Contacts of the helix formed by residues 354 - 363 (chain F) in PDB entry 5UQ9
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 ASN 354 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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172F ASP* 3.6 15.2 - - - +
173F TRP 3.7 20.4 - - - +
174F VAL* 3.1 9.5 + - - +
352F THR 3.9 0.4 + - - +
353F LEU* 1.3 69.8 - - - +
355F TYR* 1.3 65.2 + - - +
356F GLY* 3.2 2.2 - - - +
357F GLY* 3.0 29.7 + - - +
358F ILE* 3.0 25.4 + - - +
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Residues in contact with TYR 355 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339F PHE* 3.8 26.2 - + + -
342F LEU* 4.1 5.4 - - + -
343F ARG* 3.6 40.3 + - + +
346F ALA* 3.7 14.2 - - - +
353F LEU* 3.4 41.1 + - + +
354F ASN* 1.3 72.2 - - - +
356F GLY* 1.3 63.7 + - - +
358F ILE* 3.1 12.9 + - + +
359F ALA* 3.1 20.1 + - - +
380F PHE* 3.7 41.0 - + + -
384F PRO 4.7 10.5 - - - -
386F LEU 6.0 1.8 - - - -
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Residues in contact with GLY 356 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354F ASN* 3.2 4.3 + - - +
355F TYR* 1.3 79.7 - - - +
357F GLY* 1.3 55.6 + - - +
359F ALA* 3.4 1.4 + - - +
360F LEU 3.1 20.4 + - - -
377F LYS* 3.3 35.4 - - - +
380F PHE* 3.8 23.9 - - - +
381F ASP* 4.8 5.2 - - - -
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Residues in contact with GLY 357 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172F ASP* 4.8 12.3 - - - +
354F ASN* 3.0 24.5 + - - -
356F GLY* 1.3 72.2 - - - +
358F ILE* 1.3 60.2 + - - +
360F LEU* 3.3 12.2 - - - +
361F MET* 2.9 38.3 + - - +
377F LYS* 5.0 4.3 - - - +
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Residues in contact with ILE 358 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174F VAL* 3.9 25.8 - - + -
183F VAL* 3.6 42.6 - - + -
339F PHE* 4.5 3.6 - - + -
342F LEU* 4.3 14.1 - - + -
353F LEU* 4.2 17.3 - - + -
354F ASN 3.0 22.4 + - - +
355F TYR* 3.1 18.6 + - + +
357F GLY* 1.3 77.0 - - - +
359F ALA* 1.3 62.6 + - - +
361F MET* 3.1 22.7 - - - +
362F TRP* 3.4 28.5 + - + -
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Residues in contact with ALA 359 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339F PHE* 4.1 6.0 - - + -
355F TYR 3.1 10.0 + - - +
356F GLY 3.8 7.4 - - - +
358F ILE* 1.3 77.7 - - - +
360F LEU* 1.3 63.2 + - - +
362F TRP* 3.6 10.9 + - - +
363F ARG* 3.8 3.6 + - - +
373F LEU* 3.6 45.9 - - + +
376F ILE* 3.7 30.7 - - + -
377F LYS* 4.2 2.7 - - - +
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Residues in contact with LEU 360 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164F VAL* 3.7 11.7 - - + -
168F GLU* 3.9 18.8 - - + +
169F PRO 3.1 28.0 - - - +
170F CYS* 3.5 14.8 - - - -
171F CYS 4.4 2.7 - - - +
172F ASP* 5.5 6.3 - - + -
356F GLY 3.1 14.8 + - - +
357F GLY* 3.1 15.9 + - - +
359F ALA* 1.3 76.8 - - - +
361F MET* 1.3 63.5 + - + +
362F TRP 3.1 0.4 - - - -
363F ARG* 3.2 45.4 + - - +
373F LEU 5.7 0.2 - - - -
377F LYS* 3.8 23.8 - - + +
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Residues in contact with MET 361 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140F SER* 3.2 26.7 + - - -
141F LEU 3.3 13.7 - - - +
142F MET* 3.6 27.1 - - + +
170F CYS* 3.4 29.3 - - - +
171F CYS 4.4 0.2 - - - +
172F ASP* 3.1 46.0 - - + +
174F VAL* 3.6 19.5 - - + -
183F VAL* 5.1 1.8 - - - -
357F GLY 2.9 17.6 + - - +
358F ILE* 3.1 20.6 - - - +
360F LEU* 1.3 75.3 - - + +
362F TRP* 1.3 64.5 + - + +
363F ARG 3.4 0.4 - - - -
364F GLY 3.9 0.2 - - - +
366F CYS* 3.9 0.5 - - - -
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Residues in contact with TRP 362 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142F MET* 3.6 31.6 - - + +
183F VAL* 3.6 41.3 - - + +
186F VAL* 4.5 2.5 - - + -
187F HIS* 3.6 15.9 - + + +
190F ILE* 3.6 32.8 - - + -
335F TYR* 4.6 2.2 - + - -
339F PHE* 4.5 16.8 - + - -
342F LEU* 4.5 13.5 - - + -
358F ILE* 3.4 24.6 + - + -
359F ALA* 3.9 5.8 - - - +
360F LEU 3.1 1.2 - - - -
361F MET* 1.3 79.4 - - + +
363F ARG* 1.3 56.2 + - - +
364F GLY 3.2 10.0 + - - -
366F CYS* 3.2 25.6 - - - +
368F ILE* 3.7 22.4 - - + -
369F ARG* 3.6 10.7 + - - +
373F LEU* 3.6 28.9 - - + -
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Residues in contact with ARG 363 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164F VAL* 3.5 31.2 - - + +
165F GLY 5.5 1.6 + - - +
166F THR* 5.0 11.2 - - - +
168F GLU* 4.9 2.8 + - - -
170F CYS* 4.1 3.8 - - - -
359F ALA 3.8 7.4 + - - +
360F LEU* 3.2 38.6 + - - +
362F TRP* 1.3 77.1 - - - +
364F GLY* 1.3 54.4 + - - +
369F ARG* 3.6 19.9 - - - +
370F SER 3.2 36.6 - - - +
371F VAL* 4.4 11.3 + - - +
373F LEU* 3.9 3.7 - - + +
374F GLY* 3.5 30.5 - - - +
377F LYS* 5.1 5.5 - - - +
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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
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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