Contacts of the helix formed by residues 345 - 355 (chain F) in PDB entry 3HX0
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 GLY 345 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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339F SER* 4.3 7.4 - - - -
344F ALA* 1.3 75.2 - - - +
346F THR* 1.3 57.7 + - - -
348F THR* 2.9 1.8 + - - -
349F ALA* 2.7 35.0 + - - +
4H T 2.8 30.1 + - - -
5H A 4.5 6.7 - - - -
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Residues in contact with THR 346 (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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268F SER 3.9 10.2 + - - -
269F VAL* 3.0 34.0 + - - +
270F GLN 4.1 10.8 - - - +
271F GLY* 4.2 6.4 - - - +
339F SER* 4.4 4.6 + - - -
345F GLY* 1.3 68.8 - - - +
347F LYS* 1.3 66.1 + - - +
349F ALA* 3.3 6.3 + - - +
350F GLN* 2.8 48.8 + - + +
4H T 4.1 2.9 + - - -
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Residues in contact with LYS 347 (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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271F GLY* 6.1 1.8 - - - -
345F GLY 3.2 0.8 - - - -
346F THR* 1.3 86.6 - - - +
348F THR* 1.3 58.5 + - - +
350F GLN* 3.5 24.2 + - + +
351F MET* 3.0 27.9 + - - +
3H G 3.4 45.5 - - - +
4H T 3.5 17.1 + - - +
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Residues in contact with THR 348 (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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344F ALA* 4.1 1.6 - - + -
345F GLY 3.6 8.9 + - - -
347F LYS* 1.3 71.1 - - - +
349F ALA* 1.3 65.7 + - - +
351F MET* 3.5 11.7 + - + +
352F TRP* 3.2 50.7 + - + +
373F GLN* 3.4 29.1 + - - +
3H G 3.6 7.1 + - - -
4H T 2.5 31.6 + - - -
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Residues in contact with ALA 349 (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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269F VAL 6.0 0.7 - - - +
335F LEU* 3.6 26.6 - - + +
338F PHE* 3.8 23.7 - - + -
339F SER* 3.5 21.3 - - - +
344F ALA 5.4 0.2 - - - -
345F GLY 2.7 19.3 + - - +
346F THR* 3.6 5.6 - - - +
348F THR* 1.3 71.6 - - - +
350F GLN* 1.3 66.9 + - - +
352F TRP* 3.5 1.7 + - - -
353F TYR* 3.2 22.0 + - - +
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Residues in contact with GLN 350 (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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270F GLN 4.2 9.0 - - - +
335F LEU* 4.1 16.4 - - + +
346F THR* 2.8 34.0 + - + +
347F LYS* 3.5 25.2 + - + +
349F ALA* 1.3 77.0 - - - +
351F MET* 1.3 63.6 + - - +
353F TYR* 3.1 6.7 + - + +
354F GLN* 3.0 20.1 + - - +
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Residues in contact with MET 351 (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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347F LYS 3.0 14.5 + - - +
348F THR* 3.7 11.0 - - + +
349F ALA 3.3 0.2 - - - -
350F GLN* 1.3 80.7 - - - +
352F TRP* 1.3 96.4 + - + +
354F GLN* 3.0 20.3 + - + +
355F GLN* 3.1 26.9 + - + +
368F SER* 5.5 7.4 - - - +
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Residues in contact with TRP 352 (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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338F PHE* 3.7 27.8 - - + -
341F ILE* 3.8 27.4 - - + -
344F ALA* 3.8 13.0 - - + -
348F THR* 3.2 39.9 + - + +
349F ALA* 3.9 0.4 - - - +
350F GLN 3.4 0.2 - - - -
351F MET* 1.3 97.9 - - + +
353F TYR* 1.3 62.6 + - - +
355F GLN* 3.3 26.8 + - - -
357F PHE* 3.2 37.2 + + + +
363F ILE* 3.6 22.7 - - + -
367F ALA* 3.4 12.8 - - + +
368F SER* 5.0 4.4 + - - +
369F LEU* 3.4 29.8 - - + +
373F GLN* 3.7 21.3 - - + -
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Residues in contact with TYR 353 (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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330F GLU* 4.2 11.4 + - - +
331F SER* 3.0 43.3 + - - -
334F VAL* 3.8 21.8 - - + +
335F LEU* 3.6 18.8 - - + -
338F PHE* 4.2 1.8 - + + -
349F ALA 3.2 12.9 + - - +
350F GLN* 3.1 12.2 + - + +
352F TRP* 1.3 77.6 - - - +
354F GLN* 1.3 58.5 + - - +
356F GLY* 2.9 16.5 + - - -
357F PHE 3.7 8.1 - - - -
358F ARG* 3.0 66.1 + - - -
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Residues in contact with GLN 354 (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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350F GLN 3.0 9.8 + - - +
351F MET* 3.0 13.6 + - + +
353F TYR* 1.3 73.3 - - - +
355F GLN* 1.3 64.5 + - - +
356F GLY* 2.9 10.5 + - - -
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Residues in contact with GLN 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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351F MET* 3.1 26.0 + - + +
352F TRP* 3.4 25.6 - - - +
353F TYR 3.2 0.4 - - - -
354F GLN* 1.3 80.7 - - - +
356F GLY* 1.3 58.3 - - - +
357F PHE* 3.3 43.8 + - + -
367F ALA* 4.9 3.1 - - - +
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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