Contacts of the strand formed by residues 173 - 178 (chain C) in PDB entry 1XPU
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 ARG 173 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171C GLY 3.8 0.4 + - - -
172C GLN* 1.3 69.9 - - - +
174C GLY* 1.3 59.2 + - - +
301C PHE* 2.9 57.2 - - + +
302C GLY 4.1 8.5 + - - -
304C ALA* 2.7 33.3 + - + -
315C ILE 3.6 2.9 - - - -
338C THR 2.8 25.9 + - - -
339C GLY* 3.2 8.4 - - - -
340C ASN* 2.6 40.0 + - - +
341C MET 3.5 2.8 + - - +
212D ARG* 3.4 7.7 - - - +
213D PRO* 3.4 20.6 - - - +
214D GLU* 2.7 42.5 + - - -
232D PHE* 3.6 8.1 - - - -
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Residues in contact with GLY 174 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172C GLN 3.6 2.6 - - - -
173C ARG* 1.3 74.5 - - - +
175C LEU* 1.3 60.3 + - - -
176C ILE 4.1 0.2 - - - -
301C PHE* 3.4 6.4 - - - -
315C ILE 2.8 12.7 + - - +
316C ILE* 3.3 15.8 - - - +
317C ALA 2.8 27.8 + - - -
341C MET* 3.4 25.1 - - - -
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Residues in contact with LEU 175 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173C ARG 5.2 0.2 - - - +
174C GLY* 1.3 72.5 - - - -
176C ILE* 1.3 61.8 + - - +
177C VAL* 3.4 9.0 + - + +
267C ILE* 4.2 15.5 - - + -
301C PHE* 3.9 23.3 - - + -
317C ALA 3.2 14.4 - - - +
319C ALA* 4.0 21.5 - - + -
332C TYR* 4.2 24.2 - - + -
335C PHE* 4.3 26.5 - - + +
336C LYS* 5.6 1.8 - - - -
337C GLY 5.9 0.9 - - - +
339C GLY* 5.4 5.2 - - - +
341C MET* 2.9 16.0 + - - +
342C GLU* 3.2 17.4 - - + +
343C LEU 3.1 20.8 + - - -
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Residues in contact with ILE 176 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162C LEU* 5.4 2.9 - - + -
175C LEU* 1.3 71.7 - - - +
177C VAL* 1.3 63.0 + - - +
178C ALA* 3.6 3.3 + - + +
184C LYS* 5.3 1.8 - - + -
187C LEU* 3.8 26.5 - - + -
188C LEU* 5.0 5.2 - - + -
191C ILE* 6.3 2.7 - - + -
316C ILE* 3.7 29.4 - - + -
317C ALA 2.8 9.2 + - - +
318C THR* 3.1 28.5 - - + -
319C ALA 2.8 28.4 + - - -
341C MET* 4.1 10.5 - - + -
343C LEU* 3.4 36.8 - - + +
345C LEU* 4.6 9.2 - - + -
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Residues in contact with VAL 177 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175C LEU* 4.1 15.5 - - + +
176C ILE* 1.3 72.5 - - - +
178C ALA* 1.3 61.4 + - - +
179C PRO* 4.6 0.7 - - + -
319C ALA 3.8 5.2 - - - +
321C ILE* 3.7 35.4 - - + -
332C TYR* 3.5 26.2 - - + +
342C GLU* 4.4 5.6 - - - +
343C LEU 3.0 6.2 + - - +
344C HIS* 3.4 39.9 - - + +
345C LEU* 2.8 30.4 + - - +
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Residues in contact with ALA 178 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176C ILE* 3.6 5.6 + - + +
177C VAL* 1.3 77.0 - - - +
179C PRO* 1.3 72.9 - - + +
184C LYS* 3.9 30.8 + - + +
319C ALA 3.2 10.1 + - - +
320C LEU* 3.7 4.0 - - - +
321C ILE* 2.9 28.2 + - - -
345C LEU* 3.8 22.9 - - + -
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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