Contacts of the helix formed by residues 118 - 123 (chain F) in PDB entry 1U1C
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 GLY 118 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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117E ASP 4.4 2.2 - - - -
118E GLY* 3.7 13.4 - - - -
160E ASP* 3.2 17.3 - - - -
117F ASP* 1.3 73.4 - - - +
119F ALA* 1.3 66.7 + - - +
120F SER 3.3 2.5 - - - -
121F LEU* 3.1 22.9 + - - +
122F HIS* 3.2 14.4 - - - -
160F ASP* 2.9 12.4 + - - -
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Residues in contact with ALA 119 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160E ASP* 3.3 32.8 + - + +
161E THR* 4.4 5.4 - - - +
71F GLY* 3.8 12.8 - - - +
72F PRO* 4.0 2.0 - - + -
75F SER* 4.7 0.9 - - - -
117F ASP* 3.7 1.2 + - - +
118F GLY* 1.3 76.1 - - - +
120F SER* 1.3 62.9 + - - +
122F HIS* 2.9 23.9 + - - +
123F PHE* 3.3 10.7 - - - -
160F ASP* 5.0 0.4 + - - -
201F THR* 3.4 28.5 - - + +
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Residues in contact with SER 120 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115F ARG* 2.8 31.2 + - - +
117F ASP* 2.7 38.3 + - - -
119F ALA* 1.3 76.3 - - - +
121F LEU* 1.3 57.6 + - - +
123F PHE* 3.1 10.5 + - - +
124F ALA 3.1 26.0 + - - +
200F ALA 3.8 5.6 - - - -
201F THR* 3.8 5.1 + - - +
204F THR* 3.6 24.3 - - - +
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Residues in contact with LEU 121 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121E LEU* 6.2 4.0 - - + -
177E VAL* 3.8 12.3 - - - +
179E HIS* 5.1 5.6 - - + +
180E PHE* 4.3 5.2 - - + -
115F ARG* 3.7 7.0 - - - +
117F ASP 4.2 14.8 - - - +
118F GLY* 3.1 18.0 + - - +
120F SER* 1.3 76.3 + - - +
122F HIS* 1.3 63.8 + - + +
123F PHE 3.1 6.3 + - - -
124F ALA 3.4 10.6 + - - +
125F PRO* 4.3 4.5 - - + +
126F LEU* 3.6 46.4 - - + +
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Residues in contact with HIS 122 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116E LEU* 3.1 28.7 + - + -
159E SER* 3.3 18.4 - - - -
160E ASP* 3.6 8.9 - - + +
161E THR* 3.2 28.3 - - - +
164E PRO* 3.4 27.5 - - + +
165E GLY* 3.4 11.0 - - - +
175E ARG* 5.3 0.2 + - - -
177E VAL* 3.4 14.0 + - - +
180E PHE* 3.4 37.5 - + + -
118F GLY* 3.2 21.1 + - - -
119F ALA* 2.9 12.3 + - - +
121F LEU* 1.3 78.9 - - + +
123F PHE* 1.3 59.0 + - + +
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Residues in contact with PHE 123 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190B MET* 3.6 1.4 - - - +
161E THR* 3.8 15.9 - - - -
164E PRO* 3.7 27.6 - - + -
175E ARG* 3.0 36.3 + - - +
177E VAL* 3.5 9.5 - - - +
75F SER* 4.1 15.0 - - - -
79F GLU* 5.4 5.8 - - + -
119F ALA 3.3 26.7 - - - -
120F SER* 3.1 7.7 + - - +
122F HIS* 1.3 83.2 - - - +
124F ALA* 1.3 61.4 + - + +
201F THR* 5.0 1.6 - - + -
204F THR* 4.9 0.2 - - + -
205F MET* 3.6 39.9 - - + +
208F SER* 4.0 12.6 - - - +
209F GLN* 3.7 32.1 - - - -
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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