Contacts of the helix formed by residues 144 - 149 (chain I) in PDB entry 1FQV
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 144 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133I SER* 5.7 1.9 - - - -
140I TYR* 3.6 18.1 + - - -
141I ARG* 3.1 12.5 + - - -
142I LEU 2.8 1.2 - - - -
143I ALA* 1.3 79.1 + - - +
145I ASP* 1.3 67.4 + - - +
146I GLU* 3.5 2.4 + - - +
149I TRP* 3.6 12.8 - - - +
170I GLN* 3.4 34.8 + - - +
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Residues in contact with ASP 145 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118I LEU* 3.4 29.7 - - + +
141I ARG 3.7 2.2 + - - -
142I LEU* 2.7 26.6 + - - +
143I ALA 3.5 0.6 - - - -
144I SER* 1.3 79.5 - - - +
146I GLU* 1.3 78.6 + - - +
147I SER* 2.7 28.8 + - - +
148I LEU* 3.0 14.8 + - + +
149I TRP* 3.2 10.2 - - - -
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Residues in contact with GLU 146 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144I SER 3.5 1.9 + - - +
145I ASP* 1.3 77.0 + - - +
147I SER* 1.3 64.3 + - - +
149I TRP 3.1 10.9 + - - -
150I GLN* 3.6 12.7 + - - +
169I SER 5.1 1.6 - - - +
170I GLN* 3.6 22.1 - - - +
171I GLY* 3.7 18.1 + - - +
194I ARG* 2.8 50.2 + - - +
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Residues in contact with SER 147 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118I LEU* 3.9 13.6 - - - +
145I ASP* 2.7 26.9 + - - +
146I GLU* 1.3 75.6 - - - +
148I LEU* 1.3 67.7 + - - +
149I TRP 3.6 0.2 + - - -
150I GLN* 3.5 29.2 + - - +
427I ARG* 3.7 7.4 + - - -
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Residues in contact with LEU 148 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118I LEU* 3.9 14.4 - - + +
121I PHE* 3.8 12.1 - - + -
122I SER* 3.8 28.3 - - - +
129I LEU* 3.7 30.1 - - + -
142I LEU 3.3 26.2 - - - +
143I ALA 3.9 4.0 - - - +
145I ASP* 3.0 10.7 + - + +
147I SER* 1.3 86.3 - - - +
149I TRP* 1.3 66.8 + - + +
150I GLN 3.7 1.6 + - - -
151I THR 5.4 0.5 + - - -
427I ARG* 3.1 35.0 + - - +
428I LEU* 3.2 20.1 - - - +
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Residues in contact with TRP 149 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126I LEU* 3.6 30.1 - - + -
129I LEU* 3.7 22.2 - - + +
130I LEU* 3.9 20.2 - - + -
143I ALA 2.9 23.0 + - - -
144I SER* 3.6 7.9 - - - +
145I ASP 3.2 17.5 - - - -
146I GLU 3.1 3.2 + - - +
148I LEU* 1.3 81.9 - - + +
150I GLN* 1.3 60.7 + - - +
151I THR 3.4 4.4 + - - +
152I LEU* 4.1 22.0 - - + -
167I LEU* 3.5 29.6 - - + -
170I GLN* 3.0 37.8 + - + +
171I GLY 3.6 4.5 - - - -
172I VAL* 2.9 38.3 - - + +
428I LEU* 3.8 13.0 - - + -
159J TRP* 4.9 0.9 - + - -
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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