Contacts of the helix formed by residues 136 - 145 (chain A) in PDB entry 1F9O
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 ILE 136 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134A ASP* 3.0 11.3 + - - +
135A PRO* 1.3 76.7 - - - +
137A ASN* 1.3 68.3 + - - +
138A SER 3.4 2.5 - - - -
139A GLN* 3.0 18.1 + - - +
140A LEU* 3.0 21.4 + - + +
265A ASP 5.2 0.2 - - - +
268A ARG* 3.8 31.6 - - + +
269A TYR* 3.7 47.8 - - + +
272A PHE* 3.9 31.0 - - + -
289A TYR* 3.5 25.1 - - + +
348A ASP* 4.4 0.4 - - - +
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Residues in contact with ASN 137 (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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103A TYR* 3.6 30.6 - - + -
105A ALA* 4.7 9.7 - - + +
134A ASP* 3.1 22.4 + - - +
135A PRO 3.6 1.2 - - - -
136A ILE* 1.3 76.9 - - - +
138A SER* 1.3 61.3 + - - +
140A LEU* 3.0 8.3 + - - +
141A THR* 2.8 48.1 + - - +
147A SER* 4.9 6.1 + - - -
149A LEU* 5.0 5.7 - - - +
269A TYR* 3.0 21.0 + - - -
313A ILE* 4.2 7.1 - - - +
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Residues in contact with SER 138 (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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105A ALA* 6.0 0.4 - - - +
134A ASP 5.4 1.3 + - - -
135A PRO 4.1 10.8 + - - -
137A ASN* 1.3 79.8 - - - +
139A GLN* 1.3 64.5 + - - +
141A THR* 3.6 8.9 + - - -
142A SER* 3.2 26.0 + - - -
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Residues in contact with GLN 139 (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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135A PRO 3.6 18.1 + - - +
136A ILE* 3.0 13.8 + - - +
138A SER* 1.3 80.2 + - - +
140A LEU* 1.3 57.6 + - - +
142A SER* 4.1 2.2 - - - -
143A ALA* 3.3 28.1 + - - +
268A ARG* 2.9 31.1 + - - +
289A TYR* 2.9 27.1 + - - -
342A SER* 3.8 14.2 + - - -
343A SER* 3.5 21.9 + - - +
344A ASN* 3.4 21.9 + - - +
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Residues in contact with LEU 140 (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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136A ILE* 3.0 28.4 + - + +
137A ASN* 3.0 8.4 + - - +
139A GLN* 1.3 75.4 - - - +
141A THR* 1.3 67.4 + - + +
142A SER 3.1 1.3 - - - -
143A ALA* 3.3 0.8 + - - -
144A TYR* 3.1 42.8 + - + +
146A THR 4.6 0.2 - - - -
149A LEU* 5.8 0.2 - - + -
265A ASP* 3.9 40.4 - - + +
266A TYR* 4.1 31.5 + - + -
268A ARG* 4.2 6.3 - - - +
269A TYR* 3.8 30.1 - - + +
342A SER* 4.6 1.1 - - - -
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Residues in contact with THR 141 (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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137A ASN* 2.8 44.9 + - - +
138A SER* 3.6 10.6 + - - -
140A LEU* 1.3 73.6 - - + +
142A SER* 1.3 57.9 + - - +
145A GLY* 2.7 35.7 + - - -
146A THR 3.3 22.6 + - - +
147A SER* 3.8 19.3 - - - +
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Residues in contact with SER 142 (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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138A SER 3.2 19.0 + - - -
139A GLN* 4.1 2.9 - - - -
140A LEU 3.1 0.6 - - - -
141A THR* 1.3 84.0 + - - +
143A ALA* 1.3 58.7 + - - +
145A GLY* 4.3 3.1 + - - -
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Residues in contact with ALA 143 (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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139A GLN 3.3 18.7 + - - +
140A LEU 3.3 0.4 + - - -
142A SER* 1.3 76.5 - - - +
144A TYR* 1.3 77.5 + - + +
145A GLY 3.7 0.2 - - - -
341A LYS* 3.0 37.7 + - + +
342A SER* 4.0 25.8 - - - +
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Residues in contact with TYR 144 (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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140A LEU* 3.1 28.1 + - + +
143A ALA* 1.3 87.0 - - + +
145A GLY* 1.3 64.9 + - - +
146A THR* 3.2 13.3 + - + +
261A THR* 4.5 2.1 + - - +
262A LYS* 3.5 41.9 + - + -
265A ASP* 2.6 36.2 + - - +
266A TYR* 3.5 33.7 - + - +
341A LYS* 3.7 33.5 + - + +
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Residues in contact with GLY 145 (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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141A THR 2.7 21.8 + - - -
142A SER 4.2 3.2 + - - -
143A ALA 3.7 1.4 - - - -
144A TYR* 1.3 73.3 - - - +
146A THR* 1.3 56.7 + - - -
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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