A SER* 3.7 34.1 - - - -
122A ASP 3.3 14.3 + - - +
123A PRO* 3.6 10.5 - - + +
124A HIS 3.2 0.4 - - - -
125A LEU* 1.3 81.4 - - - +
127A ASP* 1.3 61.1 + - - +
129A LEU* 3.4 2.0 + - - +
130A GLU* 3.1 34.7 + - - +
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Residues in contact with ASP 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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123A PRO 2.8 20.5 + - - +
124A HIS* 3.4 18.6 - - - +
126A CYS* 1.3 71.7 - - - +
128A PHE* 1.2 62.9 + - - +
130A GLU* 3.3 10.1 + - - +
131A SER* 3.0 34.9 + - - -
202A CD 3.7 17.3 - - - -
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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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64A ARG* 3.8 23.6 - - + -
65A LEU* 3.8 9.0 - - + -
68A MET* 3.7 53.2 - - + -
71A GLN* 5.6 3.8 - - - -
124A HIS* 2.9 32.0 + + + +
125A LEU* 3.4 7.6 - - - +
127A ASP* 1.2 73.7 + - - +
129A LEU* 1.3 70.4 + - + +
131A SER* 4.9 0.2 - - - -
132A HIS* 3.0 55.8 + + - +
133A PHE* 3.3 30.7 - + - -
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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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65A LEU* 4.9 4.3 - - + -
110A LEU* 3.9 21.1 - - + +
113A LEU* 3.9 28.5 - - + -
114A HIS* 3.7 42.4 - - + +
125A LEU* 2.9 29.0 + - + +
126A CYS 3.8 3.6 - - - +
128A PHE* 1.3 87.6 - - + +
130A GLU* 1.3 66.8 + - - +
133A PHE* 3.0 21.8 + - + +
134A LEU* 3.0 31.1 + - + -
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Residues in contact with GLU 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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114A HIS* 2.8 25.9 + - - +
126A CYS* 3.1 24.1 + - - +
127A ASP* 3.8 6.8 - - - +
129A LEU* 1.3 79.0 - - - +
131A SER* 1.3 64.6 - - - +
132A HIS 3.5 0.3 + - - -
134A LEU* 3.8 34.9 + - + +
135A ASP* 4.0 10.0 + - - +
201A CD 2.6 28.8 - - - -
202A CD 4.1 10.2 - - - -
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Residues in contact with SER 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 ASP* 3.0 27.5 + - - -
130A GLU* 1.3 78.7 - - - +
132A HIS* 1.3 82.7 + - - +
135A ASP* 6.0 1.4 - - - +
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Residues in contact with HIS 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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64A ARG* 4.4 32.6 + - - -
128A PHE* 3.0 51.8 + + - -
131A SER* 1.3 97.6 + - - +
133A PHE* 1.3 82.2 + - + +
135A ASP 5.5 0.2 - - - -
136A GLU* 4.3 18.7 - - - +
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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