Contacts of the strand formed by residues 173 - 178 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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172D GLN* 1.3 72.7 - - - +
174D GLY* 1.3 61.1 + - - +
301D PHE* 2.7 65.1 + - + +
302D GLY* 3.1 14.3 + - - -
304D ALA* 2.7 32.7 + - + +
315D ILE 3.5 3.4 - - - -
338D THR 3.2 27.2 + - - -
339D GLY* 3.3 8.8 - - - -
340D ASN* 2.8 41.2 + - - +
341D MET 3.7 0.9 - - - +
212E ARG* 4.4 0.8 - - - +
213E PRO* 3.7 12.7 - - - +
214E GLU* 2.7 39.8 + - - -
232E PHE* 3.8 11.2 - - - -
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Residues in contact with GLY 174 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172D GLN* 3.6 2.4 - - - +
173D ARG* 1.3 75.3 - - - +
175D LEU* 1.3 59.8 + - - -
176D ILE 4.1 0.4 - - - -
301D PHE* 3.2 12.5 - - - -
315D ILE 2.8 13.1 + - - -
316D ILE* 4.2 4.7 - - - -
317D ALA 3.0 23.5 + - - -
341D MET* 3.3 33.1 - - - +
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Residues in contact with LEU 175 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173D ARG 5.1 0.2 - - - +
174D GLY* 1.3 72.1 - - - -
176D ILE* 1.3 62.7 + - - +
177D VAL* 3.1 14.4 + - + +
267D ILE* 4.1 23.3 - - + -
301D PHE* 3.8 29.4 - - + -
317D ALA 3.3 9.9 - - - +
319D ALA* 4.1 13.2 - - + -
332D TYR* 4.2 26.5 - - + -
335D PHE* 4.4 23.3 - - + +
336D LYS* 5.3 2.5 - - - +
337D GLY 6.0 0.2 - - - +
339D GLY* 5.6 4.3 - - - +
341D MET* 2.8 15.7 + - - +
342D GLU* 3.3 15.4 - - + +
343D LEU 3.1 19.3 + - - -
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Residues in contact with ILE 176 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162D LEU* 5.1 3.8 - - + -
168D ILE* 5.9 0.7 - - + -
175D LEU* 1.3 68.0 - - - +
177D VAL* 1.3 66.0 + - - +
178D ALA* 3.6 4.3 + - + +
184D LYS* 5.0 2.9 - - + +
187D LEU* 3.8 30.5 - - + -
188D LEU* 5.3 5.2 - - + -
191D ILE* 6.0 2.5 - - + -
316D ILE* 3.4 30.5 - - + -
317D ALA 2.7 12.8 + - - +
318D THR* 3.2 22.9 - - + -
319D ALA 3.0 23.2 + - - -
341D MET* 4.2 10.8 - - + -
343D LEU* 3.4 35.0 - - + +
345D LEU* 4.6 6.5 - - + -
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Residues in contact with VAL 177 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175D LEU* 3.1 19.5 + - + +
176D ILE* 1.3 72.4 - - - +
178D ALA* 1.3 59.4 + - - +
179D PRO* 5.9 0.2 - - + -
319D ALA* 3.9 4.5 - - + +
321D ILE* 3.5 31.6 - - + -
332D TYR* 3.7 21.1 - - + +
342D GLU* 4.8 2.2 - - + +
343D LEU 2.7 11.1 + - - +
344D HIS* 3.5 46.4 - - + +
345D LEU* 2.7 35.7 + - - +
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Residues in contact with ALA 178 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176D ILE* 3.6 5.4 + - + +
177D VAL* 1.3 78.7 - - - +
179D PRO* 1.3 73.5 - - + +
184D LYS* 4.0 28.0 - - + -
319D ALA 3.3 9.8 + - - +
320D LEU* 3.8 4.5 - - - +
321D ILE* 3.1 28.6 + - - -
345D LEU* 3.8 23.1 - - + -
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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