Contacts of the helix formed by residues 123 - 132 (chain B) in PDB entry 1IES
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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7B ASN* 3.9 8.5 - - - +
121B ALA* 3.2 14.1 - - + +
122B ASP* 1.3 85.2 - - - +
124B HIS* 1.3 56.8 + - - +
126B CYS* 3.4 8.1 + - + +
127B ASP* 2.9 28.4 + - - +
111C LEU* 3.8 26.9 - - + +
114C HIS* 3.4 48.9 - - + +
130C GLU* 4.2 4.4 - - - +
134C LEU* 3.6 11.4 - - + -
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Residues in contact with HIS 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68B MET* 4.5 15.3 - - + +
71B GLN* 4.9 3.4 - - - -
72B ARG* 3.6 27.7 + - + +
122B ASP* 3.3 7.5 + - - +
123B PRO* 1.3 81.2 - - + +
125B LEU* 1.3 60.1 + - - +
127B ASP* 3.4 8.8 + - + +
128B PHE* 2.8 35.0 + + + +
111C LEU* 6.1 2.2 - - + -
134C LEU* 4.0 15.6 - - + +
135C ASP* 3.2 40.7 + - + -
138C VAL* 3.7 39.6 - - + +
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Residues in contact with LEU 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B TYR* 5.1 2.2 - - + -
12B VAL* 3.7 30.3 - - + -
16B VAL* 4.3 5.4 - - + -
68B MET* 3.7 33.0 - - + -
72B ARG* 5.6 1.3 - - - +
113B LEU* 3.9 26.9 - - + +
114B HIS* 5.2 0.2 - - - -
117B GLY* 3.7 26.7 - - - +
122B ASP* 3.4 22.4 + - - +
123B PRO 3.4 0.6 - - - -
124B HIS* 1.3 77.1 - - - +
126B CYS* 1.3 67.1 - - - +
128B PHE* 3.1 6.2 + - - +
129B LEU* 2.9 34.3 + - + +
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Residues in contact with CYS 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114B HIS* 3.7 37.2 + - + +
117B GLY* 3.7 4.0 - - - -
118B SER* 3.5 32.1 - - - -
122B ASP 3.3 15.2 + - - +
123B PRO* 3.6 10.1 - - + +
125B LEU* 1.3 79.1 - - - +
127B ASP* 1.3 56.4 + - - +
129B LEU* 3.4 2.4 + - - +
130B GLU* 2.9 39.8 + - - +
130C GLU* 5.2 4.0 - - - +
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Residues in contact with ASP 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123B PRO 2.9 14.1 + - - +
124B HIS* 3.6 12.1 - - + +
125B LEU 3.2 0.2 - - - -
126B CYS* 1.3 75.8 - - - +
128B PHE* 1.3 55.6 + - - +
130B GLU* 3.2 10.2 + - - +
131B SER* 2.8 56.1 + - - -
202B CD 3.4 19.8 - - - -
130C GLU* 3.6 40.1 + - + +
131C SER* 4.7 1.6 + - - -
134C LEU* 5.7 1.1 - - + -
135C ASP* 5.1 9.2 - - - +
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Residues in contact with PHE 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64B ARG* 3.8 23.6 - - + -
65B LEU* 3.7 8.7 - - + -
68B MET* 3.5 53.6 - - + -
71B GLN* 6.1 2.2 - - - -
124B HIS* 2.8 32.1 + + + +
125B LEU* 3.1 6.7 + - - +
127B ASP* 1.3 75.6 + - - +
129B LEU* 1.3 66.4 + - + +
131B SER* 4.5 1.1 - - - -
132B HIS* 3.0 60.0 + + - +
133B PHE* 3.4 29.3 - + - -
135C ASP* 6.1 0.9 - - - -
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Residues in contact with LEU 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65B LEU* 4.7 5.2 - - + -
110B LEU* 3.9 28.5 - - + +
113B LEU* 3.8 29.6 - - + -
114B HIS* 3.7 40.8 - - + +
125B LEU* 2.9 25.2 + - + +
126B CYS 3.6 3.8 - - - +
128B PHE* 1.3 93.6 - - + +
130B GLU* 1.3 66.4 + - - +
133B PHE* 3.0 27.1 + - + +
134B LEU* 3.0 15.8 + - + -
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Residues in contact with GLU 130 (chain B).
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* 4.3 7.7 - - - +
126A CYS* 5.3 3.3 - - - +
127A ASP* 4.1 39.0 + - + +
130A GLU* 3.8 4.9 - - - +
201A CD 2.7 28.2 - - - -
114B HIS* 2.9 29.2 + - - +
126B CYS* 2.9 24.2 + - - +
127B ASP* 3.6 7.7 - - - +
129B LEU* 1.3 77.1 - - - +
131B SER* 1.3 64.2 + - - +
134B LEU* 3.8 27.5 + - + +
135B ASP* 4.1 10.0 + - - +
130C GLU* 3.6 6.4 - - - +
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Residues in contact with SER 131 (chain B).
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* 4.9 2.2 + - - -
127B ASP* 2.8 46.5 + - - -
128B PHE* 3.8 4.0 - - - -
130B GLU* 1.3 74.1 - - - +
132B HIS* 1.3 79.3 + - - +
135B ASP* 5.5 4.0 - - - +
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Residues in contact with HIS 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64B ARG* 3.6 39.4 + - - +
128B PHE* 3.0 50.1 + + - -
130B GLU 4.6 0.2 - - - -
131B SER* 1.3 92.1 + - - +
133B PHE* 1.3 80.3 + - + +
135B ASP 5.3 0.4 - - - -
136B GLU* 3.7 24.1 - - - +
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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