Contacts of the helix formed by residues 354 - 359 (chain F) in PDB entry 3HU1
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 ASP 354 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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310F ALA 3.2 5.3 + - - -
311F PRO 3.6 15.4 - - - +
312F LYS* 4.0 4.7 - - - +
313F ARG* 3.0 53.6 + - - +
314F GLU* 5.9 0.2 - - - -
325F VAL* 4.2 2.9 - - + -
353F ILE* 1.3 74.8 - - - +
355F PRO* 1.4 74.0 - - - +
356F ALA* 3.1 33.1 + - - +
357F LEU* 3.1 36.1 + - + +
358F ARG* 4.0 1.6 + - - +
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Residues in contact with PRO 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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312F LYS* 4.3 20.2 - - + -
314F GLU* 4.3 10.1 - - - +
353F ILE 3.2 8.2 - - - +
354F ASP* 1.4 92.3 - - - +
356F ALA* 1.3 52.3 + - - +
358F ARG* 2.8 33.0 + - + +
359F ARG* 3.3 37.3 + - - +
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Residues in contact with ALA 356 (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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305E GLU* 4.9 5.6 - - - +
313F ARG* 3.4 19.7 - - - +
329F LEU* 3.9 13.0 - - + -
354F ASP* 3.1 17.9 + - - +
355F PRO* 1.3 77.6 - - - +
357F LEU* 1.3 57.0 + - - +
358F ARG 3.4 0.3 + - - -
359F ARG* 3.5 21.2 - - - +
362F ARG* 2.8 36.1 + - - +
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Residues in contact with LEU 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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306F LEU* 4.8 3.4 - - + -
310F ALA* 3.5 27.8 - - + -
325F VAL* 3.9 11.7 - - + -
328F LEU* 3.8 28.9 - - + -
329F LEU* 4.0 18.4 - - + -
332F MET* 4.9 5.6 - - + -
353F ILE* 4.0 12.1 - - + -
354F ASP* 3.1 30.9 + - + +
356F ALA* 1.3 77.4 - - - +
358F ARG* 1.3 58.2 + - + +
359F ARG 3.3 1.8 - - - -
362F ARG* 3.3 5.9 - - + +
363F PHE* 2.9 55.9 + - + +
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Residues in contact with ARG 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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242F LEU* 3.7 21.6 - - + +
244F TYR* 6.0 0.8 - - - -
350F PRO* 3.0 39.4 + - - +
351F ASN* 3.4 22.0 + - - +
353F ILE* 5.0 17.3 + - + +
355F PRO* 2.8 18.2 + - + +
357F LEU* 1.3 78.3 - - - +
359F ARG* 1.3 63.9 + - - +
363F PHE* 3.6 21.8 - - + +
364F ASP* 4.3 4.2 - - - +
366F GLU* 2.9 35.3 + - - +
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Residues in contact with ARG 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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247E PRO* 3.4 31.8 - - + +
305E GLU* 6.1 0.2 - - - -
348E ASN* 3.6 21.8 + - - +
349E ARG* 6.0 1.2 - - - +
800E AGS 3.3 28.7 - - - -
355F PRO* 3.3 45.1 + - - +
356F ALA* 3.5 22.7 - - - +
357F LEU 3.3 2.0 - - - -
358F ARG* 1.3 84.5 - - - +
360F PHE* 1.3 70.5 + - - +
361F GLY 3.4 0.5 + - - -
362F ARG* 3.2 25.7 + - - +
364F ASP* 3.6 7.6 - - - +
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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