Contacts of the strand formed by residues 174 - 179 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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172L PRO* 3.3 2.9 - - - +
173L ASP* 1.3 83.0 - - - +
175L VAL* 1.3 63.0 + - - +
176L LEU* 4.4 0.9 - - + -
230L GLN* 3.6 25.1 - - + +
231L PHE* 4.3 18.4 - - + -
260L MET* 2.8 36.9 + - + +
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Residues in contact with VAL 175 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172L PRO* 4.7 11.0 - - + +
174L ALA* 1.3 80.7 - - - +
176L LEU* 1.3 69.1 + - - +
177L THR* 4.3 4.6 + - + +
257L GLN* 4.1 26.2 - - + -
258L THR 3.2 15.3 - - - +
259L GLU* 4.0 15.5 - - + +
260L MET* 4.8 0.2 - - - -
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Residues in contact with LEU 176 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174L ALA* 5.2 0.2 - - + -
175L VAL* 1.3 81.3 - - - +
177L THR* 1.3 64.2 + - - +
178L ASP* 4.4 1.4 - - - +
226L ARG* 3.2 46.9 - - + +
229L GLN* 4.2 4.0 - - - +
230L GLN* 3.4 36.8 - - + +
257L GLN* 3.9 0.5 - - - -
258L THR* 3.0 33.0 + - - +
260L MET* 3.5 27.1 - - + -
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Residues in contact with THR 177 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175L VAL* 5.0 5.6 - - + +
176L LEU* 1.3 75.8 - - - +
178L ASP* 1.3 64.0 + - - +
226L ARG* 2.9 21.0 + - - +
255L THR* 4.4 11.2 - - + -
256L LEU 3.3 8.5 - - - +
257L GLN* 4.0 29.8 - - + +
274L GLN* 5.5 0.9 - - + -
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Residues in contact with ASP 178 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35L GLY 5.1 0.2 - - - +
176L LEU 4.4 2.3 - - - +
177L THR* 1.3 82.4 - - - +
179L THR* 1.3 61.9 + - - +
180L THR 3.6 0.7 + - - -
222L PHE* 3.7 29.4 - - + -
225L ARG* 3.1 25.6 + - - -
226L ARG* 2.5 38.9 + - - +
255L THR* 3.3 4.3 - - - +
256L LEU* 2.8 45.4 + - + +
258L THR* 5.1 2.4 + - - -
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Residues in contact with THR 179 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178L ASP* 1.3 72.8 - - - +
180L THR* 1.3 73.7 - - - +
181L SER* 3.8 1.0 + - - -
184L GLN* 4.7 1.4 - - - +
222L PHE* 4.9 5.9 - - - -
253L GLY 4.6 4.3 - - - +
255L THR* 4.0 20.6 + - - +
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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