Contacts of the helix formed by residues 118 - 125 (chain L) in PDB entry 3IU3
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 SER 118 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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124H PHE* 3.4 17.3 - - - +
125H PRO* 3.6 29.4 + - - -
126H LEU* 6.3 0.2 - - - +
116L PRO 3.4 4.1 + - - -
117L PRO* 1.3 75.9 - - - +
119L ASP* 1.3 65.6 + - - +
120L GLU* 3.6 12.3 - - - -
121L GLN* 3.3 24.8 + - - +
122L LEU* 3.1 21.1 + - - +
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Residues in contact with ASP 119 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117L PRO 5.4 1.5 - - - +
118L SER* 1.3 72.1 - - - +
120L GLU* 1.3 71.1 + - - +
122L LEU* 3.2 20.9 + - - +
123L LYS* 3.1 38.7 + - - +
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Residues in contact with GLU 120 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124H PHE* 3.8 19.0 - - + -
125H PRO* 3.4 29.2 - - - +
211H LYS* 3.4 23.7 - - - +
118L SER* 3.6 9.2 - - - -
119L ASP* 1.3 85.0 + - - +
121L GLN* 1.3 63.3 + - - +
123L LYS* 3.2 33.4 + - + +
124L SER* 3.3 11.4 + - - -
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Residues in contact with GLN 121 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124H PHE* 3.6 33.3 - - + -
143H LEU* 4.1 5.1 - - - +
145H LYS* 3.9 15.4 - - - +
117L PRO* 4.2 0.6 - - + +
118L SER* 3.3 29.6 + - - +
119L ASP 3.2 0.4 - - - -
120L GLU* 1.3 80.1 - - - +
122L LEU* 1.3 61.9 + - - +
124L SER* 2.7 21.5 + - - +
125L GLY 3.3 1.4 + - - -
126L THR* 2.8 27.6 + - - +
127L ALA* 3.6 6.8 - - - +
128L SER* 2.8 57.1 + - - +
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Residues in contact with LEU 122 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117L PRO* 4.5 9.6 - - + +
118L SER 3.1 17.8 + - - +
119L ASP* 3.4 23.8 - - - +
121L GLN* 1.3 76.5 - - - +
123L LYS* 1.3 62.3 + - + +
125L GLY* 3.2 12.7 + - - -
126L THR 3.9 3.1 - - - +
127L ALA* 4.2 14.6 - - + -
180L LYS* 3.2 42.1 + - + +
183L TYR* 3.8 36.3 - - + -
184L GLU* 5.8 1.3 - - + +
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Residues in contact with LYS 123 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119L ASP* 3.1 26.1 + - - +
120L GLU* 3.2 25.7 + - + +
122L LEU* 1.3 77.2 - - + +
124L SER* 1.3 61.4 + - - +
125L GLY* 3.3 1.4 + - - -
180L LYS* 4.7 7.3 + - - +
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Residues in contact with SER 124 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124H PHE* 4.5 10.3 - - - -
120L GLU 3.3 7.6 + - - -
121L GLN* 2.7 23.4 + - - +
123L LYS* 1.3 79.1 - - - +
125L GLY* 1.3 56.8 + - - +
126L THR* 3.6 14.6 + - - -
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Residues in contact with GLY 125 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121L GLN 3.3 0.2 + - - -
122L LEU 3.2 10.1 + - - -
123L LYS 3.2 4.3 - - - -
124L SER* 1.3 79.4 + - - +
126L THR* 1.3 65.4 + - - +
179L SER* 3.6 6.9 - - - -
180L LYS* 2.8 33.6 + - - +
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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