Contacts of the strand formed by residues 174 - 179 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172H PRO* 3.3 2.5 - - - +
173H ASP* 1.3 84.3 - - - +
175H VAL* 1.3 62.6 + - - +
230H GLN* 3.8 16.2 - - + +
231H PHE* 4.4 17.9 - - + -
259H GLU* 3.7 0.2 - - - -
260H MET* 2.7 39.1 + - + +
175I VAL 3.3 8.1 - - - -
176I LEU* 3.5 21.5 - - + -
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Residues in contact with VAL 175 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172H PRO* 4.7 11.9 - - + +
174H ALA* 1.3 79.3 - - - +
176H LEU* 1.3 65.5 + - - +
177H THR* 5.0 3.3 - - + +
257H GLN* 3.9 28.9 - - + -
258H THR 3.2 12.1 - - - +
259H GLU* 4.0 19.1 - - + +
173I ASP 4.7 0.2 - - - -
174I ALA* 3.5 2.4 - - - -
175I VAL* 3.2 60.4 + - + +
177I THR* 6.4 1.1 - - + -
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Residues in contact with LEU 176 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174H ALA* 5.2 0.9 - - + -
175H VAL* 1.3 78.6 - - - +
177H THR* 1.3 63.7 + - - +
178H ASP* 4.3 1.7 + - - +
226H ARG* 3.3 46.4 - - + +
229H GLN* 4.4 3.4 - - - +
230H GLN* 3.7 32.1 - - + +
256H LEU 4.1 0.2 - - - +
258H THR* 2.9 32.8 + - - +
260H MET* 3.4 28.5 - - + -
173I ASP 3.6 5.2 - - - +
174I ALA* 3.3 29.8 - - + -
175I VAL 4.9 0.4 - - - +
230I GLN* 4.0 3.4 - - - +
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Residues in contact with THR 177 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175H VAL* 5.0 4.7 - - + +
176H LEU* 1.3 76.5 - - - +
178H ASP* 1.3 63.2 + - - +
226H ARG* 3.0 20.6 + - - -
255H THR* 4.2 10.8 - - + -
256H LEU 3.1 7.9 - - - +
257H GLN* 3.8 31.9 - - + +
171I PRO* 4.3 14.3 + - + +
172I PRO* 2.7 32.4 + - + +
173I ASP* 3.5 14.2 + - - +
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Residues in contact with ASP 178 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176H LEU 4.4 2.6 - - - +
177H THR* 1.3 83.1 - - - +
179H THR* 1.3 62.3 + - - +
180H THR 3.6 0.9 + - - -
222H PHE* 3.7 30.4 - - + -
225H ARG* 3.2 24.6 + - - -
226H ARG* 2.6 37.2 + - - +
255H THR* 3.3 5.3 - - - +
256H LEU* 2.6 48.1 + - + +
258H THR* 5.0 2.4 + - - -
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Residues in contact with THR 179 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178H ASP* 1.3 74.0 - - - +
180H THR* 1.3 72.4 + - - +
181H SER* 3.8 0.9 + - - -
184H GLN* 4.7 2.1 - - - +
222H PHE* 4.8 6.6 - - - -
253H GLY 4.4 5.4 - - - +
255H THR* 4.0 20.5 + - - +
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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
------------------------------------------------------------
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