Contacts of the strand formed by residues 174 - 179 (chain A) in PDB entry 1S9C
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 ALA 174 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172A PRO* 3.2 2.7 - - - +
173A ASP* 1.3 83.9 - - - +
175A VAL* 1.3 62.0 + - - +
176A LEU* 4.4 0.4 - - + -
230A GLN* 3.8 15.7 - - + +
231A PHE* 4.3 17.7 - - + -
259A GLU* 3.8 0.2 - - - -
260A MET* 2.7 36.5 + - + +
175E VAL 3.5 9.0 - - - -
176E LEU* 3.4 22.2 - - + -
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Residues in contact with VAL 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A PRO* 4.7 11.2 - - + +
174A ALA* 1.3 79.3 - - - +
176A LEU* 1.3 66.3 + - - +
177A THR* 5.0 3.6 - - + +
257A GLN* 4.0 27.6 - - + -
258A THR 3.1 15.0 - - - +
259A GLU* 4.0 16.2 - - + +
174E ALA* 3.5 2.3 - - - -
175E VAL* 3.2 56.8 + - + +
177E THR* 6.4 1.3 - - + -
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Residues in contact with LEU 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A ALA* 5.3 0.2 - - + -
175A VAL* 1.3 77.5 - - - +
177A THR* 1.3 64.7 + - - +
178A ASP* 4.3 2.4 - - - +
226A ARG* 3.3 45.1 - - + +
229A GLN* 4.4 3.1 - - + +
230A GLN* 3.6 34.3 - - + +
256A LEU 4.2 0.2 - - - +
258A THR* 3.0 32.7 + - - +
260A MET* 3.4 27.6 - - + -
173E ASP 3.5 4.5 - - - +
174E ALA* 3.2 31.4 - - + -
176E LEU* 5.4 0.4 - - + -
230E GLN* 3.9 2.9 - - - +
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Residues in contact with THR 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A VAL* 5.0 4.7 - - + +
176A LEU* 1.3 75.1 - - - +
178A ASP* 1.3 64.7 + - - +
226A ARG* 3.0 20.3 + - - -
255A THR* 4.3 10.3 - - + +
256A LEU 3.3 9.0 - - - +
257A GLN* 3.9 30.5 - - + +
170E ARG* 5.6 0.2 + - - -
171E PRO* 4.2 15.1 + - + +
172E PRO* 2.6 32.2 + - + +
173E ASP* 3.3 14.3 + - - +
175E VAL* 6.3 1.3 - - + -
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Residues in contact with ASP 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A GLY 5.0 0.5 - - - +
176A LEU 4.3 2.6 - - - +
177A THR* 1.3 79.6 - - - +
179A THR* 1.3 63.6 + - - +
180A THR 3.6 0.5 + - - -
222A PHE* 3.6 31.2 - - + +
225A ARG* 3.2 24.9 + - - -
226A ARG* 2.6 38.3 + - - +
255A THR* 3.3 4.1 - - - +
256A LEU* 2.8 45.4 + - + +
258A THR* 5.0 2.6 + - - -
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Residues in contact with THR 179 (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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178A ASP* 1.3 74.2 - - - +
180A THR* 1.3 72.9 + - - +
181A SER 3.8 0.9 + - - -
184A GLN* 4.7 2.1 - - - +
222A PHE* 4.9 5.7 - - - -
253A GLY 4.5 4.5 - - - +
255A THR* 4.1 20.2 + - - +
171E PRO* 6.0 0.7 - - - +
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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